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.