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Recent Select Publications

2021

Osvaldo D. Rivera, Michael .J Mallory, Mathieu Quesnel-Vallières, Rakesh Chatrikhi, David C. Schultz, Martin Carroll, Yoseph Barash, Sara Cherry, Kristen W. Lynch. Alternative splicing redefines landscape of commonly mutated genes in acute myeloid leukemia. Proc Natl Acad Sci USA. 2021 Apr 13 118(15)
PMID 33876749

Lindsay K. Pino, Josue Baeza, Richard Lauman, Birgit Schilling, Benjamin A. Garcia. Improved SILAC Quantification with Data-Independent Acquisition to Investigate Bortezomib-Induced Protein Degradation. J Proteome Res. 2021 Mar 25
PMID to come

Saravana G. Baskaran, Thayne P. Sharp, Kim A Sharp. Computational Graphics Software for Interactive Docking and Visualization of Ligand-Protein Complementarity. J Chem Inf Model. 2021 Mar 22;61(3):1427-1443.
PMID: 33656873

Stefan Steimle, Trevor van Eeuwen, Yavuz Ozturk, Hee Jong Kim, Merav Braitbard, Nur Selamoglu, Benjamin A Garcia, Dina Schneidman-Duhovny, Kenji Murakami, Fevzi Daldal. Cryo-EM structures of engineered active bc 1-cbb 3type CIII 2 CIV super-complexes and electronic communication between the complexes. Nat Commun. 2021 Feb 10;12(1):929.
PMID: 33568648

Santrupti Nerli, Viviane S. De Paula, Andrew C. McShan, Nikolaos G. Sgourakis. Backbone-independent NMR resonance assignments of methyl probes in large proteins. Nat Commun. 2021 Jan 29;12(1): 691
PMID 33514730

Daniel A. Jacome, Justin D. Northrup, Andrew J. Ruff, Sean W. Reilly, Iris K. Lee, Gabrielle S. Blizard, Mark A. Sellmyer. A Chemical Approach for Programmable Protein Outputs Based on Engineered Cell Interactions. ACS Chem. Biol. 2021 Jan 15;16(1): 52–57
PMID: 33351606

2020

Luca Ravotto, Stephen L Meloni, Tatiana V Esipova, Artëm E Masunov, Jessica M Anna, Sergei A Vinogradov. Three-Photon Spectroscopy of Porphyrins. J Phys Chem A. 2020 Dec 31;124(52)
PMID: 33337890

Buyan Pan, Naoki Kamo, Marie Shimogawa, Yun Huang, Anna Kashina, Elizabeth Rhoades, E. James Petersson. Effects of Glutamate Arginylation on α-Synuclein: Studying an Unusual Post-Translational Modification through Semisynthesis. J Am Chem Soc. 2020 Dec 30;142(52)
PMID: 33337869

Kushol Gupta, Audrey Allen, Carolina Giraldo, Grant Eilers, Robert Sharp, Young Hwang, Hemma Murali, Katrina Cruz, Paul Janmey, Frederic Bushman, Gregory D Van Duyne. Structure. 2020 Dec 23;S0969-2126(20)30468-8
PMID: 33357410

Zachary M March, Katelyn Sweeney, Hanna Kim, Xiaohui Yan, Laura M Castellano, Meredith E Jackrel, JiaBei Lin, Edward Chuang, Edward Gomes, Corey W Willicott, Karolina Michalska, Robert P Jedrzejczak, Andrzej Joachimiak, Kim A Caldwell, Guy A Caldwell, Ophir Shalem, James Shorter. Therapeutic genetic variation revealed in diverse Hsp104 homologs. Elife. 2020 Dec 15
PMID: 33319748

Matthew G Thompson, Mark Dittmar, Michael J Mallory, Prasanna Bhat, Max B Ferretti, Beatriz Ma Fontoura, Sara Cherry, Kristen W Lynch. Viral-induced alternative splicing of host genes promotes influenza replication. Elife. 2020 Dec 3
PMID: 33269701

Buyan Pan, Joo Hyung Park, Trudy Ramlall, David Eliezer, Elizabeth Rhoades, E James Petersson. Chemoenzymatic Semi-synthesis Enables Efficient Production of Isotopically-Labelled α-Synuclein with Site-specific Tyrosine Phosphorylation. Chembiochem. 2020 Dec 3
PMID: 33274519

Congcong Lu, Mariel Coradin, Elizabeth G. Porter, Benjamin A. Garcia. Accelerating the field of epigenetic histone modification through mass spectrometry-based approaches. Mol Cell Proteomics. 2020 Nov 17
PMID: 33203747

Jimin Yoon, John J. Ferrie, E. James Petersson. Improved Modeling of Thioamide FRET Quenching by Including Conformational Restriction and Coulomb Coupling. J Phys Chem B. 2020 Nov 25; 124(47)
PMID: 33196192

Hui Shen, Julian Stoute, Kathy Fange Liu. Structural and Catalytic Roles of the Human 18S rRNA Methyltransferases DIMT1 in Ribosome Assembly and Translation. J Biol Chem. 2020 Jul 2
PMID: 32616653

Ryan R Cupo, James Shorter. Skd3 (human CLPB) is a potent mitochondrial protein disaggregase that is inactivated by 3-methylglutaconic aciduria-linked mutations. eLife. 2020 June 23
PMID: 32573439

Caleb M Radens, Davia Blake, Paul Jewell, Yoseph Barash and Kristen W Lynch. Meta-Analysis of Transcriptomic Variation in T cell Populations Reveals both Variable and Consistent Signatures of Gene Expression and Splicing. RNA. 2020 June 17
PMID: 32554554

Austin Zimmet, Trevor Van Eeuwen, Malgorzata Boczkowska, Grzegorz Rebowski, Kenji Murakami, Roberto Dominguez. Cryo-EM Structure of NPF-bound Human Arp2/3 Complex and Activation Mechanism. Sci Adv. 2020 June 5;6(23)
PMID:32548263

R Jordan Ontiveros, Hui Shen, Julian Stoute, Amber Yanas, Yixiao Cui, Yuyu Zhang, Kathy Fange Liu. Coordination of mRNA and tRNA Methylations by TRMT10A. Proc Natl Acad Sci USA. 2020 April 7;117(14)
PMID: 32213595

Mallory MJ, McClory SP, Chatrikhi R, Gazzara MR, Ontiveros RJ, Lynch KW. Reciprocal regulation of hnRNP C and CELF2 through translation and transcription tunes splicing activity in T cells. Nucleic Acids Res. 2020 April 27
PMID: 32338744

Ye X, Lin J, Mayne L, Shorter J, Englander SW. Structural and kinetic basis for the regulation and potentiation of Hsp104 function. PNAS. 2020 April 10
PMID: 32277033

Ghanty U, Wang T, Kohli RM. Nucleobase Modifiers Identify TET Enzymes as Bifunctional DNA Dioxygenases Capable of Direct N-Demethylation. Angew Chem Int Ed Engl. 2020 April 9
PMID: 32271979

Zandarashvili L, Langelier MF, Velagapudi UK, Hancock MA, Steffen JD, Billur R, Hannan ZM, Wicks AJ, Krastev DB, Pettitt SJ, Lord CJ, Talele TT, Pascal JM, Black BE. Structural basis for allosteric PARP-1 retention on DNA breaks. Science. 2020 April 3;368(6486)
PMID: 32241924

Wein S, Andrews B, Sachsenberg T, Santos-Rosa H, Kohlbacher O, Kouzarides T, Garcia BA, Weisser H. A computational platform for high-throughput analysis of RNA sequences and modifications by mass spectrometry. Nat Commun. 2020 Feb 17;11(1):926.
PMID: 32066737

Deng S, McTiernan N, Wei X, Arnesen T, Marmorstein R. Molecular basis for N-terminal acetylation by human NatE and its modulation by HYPK. Nat Commun. 2020 Feb 10;11(1):818.
PMID: 32042062

Sweeny EA, Tariq A, Gurpinar E, Go MS, Sochor MA, Kan ZY, Mayne L, Englander SW, Shorter J. Structural and mechanistic insights into Hsp104 function revealed by synchrotron X-ray footprinting. J Biol Chem. 2020 Feb 7;295(6):1517-1538.
PMID: 31882541

Plunkett S, El Khatib M, Şencan İ, Porter JE, Kumar ATN, Collins JE, SakadŽić S, Vinogradov SA. In vivo deep-tissue microscopy with UCNP/Janus-dendrimers as imaging probes: resolution at depth and feasibility of ratiometric sensing. Nanoscale. 2020 Jan 28;12(4):2657-2672.
PMID: 31939953

Pumroy RA, Fluck EC 3rd, Ahmed T, Moiseenkova-Bell VY. Structural insights into the gating mechanisms of TRPV channels. Cell Calcium. 2020 Jan 24;87:102168.
PMID: 32004816

Oh JM, Venters CC, Di C, Pinto AM, Wan L, Younis I, Cai Z, Arai C, So BR, Duan J, Dreyfuss G. U1 snRNP regulates cancer cell migration and invasion in vitro. Nat Commun. 2020 Jan 7;11(1):1.
PMID: 31911652

Wei X, Schultz K, Bazilevsky GA, Vogt A, Marmorstein R. Molecular basis for acetyl-CoA production by ATP-citrate lyase. Nat Struct Mol Biol. 2020 Jan;27(1):33-41.
PMID: 31873304

Niaki AG, Sarkar J, Cai X, Rhine K, Vidaurre V, Guy B, Hurst M, Lee JC, Koh HR, Guo L, Fare CM, Shorter J, Myong S. Loss of Dynamic RNA Interaction and Aberrant Phase Separation Induced by Two Distinct Types of ALS/FTD-Linked FUS Mutations. Mol Cell. 2020 Jan 2;77(1):82-94.
PMID: 31630970


2019

Agosto LM, Gazzara MR, Radens CM, Sidoli S, Baeza J, Garcia BA, Lynch KW. Alcohol metabolism contributes to brain histone acetylation. Genome Res. 2019 Dec;29(12):2046-2055.
PMID: 31727681

Fujiwara R, Damodaren N, Wilusz JE, Murakami K. The capping enzyme facilitates promoter escape and assembly of a follow-on preinitiation complex for reinitiation. Proc Natl Acad Sci USA. 2019 Nov 5;116(45):22573-22582.
PMID: 31591205

Mews P, Egervari G, Nativio R, Sidoli S, Donahue G, Lombroso SI, Alexander DC, Riesche SL, Heller EA, Nestler EJ, Garcia BA, Berger SL. Alcohol metabolism contributes to brain histone acetylation. Nature. 2019 Oct;574(7780):717-721.
PMID: 31645761

Pumroy RA, Samanta A, Liu Y, Hughes TE, Zhao S, Yudin Y, Rohacs T, Han S, Moiseenkova-Bell VY. Molecular mechanism of TRPV2 channel modulation by cannabidiol. Elife. 2019 Sep 30;8.
PMID: 31566564

Sidoli S, Lopes M, Lund PJ, Goldman N, Fasolino M, Coradin M, Kulej K, Bhanu NV, Vahedi G, Garcia BA. A mass spectrometry-based assay using metabolic labeling to rapidly monitor chromatin accessibility of modified histone proteins. Sci Rep. 2019 Sep 20;9(1):13613.
PMID: 31541121

Tatomer DC, Elrod ND, Liang D, Xiao MS, Jiang JZ, Jonathan M, Huang KL, Wagner EJ, Cherry S, Wilusz JE. The Integrator complex cleaves nascent mRNAs to attenuate transcription. Genes Dev. 2019 Nov 1;33(21-22):1525-1538.
PMID: 31530651

So BR, Di C, Cai Z, Venters CC, Guo J, Oh JM, Arai C, Dreyfuss G. A Complex of U1 snRNP with Cleavage and Polyadenylation Factors Controls Telescripting, Regulating mRNA Transcription in Human Cells. Mol Cell. 2019 Nov 21;76(4):590-599.
PMID: 31522989

Chatrikhi R, Mallory MJ, Gazzara MR, Agosto LM, Zhu WS, Litterman AJ, Ansel KM, Lynch KW. RNA Binding Protein CELF2 Regulates Signal-Induced Alternative Polyadenylation by Competing with Enhancers of the Polyadenylation Machinery. Cell Rep. 2019 Sep 10;28(11)2795-2806.
PMID: 31509743

Tariq A, Lin J, Jackrel ME, Hesketh CD, Carman PJ, Mack KL, Weitzman R, Gambogi C, Hernandez Murillo OA, Sweeny EA, Gurpinar E, Yokom AL, Gates SN, Yee K, Sudesh S, Stillman J, Rizo AN, Southworth DR, Shorter J. Mining Disaggregase Sequence Space to Safely Counter TDP-43, FUS, and α-Synuclein Proteotoxicity. Cell Rep. 2019 Aug20;28(8):2080-2095.
PMID: 31433984

Wojcik JB, Marchione DM, Sidoli S, Djedid A, Lisby A, Majewski J, Garcia BA. Epigenomic Reordering Induced by Polycomb Loss Drives Oncogenesis but Leads to Therapeutic Vulnerabilities in Malignant Peripheral Nerve Sheath Tumors. Cancer Res. 2019 Jul1;79(13):3205-3219.
PMID: 30898839

Xiao MS, Wilusz JE. An improved method for circular RNA purification using RNase R that efficiently removes linear RNAs containing G-quadruplexes or structured 3' ends. Nucleic Acids Res. 2019 Sep 19;47(16):8755-8769.
PMID: 31269210

Allu PK, Dawicki-McKenna JM, Van Eeuwen T, Slavin M, Braitbard M, Xu C, Kalisman N, Murakami K, Black BE. Structure of the Human Core Centromeric Nucleosome Complex. Curr Biol. 2019 Aug 19;29(16):2625-2639.
PMID: 31353180

Logsdon GA, Gambogi CW, Liskovykh MA, Barrey EJ, Larionov V, Miga KH, Heun P, Black BE. Human Artificial Chromosomes that Bypass Centromeric DNA. Cell. 2019 Jul 25;178(3):624-639.
PMID: 31348889

Li B, Esipova TV, Sencan I, Kılıç K, Fu B, Desjardins M, Moeini M, Kura S, Yaseen MA, Lesage F, Østergaard L, Devor A, Boas DA, Vinogradov SA, Sakadžić S. More homogeneous capillary flow and oxygenation in deeper cortical layers correlate with increased oxygen extraction. Elife. 2019 Jul 15;8.
PMID: 31305237

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. Regulation of nuclear epigenome by mitochondrial DNA heteroplasmy. Proc Natl Acad Sci USA. 2019 Aug 6;116(32):16028-16035.
PMID: 31253706

Kearse MG, Goldman DH, Choi J, Nwaezeapu C, Liang D, Green KM, Goldstrohm AC, Todd PK, Green R, Wilusz JE. Ribosome queuing enables non-AUG translation to be resistant to multiple protein synthesis inhibitors. Genes Dev. 2019 July 1;33(13-14):871-885.
PMID: 31171704

Bialas C, Barnard DT, Auman DB, McBride RA, Jarocha LE, Hore PJ, Dutton PL, Stanley RJ, Moser CC. Ultrafast flavin/tryptophan radical pair kinetics in a magnetically sensitive artificial protein. Phys Chem Chem Phys. 2019 June 26;33(13-14):13453-13461.
PMID: 31187821

Ricketts MD, Dasgupta N, Fan J, Han J, Gerace M, Tang Y, Black BE, Adams PD, Marmorstein R. The HIRA histone chaperone complex subunit UBN1 harbors H3/H4- and DNA-binding activity. J Biol Chem. 2019 June 7;294(23):9239-9259.
PMID: 31040182

Bhanu NV, Sidoli S, Yuan Z-F, Molden RC, Garcia BA. Regulation of proline-directed kinases and the trans-histone code H3K9me3/H4K20me3 during human myogenesis. J Biol Chem. 2019 May 17;294(20):8296-8308.
PMID: 30872405

Bazilevsky GA, Affronti HC, Wei X, Campbell SL, Wellen KE, Marmorstein R. ATP-citrate lyase multimerization is required for coenzyme-A substrate binding and catalysis. J Biol Chem. 2019 May 3;294(18):7259-7268.
PMID: 30877197

Ye X, Lin J, Mayne L, Shorter J, Englander SW. Hydrogen exchange reveals Hydrogen exchange reveals Hsp104 architecture, structural dynamics, and energetics in physiological solution. Proc Natl Acad Sci USA. 2019 Apr 9;116(15):7333-7342.
PMID: 30918129

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 Mar 5;29(3):736-744.
PMID: 30686745

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


2018

Karch KR, Coradin M, Zandarashvili Li, Kan ZY, Gerace M, Englander SW, Black BE, Garcia 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 USA. 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 USA. 2018 Jan 16;115(3):519-524.
PMID: 29295923

 

2017

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

 

2016

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