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.