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.