Recent Select Publications


Zhang YJ, Guo L, Gonzales PK, Gendron TF, Wu Y, Jansen-West K, O'Raw AD, Pickles SR, Prudencio M, Carlomagno Y, Gachechiladze MA, Ludwig C, Tan R, Chew J, DeTure M, Lin WL, Tong J, Daughrity LM, Yue M, Song Y, Andersen JW, Castanedes-Casey M, Kurti A, Datta A, Antognetti G, McCampbell A, Rademakers R, Oskarsson B, Dickson DW, Kampmann M, Ward ME, Fryer JD, Link CD, Shorter J, Petrucelli L, Heterochromatin anomalies and double-stranded RNA accumulation underlie C9orf72 poly(PR) toxicity, Science, 2019 Feb 15;363(6428)
PMID: 30765536

Lu C, Sidoli S, Kulej K, Ross K, Wu CH, Garcia BA, Coordination between TGF-ß cellular signaling and epigenetic regulation during epithelial to mesenchymal transition, Epigenetics Chromatin, 2019 Feb 8;12(1):11
PMID: 30736855

Barra V, Logsdon GA, Shelf A, Hoffmann S, Herve S, Aslanian A, Nechemia-Arbely Y, Cleveland DW, Black BE, Fachinetti D, Phosphorylation of CENP-A on serine 7 does not control centromere function, Nat Commun, 2019 Jan 11;10(1):175
PMID: 30635586

Esipova TV, Barrett MJP, Erleback E, Masunov AE, Weber B, Vinogradov SA, Oxyphor 2P: A High-Performance Probe for Deep-Tissue Longitudinal Oxygen Imaging, Cell Metab, 2019 Jan 9
PMID: 30686745



Karch KR, Coradin M, Zandarashvili Li, Kan ZY, Gerace M, Englander SW, Black BE, Gracia BA, Hydrogen-Deuterium Exchange Coupled to Top- and Middle-Down Mass Spectrometry Reveals Histone Tail Dynamics before and after Nucleosome Assembly, Structure, 2018 Dec 4;26(12): 1651-1663
PMID: 30293810

Zasadzinska E, Huang J, Bailey AO, Guo LY, Lee NS, Srivastava S, Wong KA, French BT, Black BE, Foltz DR, Inheritance of CENP-A Nucleosomes during DNA Replication Requires HJURP, Dev Cell, 2018 Nov 5;47(3): 348-362
PMID: 30293838

Hughes TET, Pumroy RA, Yazici AT, Kasimova MA, Fluck EC, Huynh KW, Samanta A, Molugu SK, Zhou ZH, Carnevale V, Rohacs T, Moiseenkova-Bell VY, Structural insights on TRPV5 gating by endogenous modulators, Nat Commun. 2018 Oct 10;9(1): 4198
PMID: 30305626

Schutsky EK, DeNizio JE, Hu P, Liu MY, Nabel CS, Fabyanic EB, Hwang Y, Bushman FD, Wu H, Kohli RM, Nondestructive, base-resolution sequencing of 5-hydroxymethylcytosine using DNA deaminase, Nat Biotechnol, 2018 Oct 8
PMID: 30295673

Schutsky EK, DeNizio JE, Hu P, Liu MY, Nabel CS, Fabyanic EB, Hwang Y, Bushman FD, Wu H, Kohli RM, Nondestructive, base-resolution sequencing of 5-hydroxymethylcytosine using a DNA deaminase. Nat Biotechnol. 2018 Oct 8 [Epub ahead of print]
PMID: 30295673

Zasadzinska E, Huang J, Bailey AO, Guo LY, Lee NS, Srivastava S, Wong KA, French BT, Black BE, Foltz DR. Inheritance of CENP-A Nucleosomes during DNA Replication Requires HJURP. Dev Cell. 2018 Oct 3 [Epub ahead of print]
PMID: 30293838

Li, H, Sharp, R, Rutherford, K, Gupta, K, Van Duyne, GD. Serine Integrase attP Binding and Specificity. J Mol Biol. 2018 Sep 15 [Epub ahead of print]
PMID 30227134

Shields EJ, Sheng L, Weiner AK, Garcia BA, Bonasio R. High-Quality Genome Assemblies Reveal Long Non-coding RNAs Expressed in Ant Brains. Cell Rep. 2018 June 5;23(10): 3078-3090
PMID 29874592

Huang C, Liang D, Tatomer DC, Wilusz JE. A length-dependent evolutionarily conserved pathway controls nuclear export of circular RNAs. Genes Dev. 2018 May 17
PMID 29773557

Goris M, Magin RS, Foyn H, Myklebust LM, Varland S, Ree R, Drazic A, Bhambra P, Støve SI, Baumann M, Haug BE, Marmorstein R, Arnesen T. Structural determinants and cellular environment define processed actin as the sole substrate of the N-terminal acetyltransferase NAA80. Proc Natl Acad Sci U S A. 2018 Apr 24;115(17):4405-4410.
PMID: 29581307

Guo L, Kim HJ, Wang H, Monaghan J, Freyermuth F, Sung JC, O'Donovan K, Fare CM, Diaz Z, Singh N, Zhang ZC, Coughlin M, Sweeny EA, DeSantis ME, Jackrel ME, Rodell CB, Burdick JA, King OD, Gitler AD, Lagier-Tourenne C, Pandey UB, Chook YM, Taylor JP, Shorter J. Nuclear-Import Receptors Reverse Aberrant Phase Transitions of RNA-Binding Proteins with Prion-like Domains. Cell. 2018 Apr 19;173(3):677-692.
PMID: 29677512

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. Microbes vs. chemistry in the origin of the anaerobic gut lumen. Proc Natl Acad Sci U S A. 2018 Apr 17;115(16):4170-4175.
PMID: 29610310

Wilson DF, Cember ATJ, Matschinsky FM. Glutamate dehydrogenase: Role in regulating metabolism and insulin release in pancreatic β-cells. J Appl Physiol(1985). 2018 Apr 12. [Epub ahead of print] 
PMID: 29648519

Mancini JA, Sheehan M, Kodali G, Chow BY, Bryant DA, Dutton PL, Moser CC. De novo synthetic biliprotein design, assembly and excitation energy transfer. J R Soc Interface. 2018 Apr;15(141). 
PMID: 29618529

Han J, Lachance C, Ricketts MD, McCullough CE, Gerace M, Black BE, Côté J, Marmorstein R. The scaffolding protein JADE1 physically links the acetyltransferase subunit HBO1 with its histone H3-H4 substrate. J Biol Chem. 2018 Mar 23;293(12):4498-4509. 
PMID: 29382722

Langelier MF, Zandarashvili L, Aguiar PM, Black BE, Pascal JM. NAD(+) analog reveals PARP-1 substrate-blocking mechanism and allosteric communication from catalytic center to DNA-binding domains. Nat Commun. 2018 Feb 27;9(1):844.
PMID: 29487285

Ye X, Mayne L, Kan ZY, Englander SW. Folding of maltose binding protein outside of and in GroEL. Proc Natl Acad Sci U S A. 2018 Jan 16;115(3):519-524
PMID: 29295923



Becker JS, McCarthy RL, Sidoli S, Donahue G, Kaeding KE, He Z, Lin S, Garcia BA, Zaret KS. Genomic and Proteomic Resolution of Heterochromatin and Its Restriction of Alternate Fate Genes. Mol Cell. 2017 Dec 21;68(6):1023-1037.
PMID: 29272703

Damodaren N, Van Eeuwen T, Zamel J, Lin-Shiao E, Kalisman N, Murakami K. Def1 interacts with TFIIH and modulates RNA polymerase II transcription. Proc Natl Acad Sci U S A. 2017 Dec 12;114(50):13230-13235.
PMID: 29180430

Liang D, Tatomer DC, Luo Z, Wu H, Yang L, Chen LL, Cherry S, Wilusz JE. The Output of Protein-Coding Genes Shifts to Circular RNAs When the Pre-mRNA Processing Machinery Is Limiting. Mol Cell. 2017 Dec 7;68(5):940-954.
PMID: 29174924

Oh JM, Di C, Venters CC, Guo J, Arai C, So BR, Pinto AM, Zhang Z, Wan L, Younis I, Dreyfuss G. U1 snRNP telescripting regulates a size-function-stratified human genome. Nat Struct Mol Biol. 2017 Nov;24(11):993-999.
PMID: 28967884

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. Characterization of histone acylations links chromatin modifications with metabolism. Nat Commun. 2017 Oct 26;8(1):1141.
PMID: 29070843

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. Cytoplasmic chromatin triggers inflammation in senescence and cancer. Nature. 2017 Oct 19;550(7676):402-406.
PMID: 28976970

Doliba NM, Liu Q, Li C, Chen P, Liu C, Naji A, Matschinsky FM. Inhibition of cholinergic potentiation of insulin secretion from pancreatic islets by chronic elevation of glucose and fatty acids: Protection by casein kinase 2 inhibitor. Mol Metab. 2017 Oct;6(10):1240-1253.
PMID: 29031723

Armour SM, Remsberg JR, Damle M, Sidoli S, Ho WY, Li Z, Garcia BA, Lazar MA. An HDAC3-PROX1 corepressor module acts on HNF4α to control hepatic triglycerides. Nat Commun. 2017 Sep 15;8(1):549. 
PMID: 28916805

Iwata-Otsubo A, Dawicki-McKenna JM, Akera T, Falk SJ, Chmátal L, Yang K, Sullivan BA, Schultz RM, Lampson MA, Black BE. Expanded Satellite Repeats Amplify a Discrete CENP-A Nucleosome Assembly Site on Chromosomes that Drive in Female Meiosis. Curr Biol. 2017 Aug 7;27(15):2365-2373.
PMID: 28756949

Gazzara MR, Mallory MJ, Roytenberg R, Lindberg JP, Jha A, Lynch KW, Barash Y. Ancient antagonism between CELF and RBFOX families tunes mRNA splicing outcomes. Genome Res. 2017 Aug;27(8):1360-1370.
PMID: 28512194

Gates SN, Yokom AL, Lin J, Jackrel ME, Rizo AN, Kendsersky NM, Buell CE, Sweeny EA, Mack KL, Chuang E, Torrente MP, Su M, Shorter J, Southworth DR. Ratchet-like polypeptide translocation mechanism of the AAA+ disaggregase Hsp104. Science. 2017 Jul 21;357(6348):273-279.
PMID: 28619716

Gupta K, Sharp R, Yuan JB, Li H, Van Duyne GD. Coiled-coil interactions mediate serine integrase directionality. Nucleic Acids Res. 2017 Jul 7;45(12):7339-7353.
PMID: 28549184

Caro JA, Harpole KW, Kasinath V, Lim J, Granja J, Valentine KG, Sharp KA, Wand AJ. Entropy in molecular recognition by proteins. Proc Natl Acad Sci U S A. 2017 Jun 20;114(25):6563-6568.
PMID: 28584100

Guo LY, Allu PK, Zandarashvili L, McKinley KL, Sekulic N, Dawicki-McKenna JM, Fachinetti D, Logsdon GA, Jamiolkowski RM, Cleveland DW, Cheeseman IM, Black BE. Centromeres are maintained by fastening CENP-A to DNA and directing an arginine anchor-dependent nucleosome transition. Nat Commun. 2017 Jun 9;8:15775.
PMID: 28598437

Wilson DF, Cember ATJ, Matschinsky FM. The thermodynamic basis of glucose-stimulated insulin release: a model of the core mechanism. Physiol Rep. 2017 Jun;5(12).
PMID: 28655753

Liu MY, Torabifard H, Crawford DJ, DeNizio JE, Cao XJ, Garcia BA, Cisneros GA, Kohli RM. Mutations along a TET2 active site scaffold stall oxidation at 5-hydroxymethylcytosine. Nat Chem Biol. 2017 Feb;13(2):181-187.
PMID: 27918559

Fachinetti D, Logsdon GA, Abdullah A, Selzer EB, Cleveland DW, Black BE. CENP-A Modifications on Ser68 and Lys124 Are Dispensable for Establishment, Maintenance, and Long-Term Function of Human Centromeres. Dev Cell. 2017 Jan 9;40(1):104-113.
PMID: 28073008

Kodali G, Mancini JA, Solomon LA, Episova TV, Roach N, Hobbs CJ, Wagner P, Mass OA, Aravindu K, Barnsley JE, Gordon KC, Officer DL, Dutton PL, Moser CC. Design and engineering of water-soluble light-harvesting protein maquettes. Chem Sci. 2017 Jan 1;8(1):316-324.
PMID: 28261441



Grasso M, Estrada MA, Ventocilla C, Samanta M, Maksimoska J, Villanueva J, Winkler JD, Marmorstein R. Chemically Linked Vemurafenib Inhibitors Promote an Inactive BRAF(V600E) Conformation. ACS Chem Biol. 2016 Oct 21;11(10):2876-2888.
PMID: 27571413

He C, Sidoli S, Warneford-Thomson R, Tatomer DC, Wilusz JE, Garcia BA, Bonasio R. High-Resolution Mapping of RNA-Binding Regions in the Nuclear Proteome of Embryonic Stem Cells. Mol Cell. 2016 Oct 20;64(2):416-430.
PMID: 27768875

Yokom AL, Gates SN, Jackrel ME, Mack KL, Su M, Shorter J, Southworth DR. Spiral architecture of the Hsp104 disaggregase reveals the basis for polypeptide translocation. Nat Struct Mol Biol. 2016 Sep;23(9):830-7.
PMID: 27478928

Molleston JM, Sabin LR, Moy RH, Menghani SV, Rausch K, Gordesky-Gold B, Hopkins KC, Zhou R, Jensen TH, Wilusz JE, Cherry S. A conserved virus-induced cytoplasmic TRAMP-like complex recruits the exosome to target viral RNA for degradation. Genes Dev. 2016 Jul 15;30(14):1658-70.
PMID: 27474443

Lin S, Yuan ZF, Han Y, Marchione DM, Garcia BA. Preferential Phosphorylation on Old Histones during Early Mitosis in Human Cells. J Biol Chem. 2016 Jul 15;291(29):15342-57.
PMID: 27226594

Wang X, Yuan ZF, Fan J, Karch KR, Ball LE, Denu JM, Garcia BA. A Novel Quantitative Mass Spectrometry Platform for Determining Protein O-GlcNAcylation Dynamics. Mol Cell Proteomics. 2016 Jul;15(7):2462-75.
PMID: 27114449

Ajith S, Gazzara MR, Cole BS, Shankarling G, Martinez NM, Mallory MJ, Lynch KW. Position-dependent activity of CELF2 in the regulation of splicing and implications for signal-responsive regulation in T cells. RNA Biol. 2016 Jun 2;13(6):569-81.
PMID: 27096301

Laxmikanthan G, Xu C, Brilot AF, Warren D, Steele L, Seah N, Tong W, Grigorieff N, Landy A, Van Duyne GD. Structure of a Holliday junction complex reveals mechanisms governing a highly regulated DNA transaction. Elife. 2016 May  25;5.
PMID: 27223329

Smoak EM, Stein P, Schultz RM, Lampson MA, Black BE. Long-Term Retention of CENP-A Nucleosomes in Mammalian Oocytes Underpins Transgenerational Inheritance of Centromere Identity. Curr Biol. 2016 Apr 25;26(8):1110-6.
PMID: 27040782

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