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.