Publications

Latest Publications

RSS Garcia Lab Publications

Publications in 2022

Combinatorial Histone H3 Modifications Are Dynamically Altered in Distinct Cell Cycle Phases

Combinatorial Histone H3 Modifications Are Dynamically Altered in Distinct Cell Cycle Phases. Lu C, Coradin M, Janssen KA, Sidoli S, Garcia BA. J Am Soc Mass Spectrom. 2021 Apr 5. doi: 10.1021/jasms.0c00451.

Structure of TFIIK for phosphorylation of CTD of RNA polymerase II

Structure of TFIIK for phosphorylation of CTD of RNA polymerase II. van Eeuwen T, Li T, Kim HJ, Gorbea Colón JJ, Parker MI, Dunbrack RL, Garcia BA, Tsai KL, Murakami K. Sci Adv. 2021 Apr 7;7(15):eabd4420.

Sex-specific effects of in vitro fertilization on adult metabolic outcomes and hepatic transcriptome and proteome in mouse

Sex-specific effects of in vitro fertilization on adult metabolic outcomes and hepatic transcriptome and proteome in mouse. Narapareddy L, Rhon-Calderon EA, Vrooman LA, Baeza J, Nguyen DK, Mesaros C, Lan Y, Garcia BA, Schultz RM, Bartolomei MS. FASEB J. 2021 Apr;35(4):e21523.

Improved SILAC Quantification with Data-Independent Acquisition to Investigate Bortezomib-Induced Protein Degradation

Improved SILAC Quantification with Data-Independent Acquisition to Investigate Bortezomib-Induced Protein Degradation. Pino LK, Baeza J, Lauman R, Schilling B, Garcia BA. J Proteome Res. 2021 Apr 2;20(4):1918-1927.

An Esrrb and Nanog Cell Fate Regulatory Module Controlled by Feed Forward Loop Interactions

An Esrrb and Nanog Cell Fate Regulatory Module Controlled by Feed Forward Loop Interactions. Sevilla A, Papatsenko D, Mazloom AR, Xu H, Vasileva A, Unwin RD, LeRoy G, Chen EY, Garrett-Bakelman FE, Lee DF, Trinite B, Webb RL, Wang Z, Su J, Gingold J, Melnick A, Garcia BA, Whetton AD, MacArthur BD, Ma’ayan A, Lemischka IR. Front Cell Dev Biol. 2021 Mar 19;9:630067.

Long-term behavioral and cell-type-specific molecular effects of early life stress are mediated by H3K79me2 dynamics in medium spiny neurons

Long-term behavioral and cell-type-specific molecular effects of early life stress are mediated by H3K79me2 dynamics in medium spiny neurons. Kronman H, Torres-Berrío A, Sidoli S, Issler O, Godino A, Ramakrishnan A, Mews P, Lardner CK, Parise EM, Walker DM, van der Zee YY, Browne CJ, Boyce BF, Neve R, Garcia BA, Shen L, Peña CJ, Nestler EJ. Nat Neurosci. 2021 Mar 15. doi: 10.1038/s41593-021-00814-8. Online ahead of print.

Chromatin dysregulation associated with NSD1 mutation in head and neck squamous cell carcinoma

Chromatin dysregulation associated with NSD1 mutation in head and neck squamous cell carcinoma. Farhangdoost N, Horth C, Hu B, Bareke E, Chen X, Li Y, Coradin M, Garcia BA, Lu C, Majewski J. Cell Rep. 2021 Feb 23;34(8):108769.

Histone Modifications in Papillomavirus Virion Minichromosomes

Histone Modifications in Papillomavirus Virion Minichromosomes. Porter SS, Liddle JC, Browne K, Pastrana DV, Garcia BA, Buck CB, Weitzman MD, McBride AA. mBio. 2021 Feb 16;12(1):e03274-20.

Cryo-EM structures of engineered active bc1-cbb3 type CIII2CIV super-complexes and electronic communication between the complexes

Cryo-EM structures of engineered active bc1-cbb3 type CIII2CIV super-complexes and electronic communication between the complexes. Steimle S, van Eeuwen T, Ozturk Y, Kim HJ, Braitbard M, Selamoglu N, Garcia BA, Schneidman-Duhovny D, Murakami K, Daldal F. Nat Commun. 2021 Feb 10;12(1):929.

Enhancing Open Modification Searches via a Combined Approach Facilitated by Ursgal

Enhancing Open Modification Searches via a Combined Approach Facilitated by Ursgal. Schulze S, Igiraneza AB, Kösters M, Leufken J, Leidel SA, Garcia BA, Fufezan C, Pohlschroder M. J Proteome Res. 2021 Apr 2;20(4):1986-1996.

HDAC inhibition results in widespread alteration of the histone acetylation landscape and BRD4 targeting to gene bodies

HDAC inhibition results in widespread alteration of the histone acetylation landscape and BRD4 targeting to gene bodies. Slaughter MJ, Shanle EK, Khan A, Chua KF, Hong T, Boxer LD, Allis CD, Josefowicz SZ, Garcia BA, Rothbart SB, Strahl BD, Davis IJ. Cell Rep. 2021 Jan 19;34(3):108638.

Comparative proteomics identifies Schlafen 5 (SLFN5) as a herpes simplex virus restriction factor that suppresses viral transcription

 

Structure and noncanonical Cdk8 activation mechanism within an Argonaute-containing Mediator kinase module

Structure and noncanonical Cdk8 activation mechanism within an Argonaute-containing Mediator kinase module.
Li YC, Chao TC, Kim HJ, Cholko T, Chen SF, Li G, Snyder L, Nakanishi K, Chang CE, Murakami K, Garcia BA, Boyer TG, Tsai KL. Sci Adv. 2021 Jan 15;7(3):eabd4484.

Publications in 2021

Combinatorial Histone H3 Modifications Are Dynamically Altered in Distinct Cell Cycle Phases

Combinatorial Histone H3 Modifications Are Dynamically Altered in Distinct Cell Cycle Phases. Lu C, Coradin M, Janssen KA, Sidoli S, Garcia BA. J Am Soc Mass Spectrom. 2021 Apr 5. doi: 10.1021/jasms.0c00451.

Structure of TFIIK for phosphorylation of CTD of RNA polymerase II

Structure of TFIIK for phosphorylation of CTD of RNA polymerase II. van Eeuwen T, Li T, Kim HJ, Gorbea Colón JJ, Parker MI, Dunbrack RL, Garcia BA, Tsai KL, Murakami K. Sci Adv. 2021 Apr 7;7(15):eabd4420.

Sex-specific effects of in vitro fertilization on adult metabolic outcomes and hepatic transcriptome and proteome in mouse

Sex-specific effects of in vitro fertilization on adult metabolic outcomes and hepatic transcriptome and proteome in mouse. Narapareddy L, Rhon-Calderon EA, Vrooman LA, Baeza J, Nguyen DK, Mesaros C, Lan Y, Garcia BA, Schultz RM, Bartolomei MS. FASEB J. 2021 Apr;35(4):e21523.

Improved SILAC Quantification with Data-Independent Acquisition to Investigate Bortezomib-Induced Protein Degradation

Improved SILAC Quantification with Data-Independent Acquisition to Investigate Bortezomib-Induced Protein Degradation. Pino LK, Baeza J, Lauman R, Schilling B, Garcia BA. J Proteome Res. 2021 Apr 2;20(4):1918-1927.

An Esrrb and Nanog Cell Fate Regulatory Module Controlled by Feed Forward Loop Interactions

An Esrrb and Nanog Cell Fate Regulatory Module Controlled by Feed Forward Loop Interactions. Sevilla A, Papatsenko D, Mazloom AR, Xu H, Vasileva A, Unwin RD, LeRoy G, Chen EY, Garrett-Bakelman FE, Lee DF, Trinite B, Webb RL, Wang Z, Su J, Gingold J, Melnick A, Garcia BA, Whetton AD, MacArthur BD, Ma’ayan A, Lemischka IR. Front Cell Dev Biol. 2021 Mar 19;9:630067.

Long-term behavioral and cell-type-specific molecular effects of early life stress are mediated by H3K79me2 dynamics in medium spiny neurons

Long-term behavioral and cell-type-specific molecular effects of early life stress are mediated by H3K79me2 dynamics in medium spiny neurons. Kronman H, Torres-Berrío A, Sidoli S, Issler O, Godino A, Ramakrishnan A, Mews P, Lardner CK, Parise EM, Walker DM, van der Zee YY, Browne CJ, Boyce BF, Neve R, Garcia BA, Shen L, Peña CJ, Nestler EJ. Nat Neurosci. 2021 Mar 15. doi: 10.1038/s41593-021-00814-8. Online ahead of print.

Chromatin dysregulation associated with NSD1 mutation in head and neck squamous cell carcinoma

Chromatin dysregulation associated with NSD1 mutation in head and neck squamous cell carcinoma. Farhangdoost N, Horth C, Hu B, Bareke E, Chen X, Li Y, Coradin M, Garcia BA, Lu C, Majewski J. Cell Rep. 2021 Feb 23;34(8):108769.

Histone Modifications in Papillomavirus Virion Minichromosomes

Histone Modifications in Papillomavirus Virion Minichromosomes. Porter SS, Liddle JC, Browne K, Pastrana DV, Garcia BA, Buck CB, Weitzman MD, McBride AA. mBio. 2021 Feb 16;12(1):e03274-20.

Cryo-EM structures of engineered active bc1-cbb3 type CIII2CIV super-complexes and electronic communication between the complexes

Cryo-EM structures of engineered active bc1-cbb3 type CIII2CIV super-complexes and electronic communication between the complexes. Steimle S, van Eeuwen T, Ozturk Y, Kim HJ, Braitbard M, Selamoglu N, Garcia BA, Schneidman-Duhovny D, Murakami K, Daldal F. Nat Commun. 2021 Feb 10;12(1):929.

Enhancing Open Modification Searches via a Combined Approach Facilitated by Ursgal

Enhancing Open Modification Searches via a Combined Approach Facilitated by Ursgal. Schulze S, Igiraneza AB, Kösters M, Leufken J, Leidel SA, Garcia BA, Fufezan C, Pohlschroder M. J Proteome Res. 2021 Apr 2;20(4):1986-1996.

HDAC inhibition results in widespread alteration of the histone acetylation landscape and BRD4 targeting to gene bodies

HDAC inhibition results in widespread alteration of the histone acetylation landscape and BRD4 targeting to gene bodies. Slaughter MJ, Shanle EK, Khan A, Chua KF, Hong T, Boxer LD, Allis CD, Josefowicz SZ, Garcia BA, Rothbart SB, Strahl BD, Davis IJ. Cell Rep. 2021 Jan 19;34(3):108638.

Comparative proteomics identifies Schlafen 5 (SLFN5) as a herpes simplex virus restriction factor that suppresses viral transcription

 

Structure and noncanonical Cdk8 activation mechanism within an Argonaute-containing Mediator kinase module

Structure and noncanonical Cdk8 activation mechanism within an Argonaute-containing Mediator kinase module.
Li YC, Chao TC, Kim HJ, Cholko T, Chen SF, Li G, Snyder L, Nakanishi K, Chang CE, Murakami K, Garcia BA, Boyer TG, Tsai KL. Sci Adv. 2021 Jan 15;7(3):eabd4484.

Publications in 2020

Histone H3.3 beyond cancer: Germline mutations in Histone 3 Family 3A and 3B cause a previously unidentified neurodegenerative disorder in 46 patients.

Synthesis and Characterization of a Diazirine-Based Photolabel of the Nonanesthetic Fropofol

Synthesis and Characterization of a Diazirine-Based Photolabel of the Nonanesthetic Fropofol.  White ER, Leace DM, Bedell VM, Bhanu NV, Garcia BA, Dailey WP, Eckenhoff RG. ACS Chem Neurosci. 2020 Dec 23. doi: 10.1021/acschemneuro.0c00667.

Mechanistic insights into volatile anesthetic modulation of K2P channels

Mechanistic insights into volatile anesthetic modulation of K2P channels. Wague A, Joseph TT, Woll KA, Bu W, Vaidya KA, Bhanu NV, Garcia BA, Nimigean CM, Eckenhoff RG, Riegelhaupt PM. Elife. 2020 Dec 21;9:e59839. doi: 10.7554/eLife.59839. Online ahead of print.

H1 histones control the epigenetic landscape by local chromatin compaction

H1 histones control the epigenetic landscape by local chromatin compaction. Willcockson MA, Healton SE, Weiss CN, Bartholdy BA, Botbol Y, Mishra LN, Sidhwani DS, Wilson TJ, Pinto HB, Maron MI, Skalina KA, Toro LN, Zhao J, Lee CH, Hou H, Yusufova N, Meydan C, Osunsade A, David Y, Cesarman E, Melnick AM, Sidoli S, Garcia BA, Edelmann W, Macian F, Skoultchi AI. Nature. 2020 Dec 9. doi: 10.1038/s41586-020-3032-z. Online ahead of print.

Histone Purification Combined with High-Resolution Mass Spectrometry to Examine Histone Post-Translational Modifications and Histone Variants in Caenorhabditis elegans

TET2 chemically modifies tRNAs and regulates tRNA fragment levels

H3K27M in Gliomas Causes a One-Step Decrease in H3K27 Methylation and Reduced Spreading within the Constraints of H3K36 Methylation

H3K27M in Gliomas Causes a One-Step Decrease in H3K27 Methylation and Reduced Spreading within the Constraints of H3K36 Methylation. Harutyunyan AS, Chen H, Lu T, Horth C, Nikbakht H, Krug B, Russo C, Bareke E, Marchione DM, Coradin M, Garcia BA, Jabado N, Majewski J. Cell Rep. 2020 Nov 17;33(7):108390.

Accelerating the field of epigenetic histone modification through mass spectrometry-based approaches

Accelerating the field of epigenetic histone modification through mass spectrometry-based approaches. Lu C, Coradin M, Porter EG, Garcia BA. Mol Cell Proteomics. 2020 Nov 17:mcp.R120.002257.

Epigenetic and transcriptional control of the epidermal growth factor receptor (EGFR) regulates the tumor immune microenvironment in pancreatic cancer

Epigenetic and transcriptional control of the epidermal growth factor receptor (EGFR) regulates the tumor immune microenvironment in pancreatic cancer. Li J, Yuan S, Norgard RJ, Yan F, Sun YH, Kim IK, Merrell AJ, Sela Y, Jiang Y, Bhanu NV, Garcia BA, Vonderheide RH, Blanco A, Stanger BZ. Cancer Discov. 2020 Nov 6:CD-20-0519.

Histone H3.3 G34 mutations promote aberrant PRC2 activity and drive tumor progression

Histone H3.3 G34 mutations promote aberrant PRC2 activity and drive tumor progression.  Jain SU, Khazaei S, Marchione DM, Lundgren SM, Wang X, Weinberg DN, Deshmukh S, Juretic N, Lu C, Allis CD, Garcia BA, Jabado N, Lewis PW. Proc Natl Acad Sci U S A. 2020 Oct 16:202006076.

Histone Purification Combined with High-Resolution Mass Spectrometry to Examine Histone Post-Translational Modifications and Histone Variants in Caenorhabditis elegans

Histone Purification Combined with High-Resolution Mass Spectrometry to Examine Histone Post-Translational Modifications and Histone Variants in Caenorhabditis elegans.  Millan-Ariño L, Yuan ZF, Oomen ME, Brandenburg S, Chernobrovkin A, Salignon J, Körner L, Zubarev RA, Garcia BA, Riedel CG. Curr Protoc Protein Sci. 2020 Dec;102(1):e114.

An integrated multi-omics approach identifies epigenetic alterations associated with Alzheimer’s disease

An integrated multi-omics approach identifies epigenetic alterations associated with Alzheimer’s disease.  Nativio R, Lan Y, Donahue G, Sidoli S, Berson A, Srinivasan AR, Shcherbakova O, Amlie-Wolf A, Nie J, Cui X, He C, Wang LS, Garcia BA, Trojanowski JQ, Bonini NM, Berger SL. Nat Genet. 2020 Oct;52(10):1024-1035.

SIRT1 is downregulated by autophagy in senescence and ageing

H3.3G34W promotes growth and impedes differentiation of osteoblast-like mesenchymal progenitors in Giant Cell Tumour of Bone

H3.3G34W promotes growth and impedes differentiation of osteoblast-like mesenchymal progenitors in Giant Cell Tumour of Bone. Khazaei S, De Jay N, Deshmukh S, Hendrikse LD, Jawhar W, Chen CC, Mikael LG, Faury D, Marchione DM, Lanoix J, Bonneil E, Ishii T, Jain SU, Rossokhata K, Sihota TS, Eveleigh R, Lisi V, Harutyunyan AS, Jung S, Karamchandani J, Dickson BC, Turcotte R, Wunder JS, Thibault P, Lewis PW, Garcia BA, Mack SC, Taylor MD, Garzia L, Kleinman CL, Jabado N. Cancer Discov. 2020 Sep 23:CD-20-0461. doi: 10.1158/2159-8290.CD-20-0461. Online ahead of print.

Lysine and Arginine Protein Post-translational Modifications by Enhanced DIA Libraries: Quantification in Murine Liver Disease

Lysine and Arginine Protein Post-translational Modifications by Enhanced DIA Libraries: Quantification in Murine Liver Disease.  Robinson AE, Binek A, Venkatraman V, Searle BC, Holewinski RJ, Rosenberger G, Parker SJ, Basisty N, Xie X, Lund PJ, Saxena G, Mato JM, Garcia BA, Schilling B, Lu SC, Van Eyk JE. J Proteome Res. 2020 Sep 23. doi: 10.1021/acs.jproteome.0c00685. Online ahead of print.

The catalytic domain of the histone methyltransferase NSD2/MMSET is required for the generation of B1 cells in mice

The catalytic domain of the histone methyltransferase NSD2/MMSET is required for the generation of B1 cells in mice.  Dobenecker MW, Marcello J, Becker A, Rudensky E, Bhanu NV, Carrol T, Garcia BA, Prinjha R, Yurchenko V, Tarakhovsky A. FEBS Lett. 2020 Aug 9. doi: 10.1002/1873-3468.13903. Online ahead of print.

The Viral Polymerase Complex Mediates the Interaction of Viral Ribonucleoprotein Complexes with Recycling Endosomes during Sendai Virus Assembly

The Viral Polymerase Complex Mediates the Interaction of Viral Ribonucleoprotein Complexes with Recycling Endosomes during Sendai Virus Assembly. Genoyer E, Kulej K, Hung CT, Thibault PA, Azarm K, Takimoto T, Garcia BA, Lee B, Lakdawala S, Weitzman MD, López CB. mBio. 2020 Aug 25;11(4):e02028-20. doi: 10.1128/mBio.02028-20.

Extracellular Vesicle and Particle Biomarkers Define Multiple Human Cancers

Extracellular Vesicle and Particle Biomarkers Define Multiple Human Cancers.  Hoshino A, Kim HS, Bojmar L, Gyan KE, Cioffi M, Hernandez J, Zambirinis CP, Rodrigues G, Molina H, Heissel S, Mark MT, Steiner L, Benito-Martin A, Lucotti S, Di Giannatale A, Offer K, Nakajima M, Williams C, Nogués L, Pelissier Vatter FA, Hashimoto A, Davies AE, Freitas D, Kenific CM, Ararso Y, Buehring W, Lauritzen P, Ogitani Y, Sugiura K, Takahashi N, Alečković M, Bailey KA, Jolissant JS, Wang H, Harris A, Schaeffer LM, García-Santos G, Posner Z, Balachandran VP, Khakoo Y, Raju GP, Scherz A, Sagi I, Scherz-Shouval R, Yarden Y, Oren M, Malladi M, Petriccione M, De Braganca KC, Donzelli M, Fischer C, Vitolano S, Wright GP, Ganshaw L, Marrano M, Ahmed A, DeStefano J, Danzer E, Roehrl MHA, Lacayo NJ, Vincent TC, Weiser MR, Brady MS, Meyers PA, Wexler LH, Ambati SR, Chou AJ, Slotkin EK, Modak S, Roberts SS, Basu EM, Diolaiti D, Krantz BA, Cardoso F, Simpson AL, Berger M, Rudin CM, Simeone DM, Jain M, Ghajar CM, Batra SK, Stanger BZ, Bui J, Brown KA, Rajasekhar VK, Healey JH, de Sousa M, Kramer K, Sheth S, Baisch J, Pascual V, Heaton TE, La Quaglia MP, Pisapia DJ, Schwartz R, Zhang H, Liu Y, Shukla A, Blavier L, DeClerck YA, LaBarge M, Bissell MJ, Caffrey TC, Grandgenett PM, Hollingsworth MA, Bromberg J, Costa-Silva B, Peinado H, Kang Y, Garcia BA, O’Reilly EM, Kelsen D, Trippett TM, Jones DR, Matei IR, Jarnagin WR, Lyden D. Cell. 2020 Aug 20;182(4):1044-1061.e18. doi: 10.1016/j.cell.2020.07.009. Epub 2020 Aug 13.

N6-methyladenosine and RNA secondary structure affect transcript stability and protein abundance during systemic salt stress in Arabidopsis

Histone H3.3 phosphorylation amplifies stimulation-induced transcription

Histone H3.3 phosphorylation amplifies stimulation-induced transcription.  Armache A, Yang S, Martínez de Paz A, Robbins LE, Durmaz C, Cheong JQ, Ravishankar A, Daman AW, Ahimovic DJ, Klevorn T, Yue Y, Arslan T, Lin S, Panchenko T, Hrit J, Wang M, Thudium S, Garcia BA, Korb E, Armache KJ, Rothbart SB, Hake SB, Allis CD, Li H, Josefowicz SZ. Nature. 2020 Jul 22. doi: 10.1038/s41586-020-2533-0. Online ahead of print.

Plasma proteomic profiling suggests an association between antigen driven clonal B cell expansion and ME/CFS

Plasma proteomic profiling suggests an association between antigen driven clonal B cell expansion and ME/CFS.  Milivojevic M, Che X, Bateman L, Cheng A, Garcia BA, Hornig M, Huber M, Klimas NG, Lee B, Lee H, Levine S, Montoya JG, Peterson DL, Komaroff AL, Lipkin WI. PLoS One. 2020 Jul 21;15(7):e0236148.

Adenovirus-mediated ubiquitination alters protein-RNA binding and aids viral RNA processing

Adenovirus-mediated ubiquitination alters protein-RNA binding and aids viral RNA processing. Herrmann C, Dybas JM, Liddle JC, Price AM, Hayer KE, Lauman R, Purman CE, Charman M, Kim ET, Garcia BA, Weitzman MD. Nat Microbiol. 2020 Jul 13. doi: 10.1038/s41564-020-0750-9. Online ahead of print.

Histone Acetyltransferase MOF Blocks Acquisition of Quiescence in Ground-State ESCs through Activating Fatty Acid Oxidation

Histone Acetyltransferase MOF Blocks Acquisition of Quiescence in Ground-State ESCs through Activating Fatty Acid Oxidation.  Khoa LTP, Tsan YC, Mao F, Kremer DM, Sajjakulnukit P, Zhang L, Zhou B, Tong X, Bhanu NV, Choudhary C, Garcia BA, Yin L, Smith GD, Saunders TL, Bielas SL, Lyssiotis CA, Dou Y. Cell Stem Cell. 2020 Jun 24:S1934-5909(20)30272-1.

SIRT6 mono-ADP ribosylates KDM2A to locally increase H3K36me2 at DNA damage sites to inhibit transcription and promote repair

SIRT6 mono-ADP ribosylates KDM2A to locally increase H3K36me2 at DNA damage sites to inhibit transcription and promote repair. Rezazadeh S, Yang D, Biashad SA, Firsanov D, Takasugi M, Gilbert M, Tombline G, Bhanu NV, Garcia BA, Seluanov A, Gorbunova V. Aging (Albany NY). 2020 Jun 25;12.

Improvements on the quantitative analysis of Trypanosoma cruzi histone post translational modifications: Study of changes in epigenetic marks through the parasite’s metacyclogenesis and life cycle

Improvements on the quantitative analysis of Trypanosoma cruzi histone post translational modifications: Study of changes in epigenetic marks through the parasite’s metacyclogenesis and life cycle.  de Lima LP, Poubel SB, Yuan ZF, Rosón JN, de Luna Vitorino FN, Holetz FB, Garcia BA, da Cunha JPC. J Proteomics. 2020 May 29:103847. doi: 10.1016/j.jprot.2020.103847.

Metabolic Regulation of the Epigenome Drives Lethal Infantile Ependymoma

Metabolic Regulation of the Epigenome Drives Lethal Infantile Ependymoma. Michealraj KA, Kumar SA, Kim LJY, Cavalli FMG, Przelicki D, Wojcik JB, Delaidelli A, Bajic A, Saulnier O, MacLeod G, Vellanki RN, Vladoiu MC, Guilhamon P, Ong W, Lee JJY, Jiang Y, Holgado BL, Rasnitsyn A, Malik AA, Tsai R, Richman CM, Juraschka K, Haapasalo J, Wang EY, De Antonellis P, Suzuki H, Farooq H, Balin P, Kharas K, Van Ommeren R, Sirbu O, Rastan A, Krumholtz SL, Ly M, Ahmadi M, Deblois G, Srikanthan D, Luu B, Loukides J, Wu X, Garzia L, Ramaswamy V, Kanshin E, Sánchez-Osuna M, El-Hamamy I, Coutinho FJ, Prinos P, Singh S, Donovan LK, Daniels C, Schramek D, Tyers M, Weiss S, Stein LD, Lupien M, Wouters BG, Garcia BA, Arrowsmith CH, Sorensen PH, Angers S, Jabado N, Dirks PB, Mack SC, Agnihotri S, Rich JN, Taylor MD. Cell. 2020 May 20:S0092-8674(20)30553-5.

Disruption of ATRX-RNA interactions uncovers roles in ATRX localization and PRC2 function

Disruption of ATRX-RNA interactions uncovers roles in ATRX localization and PRC2 function. Ren W, Medeiros N, Warneford-Thomson R, Wulfridge P, Yan Q, Bian J, Sidoli S, Garcia BA, Skordalakes E, Joyce E, Bonasio R, Sarma K. Nat Commun. 2020 May 6;11(1):2219.

Human chimeric antigen receptor macrophages for cancer immunotherapy

Human chimeric antigen receptor macrophages for cancer immunotherapy. Klichinsky M, Ruella M, Shestova O, Lu XM, Best A, Zeeman M, Schmierer M, Gabrusiewicz K, Anderson NR, Petty NE, Cummins KD, Shen F, Shan X, Veliz K, Blouch K, Yashiro-Ohtani Y, Kenderian SS, Kim MY, O’Connor RS, Wallace SR, Kozlowski MS, Marchione DM, Shestov M, Garcia BA, June CH, Gill S. Nat Biotechnol. 2020 Mar 23. doi: 10.1038/s41587-020-0462-y. [Epub ahead of print]

Comprehensive Map of the Artemisia annua Proteome and Quantification of Differential Protein Expression in Chemotypes Producing High vs Low Content of Artemisinin

Comprehensive Map of the Artemisia annua Proteome and Quantification of Differential Protein Expression in Chemotypes Producing High vs Low Content of Artemisinin. Chen M, Yan T, Ji L, Yu D, Sidoli S, Yuan Z, Cai C, Chen J, Tang Y, Shen Q, Pan Q, Fu X, Xin K, Liao L, Garcia BA, Yan W, Tang K. Proteomics. 2020 May;20(10):e1900310.

Unraveling the RNA modification code with mass spectrometry

Unraveling the RNA modification code with mass spectrometry. Lauman R, Garcia BA. Mol Omics. 2020 Apr 14. doi: 10.1039/c8mo00247a. [Epub ahead of print]

Bacterial colonization reprograms the neonatal gut metabolome

Bacterial colonization reprograms the neonatal gut metabolome. Bittinger K, Zhao C, Li Y, Ford E, Friedman ES, Ni J, Kulkarni CV, Cai J, Tian Y, Liu Q, Patterson AD, Sarkar D, Chan SHJ, Maranas C, Saha-Shah A, Lund P, Garcia BA, Mattei LM, Gerber JS, Elovitz MA, Kelly A, DeRusso P, Kim D, Hofstaedter CE, Goulian M, Li H, Bushman FD, Zemel BS, Wu GD. Nat Microbiol. 2020 Apr 13. doi: 10.1038/s41564-020-0694-0. [Epub ahead of print]

Disruption of the Plasmodium falciparum life cycle through transcriptional reprogramming by inhibitors of Jumonji demethylases

Disruption of the Plasmodium falciparum life cycle through transcriptional reprogramming by inhibitors of Jumonji demethylases. Matthews KA, Senagbe KM, Notzel C, Gonzalez CA, Tong X, Rijo-Ferreira F, Natarajan BV, Miguel-Blanco C, Lafuente-Monasterio MJ, Garcia BA, Kafsack BF, Martinez ED. ACS Infect Dis. 2020 May 8;6(5):1058-1075.

Reproductive tract extracellular vesicles are sufficient to transmit intergenerational stress and program neurodevelopment

Reproductive tract extracellular vesicles are sufficient to transmit intergenerational stress and program neurodevelopment. Chan JC, Morgan CP, Adrian Leu N, Shetty A, Cisse YM, Nugent BM, Morrison KE, Jašarević E, Huang W, Kanyuch N, Rodgers AB, Bhanu NV, Berger DS, Garcia BA, Ament S, Kane M, Neill Epperson C, Bale TL. Nat Commun. 2020 Mar 20;11(1):1499.

Global regulation of the histone mark H3K36me2 underlies epithelial plasticity and metastatic progression

Global regulation of the histone mark H3K36me2 underlies epithelial plasticity and metastatic progression. Yuan S, Natesan R, Sanchez-Rivera FJ, Li J, Bhanu NV, Yamazoe T, Lin JH, Merrell AJ, Sela Y, Thomas SK, Jiang Y, Plesset JB, Miller EM, Shi J, Garcia BA, Lowe SW, Asangani IA, Stanger BZ. Cancer Discov. 2020 Jun;10(6):854-871.

Comparative differential cuproproteomes of Rhodobacter capsulatus reveal novel copper homeostasis related proteins

Comparative differential cuproproteomes of Rhodobacter capsulatus reveal novel copper homeostasis related proteins. Selamoglu N, Önder Ö, Öztürk Y, Khalfaoui-Hassani B, Blaby-Haas CE, Garcia BA, Koch HG, Daldal F. Metallomics. 2020 Apr 1;12(4):572-591.

Lysine 4 of histone H3.3 is required for embryonic stem cell differentiation, histone enrichment at regulatory regions and transcription accuracy

Lysine 4 of histone H3.3 is required for embryonic stem cell differentiation, histone enrichment at regulatory regions and transcription accuracy. Gehre M, Bunina D, Sidoli S, Lübke MJ, Diaz N, Trovato M, Garcia BA, Zaugg JB, Noh KM. Nat Genet. 2020 Mar;52(3):273-282.

Bullet points to evaluate the performance of the middle-down proteomics workflow for histone modification analysis

Bullet points to evaluate the performance of the middle-down proteomics workflow for histone modification analysis. Coradin M, Mendoza MR, Sidoli S, Alpert AJ, Lu C, Garcia BA. Methods. 2020 Feb 15. pii: S1046-2023(19)30173-2.

A computational platform for high-throughput analysis of RNA sequences and modifications by mass spectrometry.

A computational platform for high-throughput analysis of RNA sequences and modifications by mass spectrometry. Wein S, Andrews B, Sachsenberg T, Santos-Rosa H, Kohlbacher O, Kouzarides T, Garcia BA, Weisser H. Nat Commun. 2020 Feb 17;11(1):926.

HYPERsol: High-Quality Data from Archival FFPE Tissue for Clinical Proteomics

HYPERsol: High-Quality Data from Archival FFPE Tissue for Clinical Proteomics. Marchione DM, Ilieva I, Devins K, Sharpe D, Pappin DJ, Garcia BA, Wilson JP, Wojcik JB. J Proteome Res. 2020 Feb 7;19(2):973-983.

Quantitative live cell imaging reveals influenza virus manipulation of Rab11A transport through reduced dynein association

Quantitative live cell imaging reveals influenza virus manipulation of Rab11A transport through reduced dynein association. Bhagwat AR, Le Sage V, Nturibi E, Kulej K, Jones J, Guo M, Tae Kim E, Garcia BA, Weitzman MD, Shroff H, Lakdawala SS. Nat Commun. 2020 Jan 7;11(1):23.

Native Chromatin Proteomics Reveals a Role for Specific Nucleoporins in Heterochromatin Organization and Maintenance

Native Chromatin Proteomics Reveals a Role for Specific Nucleoporins in Heterochromatin Organization and Maintenance. Iglesias N, Paulo JA, Tatarakis A, Wang X, Edwards AL, Bhanu NV, Garcia BA, Haas W, Gygi SP, Moazed D. Mol Cell. 2020 Jan 2;77(1):51-66.

Publications in 2019

Deep profiling and custom databases improve detection of proteoforms generated by alternative splicing

Deep profiling and custom databases improve detection of proteoforms generated by alternative splicing. Agosto LM, Gazzara MR, Radens CM, Sidoli S, Baeza J, Garcia BA, Lynch KW. Genome Res. 2019 Dec;29(12):2046-2055.

Alcohol metabolism contributes to brain histone acetylation

Alcohol metabolism contributes to brain histone acetylation.  Mews P, Egervari G, Nativio R, Sidoli S, Donahue G, Lombroso SI, Alexander DC, Riesche SL, Heller EA, Nestler EJ, Garcia BA, Berger SL. Nature. 2019 Oct;574(7780):717-721.

Recognition of Histone Crotonylation by Taf14 Links Metabolic State to Gene Expression

Recognition of Histone Crotonylation by Taf14 Links Metabolic State to Gene Expression. Gowans GJ, Bridgers JB, Zhang J, Dronamraju R, Burnetti A, King DA, Thiengmany AV, Shinsky SA, Bhanu NV, Garcia BA, Buchler NE, Strahl BD, Morrison AJ. Mol Cell. 2019 Oct 23. pii: S1097-2765(19)30734-8.

Azi-medetomidine: Synthesis and Characterization of a Novel α2 Adrenergic Photoaffinity Ligand

Azi-medetomidine: Synthesis and Characterization of a Novel α2 Adrenergic Photoaffinity Ligand. McKinstry-Wu AR, Woll KA, Joseph TT, Bu W, White ER, Bhanu NV, Garcia BA, Brannigan G, Dailey WP, Eckenhoff RG. ACS Chem Neurosci. 2019 Nov 20;10(11):4716-4728.

Quantitative analysis of global protein lysine methylation by mass spectrometry

Quantitative analysis of global protein lysine methylation by mass spectrometry. Lund PJ, Lehman SM, Garcia BA. Methods Enzymol. 2019;626:475-498.

Histone H3K23-specific acetylation by MORF is coupled to H3K14 acylation

Histone H3K23-specific acetylation by MORF is coupled to H3K14 acylation. Klein BJ, Jang SM, Lachance C, Mi W, Lyu J, Sakuraba S, Krajewski K, Wang WW, Sidoli S, Liu J, Zhang Y, Wang X, Warfield BM, Kueh AJ, Voss AK, Thomas T, Garcia BA, Liu WR, Strahl BD, Kono H, Li W, Shi X, Côté J, Kutateladze TG. Nat Commun. 2019 Oct 17;10(1):4724.

A mass spectrometry-based assay using metabolic labeling to rapidly monitor chromatin accessibility of modified histone proteins

A mass spectrometry-based assay using metabolic labeling to rapidly monitor chromatin accessibility of modified histone proteins. Sidoli S, Lopes M, Lund PJ, Goldman N, Fasolino M, Coradin M, Kulej K, Bhanu NV, Vahedi G, Garcia BA. Sci Rep. 2019 Sep 20;9(1):13613.

Quantitation of Single and Combinatorial Histone Modifications by Integrated Chromatography of Bottom-up Peptides and Middle-down Polypeptide Tails

Quantitation of Single and Combinatorial Histone Modifications by Integrated Chromatography of Bottom-up Peptides and Middle-down Polypeptide Tails. Janssen KA, Coradin M, Lu C, Sidoli S, Garcia BA. J Am Soc Mass Spectrom. 2019 Dec;30(12):2449-2459.

Automethylation of PRC2 promotes H3K27 methylation and is impaired in H3K27M pediatric glioma

Automethylation of PRC2 promotes H3K27 methylation and is impaired in H3K27M pediatric glioma. Lee CH, Yu JR, Granat J, Saldaña-Meyer R, Andrade J, LeRoy G, Jin Y, Lund P, Stafford JM, Garcia BA, Ueberheide B, Reinberg D. Genes Dev. 2019 Oct 1;33(19-20):1428-1440.

The histone mark H3K36me2 recruits DNMT3A and shapes the intergenic DNA methylation landscape

The histone mark H3K36me2 recruits DNMT3A and shapes the intergenic DNA methylation landscape. Weinberg DN, Papillon-Cavanagh S, Chen H, Yue Y, Chen X, Rajagopalan KN, Horth C, McGuire JT, Xu X, Nikbakht H, Lemiesz AE, Marchione DM, Marunde MR, Meiners MJ, Cheek MA, Keogh MC, Bareke E, Djedid A, Harutyunyan AS, Jabado N, Garcia BA, Li H, Allis CD, Majewski J, Lu C. Nature. 2019 Sep;573(7773):281-286.

PHF19 promotes multiple myeloma tumorigenicity through PRC2 activation

PHF19 promotes multiple myeloma tumorigenicity through PRC2 activation. Ren Z, Ahn JH, Liu H, Tsai YH, Bhanu NV, Koss B, Allison DF, Ma A, Storey AJ, Wang P, Mackintosh SG, Edmondson RD, Groen RWJ, Martens AC, Garcia BA, Tackett AJ, Jin J, Cai L, Zheng D, Wang GG. Blood. 2019 Aug 5. pii: blood.2019000578. doi: 10.1182/blood.2019000578. [Epub ahead of print]

Regulation of nuclear epigenome by mitochondrial DNA heteroplasmy

Regulation of nuclear epigenome by mitochondrial DNA heteroplasmy. Kopinski PK, Janssen KA, Schaefer PM, Trefely S, Perry CE, Potluri P, Tintos-Hernandez JA, Singh LN, Karch KR, Campbell SL, Doan MT, Jiang H, Nissim I, Nakamaru-Ogiso E, Wellen KE, Snyder NW, Garcia BA, Wallace DC. Proc Natl Acad Sci U S A. 2019 Aug 6;116(32):16028-16035.

Glucose Metabolism Drives Histone Acetylation Landscape Transitions that Dictate Muscle Stem Cell Function

Glucose Metabolism Drives Histone Acetylation Landscape Transitions that Dictate Muscle Stem Cell Function. Yucel N, Wang YX, Mai T, Porpiglia E, Lund PJ, Markov G, Garcia BA, Bendall SC, Angelo M, Blau HM. Cell Rep. 2019 Jun 25;27(13):3939-3955.e6.

Single Cell Proteomics to Study Embryonic Asymmetry in Xenopus laevis Embryos

Single Cell Proteomics to Study Embryonic Asymmetry in Xenopus laevis Embryos. Saha-Shah A, Esmaeili M, Sidoli S, Hwang H, Yang J, Klein PS, Garcia BA. Anal Chem. 2019 Jun 13. doi: 10.1021/acs.analchem.9b00327. [Epub ahead of print]

Histone H3K27 dimethyl loss is highly specific for malignant peripheral nerve sheath tumor and distinguishes true PRC2 loss from isolated H3K27 trimethyl loss

Histone H3K27 dimethyl loss is highly specific for malignant peripheral nerve sheath tumor and distinguishes true PRC2 loss from isolated H3K27 trimethyl loss. Marchione DM, Lisby A, Viaene AN, Santi M, Nasrallah M, Wang LP, Williams EA, Larque AB, Chebib I, Garcia BA, Wojcik JB. Mod Pathol. 2019 Jun 7. doi: 10.1038/s41379-019-0287-8. [Epub ahead of print]

Novel functions of the ubiquitin-independent proteasome system in regulating Xenopus germline development

Novel functions of the ubiquitin-independent proteasome system in regulating Xenopus germline development. Hwang H, Jin Z, Krishnamurthy VV, Saha A, Klein PS, Garcia B, Mei W, King ML, Zhang K, Yang J. Development. 2019 Apr 23;146(8).

The E3 ligase adaptor molecule SPOP regulates fetal hemoglobin levels in adult erythroid cells

The E3 ligase adaptor molecule SPOP regulates fetal hemoglobin levels in adult erythroid cells. Lan X, Khandros E, Huang P, Peslak SA, Bhardwaj SK, Grevet JD, Abdulmalik O, Wang H, Keller CA, Giardine B, Baeza J, Duffner ER, El Demerdash O, Wu XS, Vakoc CR, Garcia BA, Hardison RC, Shi J, Blobel GA. Blood Adv. 2019 May 28;3(10):1586-1597

One minute analysis of 200 histone post-translational modifications by direct injection mass spectrometry

One minute analysis of 200 histone post-translational modifications by direct injection mass spectrometry. Sidoli S, Kori Y, Lopes M, Yuan ZF, Kim HJ, Kulej K, Janssen KA, Agosto LM, Cunha JPC, Andrews AJ, Garcia BA. Genome Res. 2019 Jun;29(6):978-987.

PFA ependymoma-associated protein EZHIP inhibits PRC2 activity through a H3 K27M-like mechanism

PFA ependymoma-associated protein EZHIP inhibits PRC2 activity through a H3 K27M-like mechanism. Jain SU, Do TJ, Lund PJ, Rashoff AQ, Diehl KL, Cieslik M, Bajic A, Juretic N, Deshmukh S, Venneti S, Muir TW, Garcia BA, Jabado N, Lewis PW. Nat Commun. 2019 May 13;10(1):2146.

Pervasive H3K27 Acetylation Leads to ERV Expression and a Therapeutic Vulnerability in H3K27M Gliomas

Pervasive H3K27 Acetylation Leads to ERV Expression and a Therapeutic Vulnerability in H3K27M Gliomas. Krug B, De Jay N, Harutyunyan AS, Deshmukh S, Marchione DM, Guilhamon P, Bertrand KC, Mikael LG, McConechy MK, Chen CCL, Khazaei S, Koncar RF, Agnihotri S, Faury D, Ellezam B, Weil AG, Ursini-Siegel J, De Carvalho DD, Dirks PB, Lewis PW, Salomoni P, Lupien M, Arrowsmith C, Lasko PF, Garcia BA, Kleinman CL, Jabado N, Mack SC. Cancer Cell. 2019 May 13;35(5):782-797.

Isotopic Labeling and Quantitative Proteomics of Acetylation on Histones and Beyond

Isotopic Labeling and Quantitative Proteomics of Acetylation on Histones and Beyond. Lund PJ, Kori Y, Zhao X, Sidoli S, Yuan ZF, Garcia BA. Methods Mol Biol. 2019;1977:43-70.

Interrogating Histone Acetylation and BRD4 as Mitotic Bookmarks of Transcription

Interrogating Histone Acetylation and BRD4 as Mitotic Bookmarks of Transcription. Behera V, Stonestrom AJ, Hamagami N, Hsiung CC, Keller CA, Giardine B, Sidoli S, Yuan ZF, Bhanu NV, Werner MT, Wang H, Garcia BA, Hardison RC, Blobel GA. Cell Rep. 2019 Apr 9;27(2):400-415.

The long noncoding RNA Falcor regulates Foxa2 expression to maintain lung epithelial homeostasis and promote regeneration

The long noncoding RNA Falcor regulates Foxa2 expression to maintain lung epithelial homeostasis and promote regeneration. Swarr DT, Herriges M, Li S, Morley M, Fernandes S, Sridharan A, Zhou S, Garcia BA, Stewart K, Morrisey EE. Genes Dev. 2019 Jun 1;33(11-12):656-668.

Target identification reveals lanosterol synthase as a vulnerability in glioma

Target identification reveals lanosterol synthase as a vulnerability in glioma. Phillips RE, Yang Y, Smith RC, Thompson BM, Yamasaki T, Soto-Feliciano YM, Funato K, Liang Y, Garcia-Bermudez J, Wang X, Garcia BA, Yamasaki K, McDonald JG, Birsoy K, Tabar V, Allis CD. Proc Natl Acad Sci U S A. 2019 Apr 16;116(16):7957-7962.

Epigenomic reordering induced by Polycomb loss drives oncogenesis but leads to therapeutic vulnerabilities in malignant peripheral nerve sheath tumors

Epigenomic reordering induced by Polycomb loss drives oncogenesis but leads to therapeutic vulnerabilities in malignant peripheral nerve sheath tumors. Wojcik JB, Marchione DM, Sidoli S, Djedid A, Lisby A, Majewski J, Garcia BA. Cancer Res. 2019 Jul 1;79(13):3205-3219.

H3K27M induces defective chromatin spread of PRC2-mediated repressive H3K27me2/me3 and is essential for glioma tumorigenesis

H3K27M induces defective chromatin spread of PRC2-mediated repressive H3K27me2/me3 and is essential for glioma tumorigenesis. Harutyunyan AS, Krug B, Chen H, Papillon-Cavanagh S, Zeinieh M, De Jay N, Deshmukh S, Chen CCL, Belle J, Mikael LG, Marchione DM, Li R, Nikbakht H, Hu B, Cagnone G, Cheung WA, Mohammadnia A, Bechet D, Faury D, McConechy MK, Pathania M, Jain SU, Ellezam B, Weil AG, Montpetit A, Salomoni P, Pastinen T, Lu C, Lewis PW, Garcia BA, Kleinman CL, Jabado N, Majewski J. Nat Commun. 2019 Mar 19;10(1):1262.

Regulation of proline-directed kinases and the trans-histone code H3K9me3/H4K20me3 during human myogenesis

Regulation of proline-directed kinases and the trans-histone code H3K9me3/H4K20me3 during human myogenesis. Bhanu NV, Sidoli S, Yuan ZF, Molden RC, Garcia BA.  J Biol Chem. 2019 May 17;294(20):8296-8308.

Histone serotonylation is a permissive modification that enhances TFIID binding to H3K4me3

Histone serotonylation is a permissive modification that enhances TFIID binding to H3K4me3. Farrelly LA, Thompson RE, Zhao S, Lepack AE, Lyu Y, Bhanu NV, Zhang B, Loh YE, Ramakrishnan A, Vadodaria KC, Heard KJ, Erikson G, Nakadai T, Bastle RM, Lukasak BJ, Zebroski H 3rd, Alenina N, Bader M, Berton O, Roeder RG, Molina H, Gage FH, Shen L, Garcia BA, Li H, Muir TW, Maze I. Nature. 2019, 67(7749):535-539.

RNA exploits an exposed regulatory site to inhibit the enzymatic activity of PRC2

RNA exploits an exposed regulatory site to inhibit the enzymatic activity of PRC2. Zhang Q, McKenzie NJ, Warneford-Thomson R, Gail EH, Flanigan SF, Owen BM, Lauman R, Levina V, Garcia BA, Schittenhelm RB, Bonasio R, Davidovich C. Nat Struct Mol Biol. 2019 Mar;26(3):237-247.

Histone Acetyltransferase p300 Induces De Novo Super-Enhancers to Drive Cellular Senescence

Histone Acetyltransferase p300 Induces De Novo Super-Enhancers to Drive Cellular Senescence. Sen P, Lan Y, Li CY, Sidoli S, Donahue G, Dou Z, Frederick B, Chen Q, Luense LJ, Garcia BA, Dang W, Johnson FB, Adams PD, Schultz DC, Berger SL. Mol Cell. 2019 Feb 21;73(4):684-698.

Coordination between TGF-β cellular signaling and epigenetic regulation during epithelial to mesenchymal transition

Coordination between TGF-β cellular signaling and epigenetic regulation during epithelial to mesenchymal transition. Lu C, Sidoli S, Kulej K, Ross K, Wu CH, Garcia BA. Epigenetics Chromatin. 2019 Feb 8;12(1):11.

Integrated Analysis of Acetyl-CoA and Histone Modification via Mass Spectrometry to Investigate Metabolically Driven Acetylation

Integrated Analysis of Acetyl-CoA and Histone Modification via Mass Spectrometry to Investigate Metabolically Driven Acetylation. Sidoli S, Trefely S, Garcia BA, Carrer A. Methods Mol Biol. 2019;1928:125-147.

Acetyl-CoA metabolism supports multi-step pancreatic tumorigenesis

Acetyl-CoA metabolism supports multi-step pancreatic tumorigenesis. Carrer A, Trefely S, Zhao S, Campbell S, Norgard RJ, Schultz KC, Sidoli S, Parris JLD, Affronti HC, Sivanand S, Egolf S, Sela Y, Trizzino M, Gardini A, Garcia BA, Snyder NW, Stanger BZ, Wellen K. Cancer Discov. 2019 Mar;9(3):416-435.

H3K9me3-heterochromatin loss at protein-coding genes enables developmental lineage specification

H3K9me3-heterochromatin loss at protein-coding genes enables developmental lineage specification. Nicetto D, Donahue G, Jain T, Peng T, Sidoli S, Sheng L, Montavon T, Becker JS, Grindheim JM, Blahnik K, Garcia BA, Tan K, Bonasio R, Jenuwein T, Zaret KS. Science. 2019 Jan 18;363(6424):294-297.

Publications in 2018

Impaired cocaine-induced behavioral plasticity in the male offspring of cocaine-experienced sires

Impaired cocaine-induced behavioral plasticity in the male offspring of cocaine-experienced sires. Wimmer ME, Vassoler FM, White SL, Schmidt HD, Sidoli S, Han Y, Garica BA, Pierce RC. Eur J Neurosci. 2019 May;49(9):1115-1126.

Proteomic approaches for cancer epigenetics research

Proteomic approaches for cancer epigenetics research. Marchione DM, Garcia BA, Wojcik J. Expert Rev Proteomics. 2018 Nov 27:1-15.

The HDAC3-SMARCA4-miR-27a axis promotes expression of the PAX3:FOXO1 fusion oncogene in rhabdomyosarcoma

The HDAC3-SMARCA4-miR-27a axis promotes expression of the PAX3:FOXO1 fusion oncogene in rhabdomyosarcoma. Bharathy N, Berlow NE, Wang E, Abraham J, Settelmeyer TP, Hooper JE, Svalina MN, Ishikawa Y, Zientek K, Bajwa Z, Goros MW, Hernandez BS, Wolff JE, Rudek MA, Xu L, Anders NM, Pal R, Harrold AP, Davies AM, Ashok A, Bushby D, Mancini M, Noakes C, Goodwin NC, Ordentlich P, Keck J, Hawkins DS, Rudzinski ER, Chatterjee B, Bächinger HP, Barr FG, Liddle J, Garcia BA, Mansoor A, Perkins TJ, Vakoc CR, Michalek JE, Keller C. Sci Signal. 2018 Nov 20;11(557).

Targeting CDK9 Reactivates Epigenetically Silenced Genes in Cancer

Targeting CDK9 Reactivates Epigenetically Silenced Genes in Cancer. Zhang H, Pandey S, Travers M, Sun H, Morton G, Madzo J, Chung W, Khowsathit J, Perez-Leal O, Barrero CA, Merali C, Okamoto Y, Sato T, Pan J, Garriga J, Bhanu NV, Simithy J, Patel B, Huang J, Raynal NJ, Garcia BA, Jacobson MA, Kadoch C, Merali S, Zhang Y, Childers W, Abou-Gharbia M, Karanicolas J, Baylin SB, Zahnow CA, Jelinek J, Graña X, Issa JJ. Cell. 2018 Nov 15;175(5):1244-1258.

Histone modification signatures in human sperm distinguish clinical abnormalities

Histone modification signatures in human sperm distinguish clinical abnormalities. Schon SB, Luense LJ, Wang X, Bartolomei MS, Coutifaris C, Garcia BA, Berger SL. J Assist Reprod Genet. 2019 Feb;36(2):267-275.

Target site specificity and in vivo complexity of the mammalian arginylome

Target site specificity and in vivo complexity of the mammalian arginylome. Wang J, Pejaver VR, Dann GP, Wolf MY, Kellis M, Huang Y, Garcia BA, Radivojac P, Kashina A. Sci Rep. 2018 Nov 1;8(1):16177.

Phosphorylation of TIP60 suppresses 53BP1 localization at DNA damage sites

Phosphorylation of TIP60 suppresses 53BP1 localization at DNA damage sites. Li ML, Jiang Q, Bhanu NV, Wu J, Li W, Garcia BA, Greenberg RA. Mol Cell Biol. 2018 Oct 8. pii: MCB.00209-18. doi: 10.1128/MCB.00209-18. [Epub ahead of print]

Hydrogen-Deuterium Exchange Coupled to Top- and Middle-Down Mass Spectrometry Reveals Histone Tail Dynamics before and after Nucleosome Assembly

Hydrogen-Deuterium Exchange Coupled to Top- and Middle-Down Mass Spectrometry Reveals Histone Tail Dynamics before and after Nucleosome Assembly. Karch KR, Coradin M, Zandarashvili L, Kan ZY, Gerace M, Englander SW, Black BE, Garcia BA. Structure. 2018 Dec 4;26(12):1651-1663.

Acetate Production from Glucose and Coupling to Mitochondrial Metabolism in Mammals

Acetate Production from Glucose and Coupling to Mitochondrial Metabolism in Mammals. Liu X, Cooper DE, Cluntun AA, Warmoes MO, Zhao S, Reid MA, Liu J, Lund PJ, Lopes M, Garcia BA, Wellen KE, Kirsch DG, Locasale JW. Cell. 2018 Oct 4;175(2):502-513.

Distinct Roles of Two Histone Methyltransferases in Transmitting H3K36me3-Based Epigenetic Memory Across Generations in Caenorhabditis elegans

Distinct Roles of Two Histone Methyltransferases in Transmitting H3K36me3-Based Epigenetic Memory Across Generations in Caenorhabditis elegans. Kreher J, Takasaki T, Cockrum C, Sidoli S, Garcia BA, Jensen ON, Strome S. Genetics. 2018 Nov;210(3):969-982.

Extensive Characterization of Heavily Modified Histone Tails by 193 nm Ultraviolet Photodissociation Mass Spectrometry via a Middle-Down Strategy

Extensive Characterization of Heavily Modified Histone Tails by 193 nm Ultraviolet Photodissociation Mass Spectrometry via a Middle-Down Strategy. Greer SM, Sidoli S, Coradin M, Schack Jespersen M, Schwämmle V, Jensen ON, Garcia BA, Brodbelt JS. Anal Chem. 2018 Sep 4;90(17):10425-10433.

Domain-focused CRISPR screen identifies HRI as a fetal hemoglobin regulator in human erythroid cells

Domain-focused CRISPR screen identifies HRI as a fetal hemoglobin regulator in human erythroid cells. Grevet JD, Lan X, Hamagami N, Edwards CR, Sankaranarayanan L, Ji X, Bhardwaj SK, Face CJ, Posocco DF, Abdulmalik O, Keller CA, Giardine B, Sidoli S, Garcia BA, Chou ST, Liebhaber SA, Hardison RC, Shi J, Blobel GA. Science. 2018 Jul 20;361(6399):285-290

Capturing the Onset of PRC2-Mediated Repressive Domain Formation

Capturing the Onset of PRC2-Mediated Repressive Domain Formation. Oksuz O, Narendra V, Lee CH, Descostes N, LeRoy G, Raviram R, Blumenberg L, Karch K, Rocha PP, Garcia BA, Skok JA, Reinberg D. Mol Cell. 2018 Jun 21;70(6):1149-1162.

Interrogation of nonconserved human adipose lincRNAs identifies a regulatory role of linc-ADAL in adipocyte metabolism

Interrogation of nonconserved human adipose lincRNAs identifies a regulatory role of linc-ADAL in adipocyte metabolism. Zhang X, Xue C, Lin J, Ferguson JF, Weiner A, Liu W, Han Y, Hinkle C, Li W, Jiang H, Gosai S, Hachet M, Garcia BA, Gregory BD, Soccio RE, Hogenesch JB, Seale P, Li M, Reilly MP. Sci Transl Med. 2018 Jun 20;10(446).

Rpp29 regulates histone H3.3 chromatin assembly through transcriptional mechanisms

Rpp29 regulates histone H3.3 chromatin assembly through transcriptional mechanisms. Shastrula PK, Lund PJ, Garcia BA, Janicki SM. J Biol Chem. 2018 Aug 10;293(32):12360-12377.

High-Quality Genome Assemblies Reveal Long Non-coding RNAs Expressed in Ant Brains.

High-Quality Genome Assemblies Reveal Long Non-coding RNAs Expressed in Ant Brains. Shields EJ, Sheng L, Weiner AK, Garcia BA, Bonasio R. Cell Rep. 2018 Jun 5;23(10):3078-3090.

An allosteric propofol-binding site in kinesin disrupts kinesin-mediated processive movement on microtubules

An allosteric propofol-binding site in kinesin disrupts kinesin-mediated processive movement on microtubules. Woll KA, Guzik-Lendrum S, Bensel BM, Bhanu NV, Dailey WP, Garcia BA, Gilbert SP, Eckenhoff RG. J Biol Chem. 2018 Jul 20;293(29):11283-11295.

EpiProfile 2.0: A Computational Platform for Processing Epi-Proteomics Mass Spectrometry Data

EpiProfile 2.0: A Computational Platform for Processing Epi-Proteomics Mass Spectrometry Data. Yuan ZF, Sidoli S, Marchione DM, Simithy J, Janssen KA, Szurgot MR, Garcia BA. J Proteome Res. 2018 Jul 6;17(7):2533-2541.

Allosteric Activation Dictates PRC2 Activity Independent of Its Recruitment to Chromatin

Allosteric Activation Dictates PRC2 Activity Independent of Its Recruitment to Chromatin. Lee CH, Yu JR, Kumar S, Jin Y, LeRoy G, Bhanu N, Kaneko S, Garcia BA, Hamilton AD, Reinberg D. Mol Cell. 2018 May 3;70(3):422-434.

Wnt5a signaling induced phosphorylation increases APT1 activity and promotes melanoma metastatic behavior

Wnt5a signaling induced phosphorylation increases APT1 activity and promotes melanoma metastatic behavior. Sadeghi RS, Kulej K, Kathayat RS, Garcia BA, Dickinson BC, Brady DC, Witze E. Elife. 2018 Apr 12;7. pii: e34362.

Microbes vs. chemistry in the origin of the anaerobic gut lumen

Microbes vs. chemistry in the origin of the anaerobic gut lumen. Friedman ES, Bittinger K, Esipova TV, Hou L, Chau L, Jiang J, Mesaros C, Lund PJ, Liang X, FitzGerald GA, Goulian M, Lee D, Garcia BA, Blair IA, Vinogradov SA, Wu GD. Proc Natl Acad Sci U S A. 2018 Apr 17;115(16):4170-4175.

Integrating Proteomics and Targeted Metabolomics to Understand Global Changes in Histone Modifications

Integrating Proteomics and Targeted Metabolomics to Understand Global Changes in Histone Modifications. Simithy J, Sidoli S, Garcia BA. Proteomics. 2018 Sep;18(18):e1700309.

Identification of binding sites contributing to volatile anesthetic effects on GABA type A receptors

Identification of binding sites contributing to volatile anesthetic effects on GABA type A receptors. Woll KA, Zhou X, Bhanu NV, Garcia BA, Covarrubias M, Miller KW, Eckenhoff RG. FASEB J. 2018 Aug;32(8):4172-4189.

How many human proteoforms are there?

How many human proteoforms are there? Aebersold R, Agar JN, Amster IJ, Baker MS, Bertozzi CR, Boja ES, Costello CE, Cravatt BF, Fenselau C, Garcia BA, Ge Y, Gunawardena J, Hendrickson RC, Hergenrother PJ, Huber CG, Ivanov AR, Jensen ON, Jewett MC, Kelleher NL, Kiessling LL, Krogan NJ, Larsen MR, Loo JA, Ogorzalek Loo RR, Lundberg E, MacCoss MJ, Mallick P, Mootha VK, Mrksich M, Muir TW, Patrie SM, Pesavento JJ, Pitteri SJ, Rodriguez H, Saghatelian A, Sandoval W, Schlüter H, Sechi S, Slavoff SA, Smith LM, Snyder MP, Thomas PM, Uhlén M, Van Eyk JE, Vidal M, Walt DR, White FM, Williams ER, Wohlschlager T, Wysocki VH, Yates NA, Young NL, Zhang B. Nat Chem Biol. 2018 Feb 14;14(3):206-214.

KMT2D regulates p63 target enhancers to coordinate epithelial homeostasis

KMT2D regulates p63 target enhancers to coordinate epithelial homeostasis. Lin-Shiao E, Lan Y, Coradin M, Anderson A, Donahue G, Simpson CL, Sen P, Saffie R, Busino L, Garcia BA, Berger SL, Capell BC. Genes Dev. 2018 Jan 15;32(2):181-193.

Publications in 2017

Genomic and Proteomic Resolution of Heterochromatin and Its Restriction of Alternate Fate Genes

Genomic and Proteomic Resolution of Heterochromatin and Its Restriction of Alternate Fate Genes. Becker JS, McCarthy RL, Sidoli S, Donahue G, Kaeding KE, He Z, Lin S, Garcia BA, Zaret KS. Mol Cell. 2017 Dec 21;68(6):1023-1037.

TDP-43 Promotes Neurodegeneration by Impairing Chromatin Remodeling

TDP-43 Promotes Neurodegeneration by Impairing Chromatin Remodeling. Berson A, Sartoris A, Nativio R, Van Deerlin V, Toledo JB, Porta S, Liu S, Chung CY, Garcia BA, Lee VM, Trojanowski JQ, Johnson FB, Berger SL, Bonini NM. Curr Biol. 2017 Nov 9. pii: S0960-9822(17)31327-1.

GiaPronto: a one-click graph visualization software for proteomics datasets

GiaPronto: a one-click graph visualization software for proteomics datasets. Weiner AK, Sidoli S, Diskin SJ, Garcia B. Mol Cell Proteomics. 2018 Jul;17(7):1426-1431.

PKC epsilon is a Key Regulator of Mitochondrial Redox Homeostasis in Acute Myeloid Leukemia

PKC epsilon is a Key Regulator of Mitochondrial Redox Homeostasis in Acute Myeloid Leukemia. Di Marcantonio D, Martinez E, Sidoli S, Vadaketh J, Nieborowska-Skorska M, Gupta A, Meadows JM, Ferraro F, Masselli E, Challen GA, Milsom MD, Scholl C, Froehling S, Balachandran S, Skorski T, Garcia B, Mirandola P, Gobbi G, Garzon R, Vitale M, Sykes SM. Clin Cancer Res. 2018 Feb 1;24(3):608-618.

Assessment of quantification precision of histone post-translational modifications by using an ion trap and down to 50,000 cells as starting material

Assessment of quantification precision of histone post-translational modifications by using an ion trap and down to 50,000 cells as starting material. Guo Q, Sidoli S, Garcia BA, Zhao X. J Proteome Res. 2018 Jan 5;17(1):234-242.

Naked Mole Rat Cells Have a Stable Epigenome that Resists iPSC Reprogramming

Naked Mole Rat Cells Have a Stable Epigenome that Resists iPSC Reprogramming. Tan L, Ke Z, Tombline G, Macoretta N, Hayes K, Tian X, Lv R, Ablaeva J, Gilbert M, Bhanu NV, Yuan ZF, Garcia BA, Shi YG, Shi Y, Seluanov A, Gorbunova V. Stem Cell Reports. 2017 Nov 14;9(5):1721-1734

Characterization of histone acylations links chromatin modifications with metabolism

Characterization of histone acylations links chromatin modifications with metabolism. Simithy J, Sidoli S, Yuan ZF, Coradin M, Bhanu NV, Marchione DM, Klein BJ, Bazilevsky GA, McCullough CE, Magin RS, Kutateladze TG, Snyder NW, Marmorstein R, Garcia BA. Nat Commun. 2017 Oct 26;8(1):1141.

The nucleosomal surface is the main target of histone ADP-ribosylation in response to DNA damage

The nucleosomal surface is the main target of histone ADP-ribosylation in response to DNA damage. Karch KR, Langelier MF, Pascal JM, Garcia BA. Mol Biosyst. 2017 Nov 21;13(12):2660-2671.

Cytoplasmic chromatin triggers inflammation in senescence and cancer

Cytoplasmic chromatin triggers inflammation in senescence and cancer. Dou Z, Ghosh K, Vizioli MG, Zhu J, Sen P, Wangensteen KJ, Simithy J, Lan Y, Lin Y, Zhou Z, Capell BC, Xu C, Xu M, Kieckhaefer JE, Jiang T, Shoshkes-Carmel M, Tanim KMAA, Barber GN, Seykora JT, Millar SE, Kaestner KH, Garcia BA, Adams PD, Berger SL. Nature. 2017 Oct 19;550(7676):402-406.

Sites Contributing to TRPA1 Activation by the Anesthetic Propofol Identified by Photoaffinity Labeling

Sites Contributing to TRPA1 Activation by the Anesthetic Propofol Identified by Photoaffinity Labeling. Woll KA, Skinner KA, Gianti E, Bhanu NV, Garcia BA, Carnevale V, Eckenhoff RG, Gaudet R. Biophys J. 2017 Sep 19. pii: S0006-3495(17)30963-3.

An HDAC3-PROX1 corepressor module acts on HNF4α to control hepatic triglycerides

An HDAC3-PROX1 corepressor module acts on HNF4α to control hepatic triglycerides. Armour SM, Remsberg JR, Damle M, Sidoli S, Ho WY, Li Z, Garcia BA, Lazar MA. Nat Commun. 2017 Sep 15;8(1):549.

Phosphoproteomics reveals that glycogen synthase kinase-3 phosphorylates multiple splicing factors and is associated with alternative splicing

Phosphoproteomics reveals that glycogen synthase kinase-3 phosphorylates multiple splicing factors and is associated with alternative splicing. Shinde MY, Sidoli S, Kulej K, Mallory MJ, Radens CM, Reicherter A, Myers RL, Barash Y, Lynch KW, Garcia BA, Klein PS. J Biol Chem. 2017 Nov 3;292(44):18240-18255.

Proteome-wide acetylation dynamics in human cells

Proteome-wide acetylation dynamics in human cells. Kori Y, Sidoli S, Yuan ZF, Lund PJ, Zhao X, Garcia BA. Sci Rep. 2017 Aug 31;7(1):10296.

Identification of Nidogen 1 as a lung metastasis protein through secretome analysis

Identification of Nidogen 1 as a lung metastasis protein through secretome analysis.  Alečković M, Wei Y, LeRoy G, Sidoli S, Liu DD, Garcia BA, Kang Y. Genes Dev. 2017 Jul 15;31(14):1439-1455.

The Neuropeptide Corazonin Controls Social Behavior and Caste Identity in Ants

The Neuropeptide Corazonin Controls Social Behavior and Caste Identity in Ants. Gospocic J, Shields EJ, Glastad KM, Lin Y, Penick CA, Yan H, Mikheyev AS, Linksvayer TA, Garcia BA, Berger SL, Liebig J, Reinberg D, Bonasio R. Cell. 2017 Aug 10;170(4):748-759.e12.

Detection of early pancreatic ductal adenocarcinoma with thrombospondin-2 and CA19-9 blood markers

Detection of early pancreatic ductal adenocarcinoma with thrombospondin-2 and CA19-9 blood markers. Kim J, Bamlet WR, Oberg AL, Chaffee KG, Donahue G, Cao XJ, Chari S, Garcia BA, Petersen GM, Zaret KS. Sci Transl Med. 2017 Jul 12;9(398).

Vitamin C induces specific demethylation of H3K9me2 in mouse embryonic stem cells via Kdm3a/b

Vitamin C induces specific demethylation of H3K9me2 in mouse embryonic stem cells via Kdm3a/b. Ebata KT, Mesh K, Liu S, Bilenky M, Fekete A, Acker MG, Hirst M, Garcia BA, Ramalho-Santos M. Epigenetics Chromatin. 2017 Jul 12;10(1):36.

Metabolic labeling in middle-down proteomics allows for investigation of the dynamics of the histone code

Metabolic labeling in middle-down proteomics allows for investigation of the dynamics of the histone code. Sidoli S, Lu C, Coradin M, Wang X, Karch KR, Ruminowicz C, Garcia BA. Epigenetics Chromatin. 2017 Jul 6;10(1):34.

Unique roles for histone H3K9me states in RNAi and heritable silencing of transcription

Unique roles for histone H3K9me states in RNAi and heritable silencing of transcription. Jih G, Iglesias N, Currie MA, Bhanu NV, Paulo JA, Gygi SP, Garcia BA, Moazed D. Nature. 2017 Jul 27; 547 (7664): 463-467.

Middle-down proteomics: a still unexploited resource for chromatin biology

Middle-down proteomics: a still unexploited resource for chromatin biology. Sidoli S, Garcia BA. Expert Rev Proteomics. 2017 Jul;14(7):617-626.

Uncovering BRD4 hyperphosphorylation associated with cellular transformation in NUT midline carcinoma

Uncovering BRD4 hyperphosphorylation associated with cellular transformation in NUT midline carcinoma. Wang R, Cao XJ, Kulej K, Liu W, Ma T, MacDonald M, Chiang CM, Garcia BA, You J. Proc Natl Acad Sci U S A. 2017 Jul 3;114(27):E5352-E5361.

The NANCI-Nkx2.1 gene duplex buffers Nkx2.1 expression to maintain lung development and homeostasis

The NANCI-Nkx2.1 gene duplex buffers Nkx2.1 expression to maintain lung development and homeostasis. Herriges MJ, Tischfield DJ, Cui Z, Morley MP, Han Y, Babu A, Li S, Lu M, Cendan I, Garcia BA, Anderson SA, Morrisey EE. Genes Dev. 2017 May 1;31(9):889-903.

Taxane-Platin-Resistant Lung Cancers Co-develop Hypersensitivity to JumonjiC Demethylase Inhibitors

Taxane-Platin-Resistant Lung Cancers Co-develop Hypersensitivity to JumonjiC Demethylase Inhibitors. Dalvi MP, Wang L, Zhong R, Kollipara RK, Park H, Bayo J, Yenerall P, Zhou Y, Timmons BC, Rodriguez-Canales J, Behrens C, Mino B, Villalobos P, Parra ER, Suraokar M, Pataer A, Swisher SG, Kalhor N, Bhanu NV, Garcia BA, Heymach JV, Coombes K, Xie Y, Girard L, Gazdar AF, Kittler R, Wistuba II, Minna JD, Martinez ED. Cell Rep. 2017 May 23;19(8):1669-1684.

Mll3 and Mll4 Facilitate Enhancer RNA Synthesis and Transcription from Promoters Independently of H3K4 Monomethylation

Mll3 and Mll4 Facilitate Enhancer RNA Synthesis and Transcription from Promoters Independently of H3K4 Monomethylation. Dorighi KM, Swigut T, Henriques T, Bhanu NV, Scruggs BS, Nady N, Still CD 2nd, Garcia BA, Adelman K, Wysocka J. Mol Cell. 2017 May 18;66(4):568-576.

Systematic Epigenomic Analysis Reveals Chromatin States Associated with Melanoma Progression

Systematic Epigenomic Analysis Reveals Chromatin States Associated with Melanoma Progression. Fiziev P, Akdemir KC, Miller JP, Keung EZ, Samant NS, Sharma S, Natale CA, Terranova CJ, Maitituoheti M, Amin SB, Martinez-Ledesma E, Dhamdhere M, Axelrad JB, Shah A, Cheng CS, Mahadeshwar H, Seth S, Barton MC, Protopopov A, Tsai KY, Davies MA, Garcia BA, Amit I, Chin L, Ernst J, Rai K. Cell Rep. 2017 Apr 25;19(4):875-889.

A Global View of RNA-Protein Interactions Identifies Post-transcriptional Regulators of Root Hair Cell Fate

A Global View of RNA-Protein Interactions Identifies Post-transcriptional Regulators of Root Hair Cell Fate. Foley SW, Gosai SJ, Wang D, Selamoglu N, Sollitti AC, Köster T, Steffen A, Lyons E, Daldal F, Garcia BA, Staiger D, Deal RB, Gregory BD. Dev Cell. 2017 Apr 24;41(2):204-220.e5.

Monitoring proteolytic processing events by quantitative mass spectrometry

Monitoring proteolytic processing events by quantitative mass spectrometry. Coradin M, Karch KR, Garcia BA. Expert Rev Proteomics. 2017 May;14(5):409-418.

Quantitative chromatin proteomics reveals a dynamic histone post-translational modification landscape that defines asexual and sexual Plasmodium falciparum parasites

Quantitative chromatin proteomics reveals a dynamic histone post-translational modification landscape that defines asexual and sexual Plasmodium falciparum parasites. Coetzee N, Sidoli S, van Biljon R, Painter H, Llinás M, Garcia BA, Birkholtz LM. Sci Rep. 2017 Apr 4;7(1):607.

Photoaffinity ligand for the inhalational anesthetic sevoflurane allows mechanistic insight into potassium channel modulation

Photoaffinity ligand for the inhalational anesthetic sevoflurane allows mechanistic insight into potassium channel modulation. Woll KA, Peng W, Liang Q, Zhi L, Jacobs JA, Maciunas L, Bhanu N, Garcia BA, Covarrubias M, Loll PJ, Dailey WP, Eckenhoff RG. ACS Chem Biol. 2017 May 19;12(5):1353-1362.

Recognition of Histone H3K14 Acylation by MORF

Recognition of Histone H3K14 Acylation by MORF. Klein BJ, Simithy J, Wang X, Ahn J, Andrews FH, Zhang Y, Côté J, Shi X, Garcia BA, Kutateladze TG. Structure. 2017 Apr 4;25(4):650-654.

Paternal cocaine taking elicits epigenetic remodeling and memory deficits in male progeny

Paternal cocaine taking elicits epigenetic remodeling and memory deficits in male progeny. Wimmer ME, Briand LA, Fant B, Guercio LA, Arreola AC, Schmidt HD, Sidoli S, Han Y, Garcia BA, Pierce RC. Mol Psychiatry. 2017 Nov;22(11):1641-1650.

Multicellular Tumor Spheroids Combined with Mass Spectrometric Histone Analysis To Evaluate Epigenetic Drugs

Multicellular Tumor Spheroids Combined with Mass Spectrometric Histone Analysis To Evaluate Epigenetic Drugs. Feist PE, Sidoli S, Liu X, Schroll MM, Rahmy S, Fujiwara R, Garcia BA, Hummon AB. Anal Chem. 2017, 89(5):2773-2781.

Time-resolved global and chromatin proteomics during herpes simplex virus (HSV-1) infection

Time-resolved global and chromatin proteomics during herpes simplex virus (HSV-1) infection. Kulej K, Avgousti DC, Sidoli S, Herrmann C, Della Fera AN, Kim ET, Garcia BA, Weitzman MD. Mol Cell Proteomics. 2017 Apr;16(4 suppl 1):S92-S107.

Recent Achievements in Characterizing the Histone Code and Approaches to Integrating Epigenomics and Systems Biology

Recent Achievements in Characterizing the Histone Code and Approaches to Integrating Epigenomics and Systems Biology. Janssen KA, Sidoli S, Garcia BA. Methods Enzymol. 2017;586:359-378.

Impaired H3K36 methylation defines a subset of head and neck squamous cell carcinomas

Impaired H3K36 methylation defines a subset of head and neck squamous cell carcinomas. Papillon-Cavanagh S, Lu C, Gayden T, Mikael LG, Bechet D, Karamboulas C, Ailles L, Karamchandani J, Marchione DM, Garcia BA, Weinreb I, Goldstein D, Lewis PW, Dancu OM, Dhaliwal S, Stecho W, Howlett CJ, Mymryk JS, Barrett JW, Nichols AC, Allis CD, Majewski J, Jabado N.  Nat Genet. 2017 Feb;49(2):180-185.

Optical High Content Nanoscopy of Epigenetic Marks Decodes Phenotypic Divergence in Stem Cells

Optical High Content Nanoscopy of Epigenetic Marks Decodes Phenotypic Divergence in Stem Cells. Kim JJ, Bennett NK, Devita MS, Chahar S, Viswanath S, Lee EA, Jung G, Shao PP, Childers EP, Liu S, Kulesa A, Garcia BA, Becker ML, Hwang NS, Madabhushi A, Verzi MP, Moghe PV. Sci Rep. 2017 Jan 4;7:39406.

Roles of H3K27me2 and H3K27me3 Examined during Fate Specification of Embryonic Stem Cells

Roles of H3K27me2 and H3K27me3 Examined during Fate Specification of Embryonic Stem Cells. Juan AH, Wang S, Ko KD, Zare H, Tsai PF, Feng X, Vivanco KO, Ascoli AM, Gutierrez-Cruz G, Krebs J, Sidoli S, Knight AL, Pedersen RA, Garcia BA, Casellas R, Zou J, Sartorelli V. Cell Rep. 2016, 17(5):1369-1382.

Publications in 2016

A Dual Inhibitory Mechanism Sufficient to Maintain Cell-Cycle-Restricted CENP-A Assembly

A Dual Inhibitory Mechanism Sufficient to Maintain Cell-Cycle-Restricted CENP-A Assembly. Stankovic A, Guo LY, Mata JF, Bodor DL, Cao XJ, Bailey AO, Shabanowitz J, Hunt DF, Garcia BA, Black BE, Jansen LE.  Mol Cell. 2017 Jan 19;65(2):231-246.

Why proteomics is not the new genomics and the future of mass spectrometry in cell biology

Why proteomics is not the new genomics and the future of mass spectrometry in cell biology. Sidoli S, Kulej K, Garcia BA. J Cell Biol. 2017 Jan 2;216(1):21-24.

Mutations along a TET2 active site scaffold stall oxidation at 5-hydroxymethylcytosine

Mutations along a TET2 active site scaffold stall oxidation at 5-hydroxymethylcytosine. Liu MY, Torabifard H, Crawford DJ, DeNizio JE, Cao XJ, Garcia BA, Cisneros GA, Kohli RM.  Nat Chem Biol. 2017 Feb;13(2):181-187.

Lowered H3K27me3 and DNA hypomethylation define poorly prognostic pediatric posterior fossa ependymomas

Lowered H3K27me3 and DNA hypomethylation define poorly prognostic pediatric posterior fossa ependymomas. Bayliss J, Mukherjee P, Lu C, Jain SU, Chung C, Martinez D, Sabari B, Margol AS, Panwalkar P, Parolia A, Pekmezci M, McEachin RC, Cieslik M, Tamrazi B, Garcia BA, La Rocca G, Santi M, Lewis PW, Hawkins C, Melnick A, David Allis C, Thompson CB, Chinnaiyan AM, Judkins AR, Venneti S. Sci Transl Med. 2016 Nov 23;8(366):366ra161.

Characterization of Individual Histone Posttranslational Modifications and Their Combinatorial Patterns by Mass Spectrometry-Based Proteomics Strategies

Characterization of Individual Histone Posttranslational Modifications and Their Combinatorial Patterns by Mass Spectrometry-Based Proteomics Strategies. Sidoli S, Garcia BA. Methods Mol Biol. 2017;1528:121-148.

Global Proteomics Analysis of Protein Lysine Methylation

Global Proteomics Analysis of Protein Lysine Methylation. Cao XJ, Garcia BA. Curr Protoc Protein Sci. 2016 Nov 1;86:24.8.1-24.8.19.

High-Resolution Mapping of RNA-Binding Regions in the Nuclear Proteome of Embryonic Stem Cells

High-Resolution Mapping of RNA-Binding Regions in the Nuclear Proteome of Embryonic Stem Cells. He C, Sidoli S, Warneford-Thomson R, Tatomer DC, Wilusz JE, Garcia BA, Bonasio R. Mol Cell. 2016 Oct 20;64(2):416-430.

Chromatin Kinases Act on Transcription Factors and Histone Tails in Regulation of Inducible Transcription

Chromatin Kinases Act on Transcription Factors and Histone Tails in Regulation of Inducible Transcription. Josefowicz SZ, Shimada M, Armache A, Li CH, Miller RM, Lin S, Yang A, Dill BD, Molina H, Park HS, Garcia BA, Taunton J, Roeder RG, Allis CD. Mol Cell. 2016 Oct 20;64(2):347-361.

Identification and Quantification of Histone PTMs Using High-Resolution Mass Spectrometry

Identification and Quantification of Histone PTMs Using High-Resolution Mass Spectrometry. Karch KR, Sidoli S, Garcia BA. Methods Enzymol. 2016;574:3-29.

A Novel Bifunctional Alkylphenol Anesthetic Allows Characterization of GABAA Receptor Subunit Binding Selectivity in Synaptosomes

A Novel Bifunctional Alkylphenol Anesthetic Allows Characterization of GABAA Receptor Subunit Binding Selectivity in Synaptosomes. Woll KA, Murlidaran S, Pinch BJ, Hénin J, Wang X, Salari R, Covarrubias M, Dailey WP, Brannigan G, Garcia BA, Eckenhoff RG.  J Biol Chem. 2016 Sep 23;291(39):20473-86.

Mapping H4K20me3 onto the chromatin landscape of senescent cells indicates a function in control of cell senescence and tumor suppression through preservation of genetic and epigenetic stability

Mapping H4K20me3 onto the chromatin landscape of senescent cells indicates a function in control of cell senescence and tumor suppression through preservation of genetic and epigenetic stability. Nelson DM, Jaber-Hijazi F, Cole JJ, Robertson NA, Pawlikowski JS, Norris KT, Criscione SW, Pchelintsev NA, Piscitello D, Stong N, Rai TS, McBryan T, Otte GL, Nixon C, Clark W, Riethman H, Wu H, Schotta G, Garcia BA, Neretti N, Baird DM, Berger SL, Adams PD. Genome Biol. 2016 Jul 25;17(1):158.

A core viral protein binds host nucleosomes to sequester immune danger signals

A core viral protein binds host nucleosomes to sequester immune danger signals.  Avgousti DC, Herrmann C, Kulej K, Pancholi NJ, Sekulic N, Petrescu J, Molden RC, Blumenthal D, Paris AJ, Reyes ED, Ostapchuk P, Hearing P, Seeholzer SH, Worthen GS, Black BE, Garcia BA, Weitzman MD. Nature. 2016 Jul 7;535(7610):173-7.

Comprehensive analysis of histone post-translational modifications in mouse and human male germ cells

Comprehensive analysis of histone post-translational modifications in mouse and human male germ cells. Luense LJ, Wang X, Schon SB, Weller AH, Lin Shiao E, Bryant JM, Bartolomei MS, Coutifaris C, Garcia BA, Berger SL. Epigenetics Chromatin. 2016 Jun 21;9:24.

Differential quantification of isobaric phosphopeptides using data-independent acquisition mass spectrometry

Differential quantification of isobaric phosphopeptides using data-independent acquisition mass spectrometry. Sidoli S, Fujiwara R, Kulej K, Garcia BA. Mol Biosyst. 2016 Jul 19;12(8):2385-8.

Co-repressor CBFA2T2 regulates pluripotency and germline development

Co-repressor CBFA2T2 regulates pluripotency and germline development. Tu S, Narendra V, Yamaji M, Vidal SE, Rojas LA, Wang X, Kim SY, Garcia BA, Tuschl T, Stadtfeld M, Reinberg D. Nature. 2016 Jun 8;534(7607):387-90.

Complete workflow for analysis of histone post-translational modifications using bottom-up mass spectrometry: From histone extraction to data analysis

Sidoli, S., Bhanu, N. V., Karch, K. R., Wang, X., Garcia, B. A. Complete Workflow for Analysis of Histone Post-translational Modifications Using Bottom-up Mass Spectrometry: From Histone Extraction to Data Analysis.  J. Vis. Exp. (111), e54112, doi:10.3791/54112 (2016).

Preferential phosphorylation on old histones during early mitosis in human cells

Preferential phosphorylation on old histones during early mitosis in human cells. Lin S, Yuan ZF, Han Y, Marchione DM, Garcia BA. J Biol Chem. 2016 Jul 15;291(29):15342-57.

Multiplexed data independent acquisition (MSX-DIA) applied by high resolution mass spectrometry improves quantification quality for the analysis of histone peptides

Multiplexed data independent acquisition (MSX-DIA) applied by high resolution mass spectrometry improves quantification quality for the analysis of histone peptides. Sidoli S, Fujiwara R, Garcia BA. Proteomics. 2016 Aug;16(15-16):2095-105.

Histone H3K36 mutations promote sarcomagenesis through altered histone methylation landscape.

Histone H3K36 mutations promote sarcomagenesis through altered histone methylation landscape. Lu C, Jain SU, Hoelper D, Bechet D, Molden RC, Ran L, Murphy D, Venneti S, Hameed M, Pawel BR, Wunder JS, Dickson BC, Lundgren SM, Jani KS, De Jay N, Papillon-Cavanagh S, Andrulis IL, Sawyer SL, Grynspan D, Turcotte RE, Nadaf J, Fahiminiyah S, Muir TW, Majewski J, Thompson CB, Chi P, Garcia BA, Allis CD, Jabado N, Lewis PW. Science. 2016 May 13;352(6287):844-9.

Inhibition of DHHC20-Mediated EGFR Palmitoylation Creates a Dependence on EGFR Signaling

Inhibition of DHHC20-Mediated EGFR Palmitoylation Creates a Dependence on EGFR Signaling. Runkle KB, Kharbanda A, Stypulkowski E, Cao XJ, Wang W, Garcia BA, Witze ES. Mol Cell. 2016 May 5;62(3):385-396.

PRDM16 Suppresses MLL1r Leukemia via Intrinsic Histone Methyltransferase Activity

PRDM16 Suppresses MLL1r Leukemia via Intrinsic Histone Methyltransferase Activity. Zhou B, Wang J, Lee SY, Xiong J, Bhanu N, Guo Q, Ma P, Sun Y, Rao RC, Garcia BA, Hess JL, Dou Y. Mol Cell. 2016 Apr 12. pii: S1097-2765(16)00188-X.

A novel quantitative mass spectrometry platform for determining site-specific protein O-GlcNAcylation dynamics

A novel quantitative mass spectrometry platform for determining site-specific protein O-GlcNAcylation dynamics. Wang X, Yuan ZF, Fan J, Karch KR, Ball LE, Denu JM, Garcia BA. Mol Cell Proteomics. 2016 Jul;15(7):2462-75.

Folate deficiency affects histone methylation

Folate deficiency affects histone methylation. Garcia BA, Luka Z, Loukachevitch LV, Bhanu NV, Wagner C. Med Hypotheses. 2016 Mar;88:63-7.

Histone H4 acetylation and the epigenetic reader Brd4 are critical regulators of pluripotency in embryonic stem cells

Histone H4 acetylation and the epigenetic reader Brd4 are critical regulators of pluripotency in embryonic stem cells. Gonzales-Cope M, Sidoli S, Bhanu NV, Won KJ, Garcia BA. BMC Genomics. 2016 Feb 4;17(1):95.

Reshaping the chromatin and epigenetic landscapes with quantitative mass spectrometry

Reshaping the chromatin and epigenetic landscapes with quantitative mass spectrometry. Washburn MP, Zhao Y, Garcia BA. Mol Cell Proteomics, 2016 15: 753-754.

Bioorthogonal Chemistry for the Isolation and Study of Newly Synthesized Histones and their Modifications

Bioorthogonal Chemistry for the Isolation and Study of Newly Synthesized Histones and their Modifications. Arnaudo AM, Link AJ, Garcia BA. ACS Chem Biol. 2016 Mar 18;11(3):782-91.

Analyses of Histone Proteoforms Using Front-End Electron Transfer Dissociation-Enabled Orbitrap Instruments

Analyses of Histone Proteoforms Using Front-End Electron Transfer Dissociation-Enabled Orbitrap Instruments. Anderson LC, Karch KR, Ugrin SA, Coradin M, English AM, Sidoli S, Shabanowitz J, Garcia BA, Hunt DF. Mol Cell Proteomics 2016 15: 975-988.

Quantitative profiling of the activity of protein lysine methyltransferase SMYD2 using SILAC-based proteomics

Quantitative profiling of the activity of protein lysine methyltransferase SMYD2 using SILAC-based proteomics. Olsen JB, Cao XJ, Han B, Chen LH, Horvath A, Richardson TI, Campbell RM, Garcia BA, Nguyen H. Mol Cell Proteomics 2016 15: 892-905.

Tet2 catalyzes stepwise 5-methylcytosine oxidation by an iterative and de novo mechanism

Tet2 catalyzes stepwise 5-methylcytosine oxidation by an iterative and de novo mechanism. Crawford DJ, Liu MY, Nabel CS, Cao XJ, Garcia BA, Kohli RM. J Am Chem Soc. 2016 Jan 27;138(3):730-3.

Publications in 2015

Permuting the PGF-CTERM signature motif blocks both archaeosortase-dependent C-terminal cleavage and prenyl lipid attachment for the Haloferax volcanii S-layer glycoprotein

Permuting the PGF-CTERM signature motif blocks both archaeosortase-dependent C-terminal cleavage and prenyl lipid attachment for the Haloferax volcanii S-layer glycoprotein. Abdul Halim MF, Karch KR, Zhou Y, Haft DH, Garcia BA, Pohlschroder M. J Bacteriol. 2015 Dec 28;198(5):808-15.

Histone modification profiling reveals differential signatures associated with human embryonic stem cell self-renewal and differentiation

Histone modification profiling reveals differential signatures associated with human embryonic stem cell self-renewal and differentiation. Bhanu NV, Sidoli S, Garcia BA. Proteomics. 2016 Feb;16(3):448-58.

H4K44 Acetylation Facilitates Chromatin Accessibility during Meiosis

H4K44 Acetylation Facilitates Chromatin Accessibility during Meiosis. Hu J, Donahue G, Dorsey J, Govin J, Yuan Z, Garcia BA, Shah PP, Berger SL. Cell Rep. 2015, 13(9):1772-1780.

Monitoring cellular phosphorylation signaling pathways into chromatin and down to the gene level

Monitoring cellular phosphorylation signaling pathways into chromatin and down to the gene level. Han Y, Yuan ZF, Molden RC, Garcia, BA. Mol Cell Proteomics 2016 15: 834-853.

Nitric oxide regulates gene expression in cancers by controlling histone posttranslational modifications

Nitric oxide regulates gene expression in cancers by controlling histone posttranslational modifications. Vasudevan D, Hickok JR, Bovee RC, Pham V, Mantell LL, Bahroos N, Kanabar P, Cao XJ, Maienschein-Cline M, Garcia BA, Thomas DD. Cancer Res. 2015, 75(24):5299-5308.

Loss of HP1 causes depletion of H3K27me3 from facultative heterochromatin and gain of H3K27me2 at constitutive heterochromatin

Loss of HP1 causes depletion of H3K27me3 from facultative heterochromatin and gain of H3K27me2 at constitutive heterochromatin. Jamieson K, Wiles ET, McNaught KJ, Sidoli S, Leggett N, Shao Y, Garcia BA, Selker EU. Genome Res. 2016 Jan;26(1):97-107

Tumour exosome integrins determine organotropic metastasis

Tumour exosome integrins determine organotropic metastasis. Hoshino A, Costa-Silva B, Shen TL, Rodrigues G, Hashimoto A, Tesic Mark M, Molina H, Kohsaka S, Di Giannatale A, Ceder S, Singh S, Williams C, Soplop N, Uryu K, Pharmer L, King T, Bojmar L, Davies AE, Ararso Y, Zhang T, Zhang H, Hernandez J, Weiss JM, Dumont-Cole VD, Kramer K, Wexler LH, Narendran A, Schwartz GK, Healey JH, Sandstrom P, Jørgen Labori K, Kure EH, Grandgenett PM, Hollingsworth MA, de Sousa M, Kaur S, Jain M, Mallya K, Batra SK, Jarnagin WR, Brady MS, Fodstad O, Muller V, Pantel K, Minn AJ, Bissell MJ, Garcia BA, Kang Y, Rajasekhar VK, Ghajar CM, Matei I, Peinado H, Bromberg J, Lyden D. Nature. 2015, 527(7578):329-35.

Low Resolution Data-Independent Acquisition in an LTQ-Orbitrap Allows for Simplified and Fully Untargeted Analysis of Histone Modifications

Low Resolution Data-Independent Acquisition in an LTQ-Orbitrap Allows for Simplified and Fully Untargeted Analysis of Histone Modifications. Sidoli S, Simithy J, Karch KR, Kulej K, Garcia BA. Anal Chem. 2015, 87(22):11448-54.

The PZP Domain of AF10 Senses Unmodified H3K27 to Regulate DOT1L-Mediated Methylation of H3K79

The PZP Domain of AF10 Senses Unmodified H3K27 to Regulate DOT1L-Mediated Methylation of H3K79. Chen S, Yang Z, Wilkinson AW, Deshpande AJ, Sidoli S, Krajewski K, Strahl BD, Garcia BA, Armstrong SA, Patel DJ, Gozani O. Mol Cell. 2015, 60(2):319-27.

Progress in epigenetic histone modification analysis by mass spectrometry for clinical investigations

Progress in epigenetic histone modification analysis by mass spectrometry for clinical investigations. Önder Ö, Sidoli S, Carroll M, Garcia BA. Expert Rev Proteomics. 2015, 12(5):499-517.

Comprehensive Catalog of Currently Documented Histone Modifications

Comprehensive Catalog of Currently Documented Histone Modifications. Zhao Y, Garcia BA. Cold Spring Harb Perspect Biol. 2015 Sep 1;7(9). pii: a025064.

The histone lysine methyltransferase KMT2D sustains a gene expression program that represses B cell lymphoma development

The histone lysine methyltransferase KMT2D sustains a gene expression program that represses B cell lymphoma development. Ortega-Molina A, Boss IW, Canela A, Pan H, Jiang Y, Zhao C, Jiang M, Hu D, Agirre X, Niesvizky I, Lee JE, Chen HT, Ennishi D, Scott DW, Mottok A, Hother C, Liu S, Cao XJ, Tam W, Shaknovich R, Garcia BA, Gascoyne RD, Ge K, Shilatifard A, Elemento O, Nussenzweig A, Melnick AM, Wendel HG. Nat Med. 2015, 21(10):1199-208.

Analysis of Histones H3 and H4 Reveals Novel and Conserved Post-Translational Modifications in Sugarcane

Analysis of Histones H3 and H4 Reveals Novel and Conserved Post-Translational Modifications in Sugarcane. Moraes I, Yuan ZF, Liu S, Souza GM, Garcia BA, Casas-Mollano JA. PLoS One. 2015, 10(7):e0134586.

Properly reading the histone code by MS based proteomics

Properly reading the histone code by MS based proteomics. Sidoli S, Garcia BA. Proteomics. 2015, 15(17):2901-2.

Critical Role of Histone Turnover in Neuronal Transcription and Plasticity

Critical Role of Histone Turnover in Neuronal Transcription and Plasticity. Maze I, Wenderski W, Noh KM, Bagot RC, Tzavaras N, Purushothaman I, Elsässer SJ, Guo Y, Ionete C, Hurd YL, Tamminga CA, Halene T, Farrelly L, Soshnev AA, Wen D, Rafii S, Birtwistle MR, Akbarian S, Buchholz BA, Blitzer RD, Nestler EJ, Yuan ZF, Garcia BA, Shen L, Molina H, Allis CD. Neuron. 2015, 87(1):77-94.

Characterization of histone post-translational modifications during virus infection using mass spectrometry-based proteomics

Characterization of histone post-translational modifications during virus infection using mass spectrometry-based proteomics. Kulej K, Avgousti DC, Weitzman MD, Garcia BA. Methods. 2015 pii: S1046-2023(15)00249-2.

Memory acquisition and retrieval impact different epigenetic processes that regulate gene expression

Memory acquisition and retrieval impact different epigenetic processes that regulate gene expression. Peixoto LL, Wimmer ME, Poplawski SG, Tudor JC, Kenworthy CA, Liu S, Mizuno K, Garcia BA, Zhang NR, Giese K, Abel T. BMC Genomics. 2015 May 26;16 Suppl 5:S5. doi: 10.1186/1471-2164-16-S5-S5.

Human cytomegalovirus TRS1 protein associates with the 7-methylguanosine mRNA cap and facilitates translation

Human cytomegalovirus TRS1 protein associates with the 7-methylguanosine mRNA cap and facilitates translation. Ziehr B, Lenarcic E, Vincent HA, Cecil C, Garcia B, Shenk T, Moorman NJ. Proteomics. 2015, 15(12):1983-94.

Multi-faceted quantitative proteomics analysis of histone H2B isoforms and their modifications

Multi-faceted quantitative proteomics analysis of histone H2B isoforms and their modifications. Molden RC, Bhanu NV, LeRoy G, Arnaudo AM, Garcia BA. Epigenetics Chromatin. 2015, 8:15.

Proteogenomics analysis reveals specific genomic orientations of distal regulatory regions composed by non-canonical histone variants

Proteogenomics analysis reveals specific genomic orientations of distal regulatory regions composed by non-canonical histone variants. Won KJ, Choi I, LeRoy G, Zee BM, Sidoli S, Gonzales-Cope M, Garcia BA. Epigenetics Chromatin. 2015, 8:13.

LLY-507, a Cell-Active, Potent and Selective Inhibitor of Protein Lysine Methyltransferase SMYD2

LLY-507, a Cell-Active, Potent and Selective Inhibitor of Protein Lysine Methyltransferase SMYD2. Nguyen H, Allali-Hassani A, Antonysamy S, Chang S, Chen LH, Curtis C, Emtage S, Fan L, Gheyi T, Li F, Liu S, Martin JR, Mendel D, Olsen JB, Pelletier L, Shatseva T, Wu S, Zhang FF, Arrowsmith CH, Brown PJ, Campbell RM, Garcia BA, Barsyte-Lovejoy D, Mader M, Vedadi M. J Biol Chem. 2015, 290(22):13641-53.

EpiProfile quantifies histone modifications by extracting retention time and intensity in high-resolution mass spectra

EpiProfile quantifies histone modifications by extracting retention time and intensity in high-resolution mass spectra. Yuan ZF, Lin S, Molden RC, Cao XJ, Bhanu NV, Wang X, Sidoli S, Liu S, Garcia BA. Mol Cell Proteomics. 2015, 14(6):1696-707.

Bottom-Up and Middle-Down Proteomics Have Comparable Accuracies in Defining Histone Post-Translational Modification Relative Abundance and Stoichiometry

Bottom-Up and Middle-Down Proteomics Have Comparable Accuracies in Defining Histone Post-Translational Modification Relative Abundance and Stoichiometry. Sidoli S, Lin S, Karch KR, Garcia BA. Anal Chem. 2015, 87(6):3129-33.

Characterization of BRD4 during mammalian post-meiotic sperm development

Characterization of BRD4 during mammalian post-meiotic sperm development. Bryant JM, Donahue G, Wang X, Meyer-Ficca M, Luense LJ, Weller AH, Bartolomei MS, Blobel GA, Meyer RG, Garcia BA, Berger SL. Mol Cell Biol. 2015, 35(8):1433-48.

Quantitative Proteomic Analysis of Histone Modifications

Quantitative Proteomic Analysis of Histone Modifications. Huang H, Lin S, Garcia BA, Zhao Y. Chem Rev. 2015 Mar 25;115(6):2376-418.

A Specific LSD1/KDM1A Isoform Regulates Neuronal Differentiation through H3K9 Demethylation

A Specific LSD1/KDM1A Isoform Regulates Neuronal Differentiation through H3K9 Demethylation. Laurent B, Ruitu L, Murn J, Hempel K, Ferrao R, Xiang Y, Liu S, Garcia BA, Wu H, Wu F, Steen H, Shi Y. Mol Cell. 2015, 57(6):957-70.

Drawbacks in the use of unconventional hydrophobic anhydrides for histone derivatization in bottom-up proteomics PTM analysis

Drawbacks in the use of unconventional hydrophobic anhydrides for histone derivatization in bottom-up proteomics PTM analysis. Sidoli S, Yuan ZF, Lin S, Karch K, Wang X, Bhanu N, Arnaudo AM, Britton LM, Cao XJ, Gonzales-Cope M, Han Y, Liu S, Molden RC, Wein S, Afjehi-Sadat L, Garcia BA. Proteomics. 2015, 15(9):1459-69.

SWATH Analysis for Characterization and Quantification of Histone Post-translational Modifications

SWATH Analysis for Characterization and Quantification of Histone Post-translational Modifications. Sidoli S, Lin S, Xiong L, Bhanu NV, Karch KR, Johansen E, Hunter C, Mollah S, Garcia BA. Mol Cell Proteomics. 2015, 14(9):2420-8.

The Cerebral Cavernous Malformation Pathway Controls Cardiac Development via Regulation of Endocardial MEKK3 Signaling and KLF Expression

Zhou Z, Rawnsley DR, Goddard LM, Pan W, Cao XJ, Jakus Z, Zheng H, Yang J, Arthur JS, Whitehead KJ, Li D, Zhou B, Garcia BA, Zheng X, Kahn ML. The Cerebral Cavernous Malformation Pathway Controls Cardiac Development via Regulation of Endocardial MEKK3 Signaling and KLF Expression. Dev Cell. 2015, 32(2):168-180.

Identification of nuclear hormone receptor pathways causing insulin resistance by transcriptional and epigenomic analysis

Kang S, Tsai LT, Zhou Y, Evertts A, Xu S, Griffin MJ, Issner R, Whitton HJ, Garcia BA, Epstein CB, Mikkelsen TS, Rosen ED. Identification of nuclear hormone receptor pathways causing insulin resistance by transcriptional and epigenomic analysis. Nat Cell Biol. 2015, 17(1):44-56.

Defining heterochromatin in C. elegans through genome-wide analysis of the heterochromatin protein 1 homolog HPL-2

Garrigues JM, Sidoli S, Garcia BA, Strome S. Defining heterochromatin in C. elegans through genome-wide analysis of the heterochromatin protein 1 homolog HPL-2. Genome Res. 2015, 25(1):76-88.

Selective inhibition of EZH2 and EZH1 enzymatic activity by a small molecule suppresses MLL-rearranged leukemia

Xu B, On DM, Ma A, Parton T, Konze KD, Pattenden SG, Allison DF, Cai L, Rockowitz S, Liu S, Liu Y, Li F, Vedadi M, Frye SV, Garcia BA, Zheng D, Jin J, Wang GG. Selective inhibition of EZH2 and EZH1 enzymatic activity by a small molecule suppresses MLL-rearranged leukemia. Blood. 2015, 125(2):346-57.

Publications in 2014

BRD4 assists elongation of both coding and enhancer RNAs by interacting with acetylated histones

Kanno T, Kanno Y, LeRoy G, Campos E, Sun HW, Brooks SR, Vahedi G, Heightman TD, Garcia BA, Reinberg D, Siebenlist U, O’Shea JJ, Ozato K. BRD4 assists elongation of both coding and enhancer RNAs by interacting with acetylated histones. Nat Struct Mol Biol. 2014, 21(12):1047-57.

In vivo proximity labeling for the detection of protein-protein and protein-RNA interactions

Beck DB, Narendra V, Drury WJ 3rd, Casey R, Jansen PW, Yuan ZF, Garcia BA, Vermeulen M, Bonasio R. In vivo proximity labeling for the detection of protein-protein and protein-RNA interactions. J Proteome Res. 2014, 13(12):6135-43.

Analytical tools and current challenges in the modern era of neuroepigenomics

Maze I, Shen L, Zhang B, Garcia BA, Shao N, Mitchell A, Sun H, Akbarian S, Allis CD, Nestler EJ. Analytical tools and current challenges in the modern era of neuroepigenomics. Nat Neurosci. 2014, 17(11):1476-1490.

High resolution is not a strict requirement for characterization and quantification of histone post-translational modifications

Karch KR, Zee BM, Garcia BA. High resolution is not a strict requirement for characterization and quantification of histone post-translational modifications. J Proteome Res. 2014, 13(12):6152-9.

SnapShot: Histone Modifications

Huang H, Sabari BR, Garcia BA, Allis CD, Zhao Y. SnapShot: Histone Modifications. Cell. 2014, 159(2):458-458.

Evaluation of proteomic search engines for the analysis of histone modifications

Yuan ZF, Lin S, Molden RC, Garcia BA. Evaluation of proteomic search engines for the analysis of histone modifications. J Proteome Res. 2014, 13(10):4470-8.

Histone methylation has distinct dynamics from histone acetylation in cell cycle re-entry from quiescence

Mews P, Zee BM, Liu S, Donahue G, Garcia BA, Berger SL. Histone methylation has distinct dynamics from histone acetylation in cell cycle re-entry from quiescence. Mol Cell Biol. 2014, 34(21):3968-80.

A Proteomic Glimpse into the Initial Global Epigenetic Changes During HIV Infection

Britton LM, Sova P, Belisle S, Liu S, Chan EY, Katze MG, Garcia BA. A Proteomic Glimpse into the Initial Global Epigenetic Changes During HIV Infection. Proteomics. 2014, 14(19):2226-30.

Middle-Down and Top-Down Mass Spectrometric Analysis of Co-occurring Histone Modifications

Molden RC, Garcia BA. Middle-Down and Top-Down Mass Spectrometric Analysis of Co-occurring Histone Modifications. Curr Protoc Protein Sci. 2014, 77:23.7.1-23.7.28.

Stable Isotope labeled histone peptide library for histone post-translational modification and variant quantification by mass spectrometry

Lin S, Wein S, Gonzales-Cope M, Otte GL, Yuan ZF, Afjehi-Sadat L, Maile T, Berger SL, Rush J, Lill JR, Arnott D, Garcia BA. Stable Isotope labeled histone peptide library for histone post-translational modification and variant quantification by mass spectrometry. Mol Cell Proteomics. 2014, 13(9):2450-66.

Akt-Dependent Metabolic Reprogramming Regulates Tumor Cell Histone Acetylation

Lee JV, Carrer A, Shah S, Snyder NW, Wei S, Venneti S, Worth AJ, Yuan ZF, Lim HW, Liu S, Jackson E, Aiello NM, Haas NB, Rebbeck TR, Judkins A, Won KJ, Chodosh LA, Garcia BA, Stanger BZ, Feldman MD, Blair IA, Wellen KE. Akt-Dependent Metabolic Reprogramming Regulates Tumor Cell Histone Acetylation. Cell Metab. 2014, 20(2):306-19.

Quantitative Proteomic Discovery of Dynamic Epigenome Changes that Control Human Cytomegalovirus Infection

O’Connor C, DiMaggio PA Jr, Shenk T, Garcia BA. Quantitative Proteomic Discovery of Dynamic Epigenome Changes that Control Human Cytomegalovirus Infection. Mol Cell Proteomics. 2014, 13(9):2399-410.

Mass spectrometric analysis of histone proteoforms

Yuan ZF, Arnaudo AM, Garcia BA. Mass spectrometric analysis of histone proteoforms. Annu Rev Anal Chem. 2014, 7(1):113-28.

ChIP-less analysis of chromatin states

Su Z, Boersma MD, Lee JH, Oliver SS, Liu S, Garcia BA, Denu JM. ChIP-less analysis of chromatin states. Epigenetics Chromatin. 2014 Apr 24;7:7.

SMYD3 links lysine methylation of MAP3K2 to Ras-driven cancer

Mazur PK, Reynoird N, Khatri P, Jansen PW, Wilkinson AW, Liu S, Barbash O, Van Aller GS, Huddleston M, Dhanak D, Tummino PJ, Kruger RG, Garcia BA, Butte AJ, Vermeulen M, Sage J, Gozani O. SMYD3 links lysine methylation of MAP3K2 to Ras-driven cancer. Nature. 2014, 510(7504):283-7.

De novo Peptide design and experimental validation of histone methyltransferase inhibitors

Smadbeck J, Peterson MB, Zee BM, Garapaty S, Mago A, Lee C, Giannis A, Trojer P, Garcia BA, Floudas CA. De novo Peptide design and experimental validation of histone methyltransferase inhibitors. PLoS One. 2014, 9(2):e90095.

Stable isotope labeling of phosphoproteins for large-scale phosphorylation rate determination

Molden RC, Goya J, Kahn Z, Garcia BA. Stable isotope labeling of phosphoproteins for large-scale phosphorylation rate determination. Mol Cell Proteomics. 2014, 13(4):1106-18.

Tyr Phosphorylation of PDP1 Toggles Recruitment between ACAT1 and SIRT3 to Regulate the Pyruvate Dehydrogenase Complex

Fan J, Shan C, Kang HB, Elf S, Xie J, Tucker M, Gu TL, Aguiar M, Lonning S, Chen H, Mohammadi M, Britton LM, Garcia BA, Alečković M, Kang Y, Kaluz S, Devi N, Van Meir EG, Hitosugi T, Seo JH, Lonial S, Gaddh M, Arellano M, Khoury HJ, Khuri FR, Boggon TJ, Kang S, Chen J. Tyr Phosphorylation of PDP1 Toggles Recruitment between ACAT1 and SIRT3 to Regulate the Pyruvate Dehydrogenase Complex. Mol Cell. 2014, 53(4):534-48.

Neutron-encoded mass signatures for quantitative top down proteomics

Rhoads TW, Rose CM, Bailey DJ, Riley NM, Molden RC, Nestler AJ, Merrill AE, Hebert AS, Westphall MS, Pagliarini DJ, Garcia BA, Coon JJ. Neutron-encoded mass signatures for quantitative top down proteomics. Anal Chem. 2014, 86(5):2314-9.