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Select item 108724771.

Protein interaction network revealed by quantitative proteomic analysis links TFIIB to multiple aspects of the transcription cycle

Michael J. O’Brien, Athar Ansari

Biochim Biophys Acta Proteins Proteom. Author manuscript; available in PMC 2024 Feb 16.

Published in final edited form as: Biochim Biophys Acta Proteins Proteom. 2024 Jan 1; 1872(1): 140968. Published online 2023 Oct 19. doi: 10.1016/j.bbapap.2023.140968

PMCID:: PMC10872477

Abstract Article PDF–1.7M

Select item 107988582.

Fast-evolving cofactors regulate the role of HEATR5 complexes in intra-Golgi trafficking

Lucas J. Marmorale, Huan Jin, Thomas G. Reidy, Brandon Palomino-Alonso, Christopher J. Zysnarski, Fatima Jordan-Javed, Sagar Lahiri, Mara C. Duncan

J Cell Biol. 2024 Mar 4; 223(3): e202309047. Published online 2024 Jan 19. doi: 10.1083/jcb.202309047

PMCID:: PMC10798858

Abstract Article PDF–6.4M

Select item 105166423.

ISW1a modulates cohesin distribution in centromeric and pericentromeric regions

Ireneusz Litwin, Małgorzata Nowicka, Katarzyna Markowska, Ewa Maciaszczyk-Dziubińska, Paulina Tomaszewska, Robert Wysocki, Karol Kramarz

Nucleic Acids Res. 2023 Sep 22; 51(17): 9101–9121. Published online 2023 Jul 24. doi: 10.1093/nar/gkad612

PMCID:: PMC10516642

Abstract Article PDF–2.8M

Select item 96309864.

A balancing act: interactions within NuA4/TIP60 regulate picNuA4 function in Saccharomyces cerevisiae and humans

Phoebe Y T Lu, Alyssa C Kirlin, Maria J Aristizabal, Hilary T Brewis, Nancy Lévesque, Dheva T Setiaputra, Nikita Avvakumov, Joris J Benschop, Marian Groot Koerkamp, Frank C P Holstege, Nevan J Krogan, Calvin K Yip, Jacques Côté, Michael S Kobor

Genetics. 2022 Nov; 222(3): iyac136. Published online 2022 Sep 6. doi: 10.1093/genetics/iyac136

PMCID:: PMC9630986

Abstract Article PDF–2.2M

Select item 92098115.

New data and collaborations at the Saccharomyces Genome Database: updated reference genome, alleles, and the Alliance of Genome Resources

Stacia R Engel, Edith D Wong, Robert S Nash, Suzi Aleksander, Micheal Alexander, Eric Douglass, Kalpana Karra, Stuart R Miyasato, Matt Simison, Marek S Skrzypek, Shuai Weng, J Michael Cherry

Genetics. 2022 Apr; 220(4): iyab224. Published online 2021 Dec 13. doi: 10.1093/genetics/iyab224

PMCID:: PMC9209811

Abstract Article PDF–818K

Select item 85119506.

The histone chaperone Spt6 is required for normal recruitment of the capping enzyme Abd1 to transcribed regions

Rajaraman Gopalakrishnan, Fred Winston

J Biol Chem. 2021 Oct; 297(4): 101205. Published online 2021 Sep 17. doi: 10.1016/j.jbc.2021.101205

PMCID:: PMC8511950

Abstract Article PDF–3.1M

Select item 84212297.

Testing mechanisms of DNA sliding by architectural DNA-binding proteins: dynamics of single wild-type and mutant protein molecules in vitro and in vivo

Kiyoto Kamagata, Yuji Itoh, Cheng Tan, Eriko Mano, Yining Wu, Sridhar Mandali, Shoji Takada, Reid C Johnson

Nucleic Acids Res. 2021 Sep 7; 49(15): 8642–8664. Published online 2021 Aug 5. doi: 10.1093/nar/gkab658

PMCID:: PMC8421229

Abstract Article PDF–6.0M

Select item 77187518.

Comprehensive Synthetic Genetic Array Analysis of Alleles That Interact with Mutation of the Saccharomyces cerevisiae RecQ Helicases Hrq1 and Sgs1

Elsbeth Sanders, Phoebe A. Nguyen, Cody M. Rogers, Matthew L. Bochman

G3 (Bethesda) 2020 Dec; 10(12): 4359–4368. Published online 2020 Oct 28. doi: 10.1534/g3.120.401709

PMCID:: PMC7718751

Abstract Article PDF–1.2M

Select item 76417349.

The HMGB chromatin protein Nhp6A can bypass obstacles when traveling on DNA

Kiyoto Kamagata, Kana Ouchi, Cheng Tan, Eriko Mano, Sridhar Mandali, Yining Wu, Shoji Takada, Satoshi Takahashi, Reid C Johnson

Nucleic Acids Res. 2020 Nov 4; 48(19): 10820–10831. Published online 2020 Sep 30. doi: 10.1093/nar/gkaa799

PMCID:: PMC7641734

Abstract Article PDF–4.8M

Select item 727317710.

Chaperone-Mediated Protein Disaggregation Triggers Proteolytic Clearance of Intra-nuclear Protein Inclusions

Fabian den Brave, Lucas V. Cairo, Chandhuru Jagadeesan, Carmen Ruger-Herreros, Axel Mogk, Bernd Bukau, Stefan Jentsch

Cell Rep. 2020 Jun 2; 31(9): 107680. Published online 2020 Jun 2. doi: 10.1016/j.celrep.2020.107680

PMCID:: PMC7273177

Abstract Article

Select item 645113711.

Evidence for a bind-then-bend mechanism for architectural DNA binding protein yNhp6A

Manas Kumar Sarangi, Viktoriya Zvoda, Molly Nelson Holte, Nicole A Becker, Justin P Peters, L James Maher, III, Anjum Ansari

Nucleic Acids Res. 2019 Apr 8; 47(6): 2871–2883. Published online 2019 Jan 30. doi: 10.1093/nar/gkz022

PMCID:: PMC6451137

Abstract Article PDF–1.6M

Select item 634489512.

Single and double box HMGB proteins differentially destabilize nucleosomes

Micah J McCauley, Ran Huo, Nicole Becker, Molly Nelson Holte, Uma M Muthurajan, Ioulia Rouzina, Karolin Luger, L James Maher, III, Nathan E Israeloff, Mark C Williams

Nucleic Acids Res. 2019 Jan 25; 47(2): 666–678. Published online 2018 Nov 16. doi: 10.1093/nar/gky1119

PMCID:: PMC6344895

Abstract Article PDF–4.1M

Select item 620982313.

Pathologic Replication-Independent Endogenous DNA Double-Strand Breaks Repair Defect in Chronological Aging Yeast

Monnat Pongpanich, Maturada Patchsung, Apiwat Mutirangura

Front Genet. 2018; 9: 501. Published online 2018 Oct 25. doi: 10.3389/fgene.2018.00501

PMCID:: PMC6209823

Abstract Article PDF–714K

Select item 594018014.

Network inference reveals novel connections in pathways regulating growth and defense in the yeast salt response

Matthew E. MacGilvray, Evgenia Shishkova, Deborah Chasman, Michael Place, Anthony Gitter, Joshua J. Coon, Audrey P. Gasch

PLoS Comput Biol. 2018 May; 13(5): e1006088. Published online 2018 May 8. doi: 10.1371/journal.pcbi.1006088

PMCID:: PMC5940180

Abstract Article PDF–3.0M

Select item 591375215.

Role of Nhp6 and Hmo1 in SWI/SNF occupancy and nucleosome landscape at gene regulatory regions

Matias I. Hepp, Michaela Smolle, Cristian Gidi, Roberto Amigo, Nicole Valenzuela, Axel Arriagada, Alejandro Maureira, Madelaine M. Gogol, Marcela Torrejón, Jerry L. Workman, José L. Gutiérrez

Biochim Biophys Acta. Author manuscript; available in PMC 2018 Apr 24.

Published in final edited form as: Biochim Biophys Acta. 2017 Mar; 1860(3): 316–326. Published online 2017 Jan 9. doi: 10.1016/j.bbagrm.2017.01.002

PMCID:: PMC5913752

Abstract Article PDF–2.3M

Select item 591246016.

Functional roles of the DNA-binding HMGB domain in the histone chaperone FACT in nucleosome reorganization

Laura L. McCullough, Zaily Connell, Hua Xin, Vasily M. Studitsky, Alexey V. Feofanov, Maria E. Valieva, Tim Formosa

J Biol Chem. 2018 Apr 20; 293(16): 6121–6133. Published online 2018 Mar 7. doi: 10.1074/jbc.RA117.000199

PMCID:: PMC5912460

Abstract Article PDF–2.2M

Select item 576535917.

Genome-Wide Mapping of Decay Factor–mRNA Interactions in Yeast Identifies Nutrient-Responsive Transcripts as Targets of the Deadenylase Ccr4

Jason E. Miller, Liye Zhang, Haoyang Jiang, Yunfei Li, B. Franklin Pugh, Joseph C. Reese

G3 (Bethesda) 2018 Jan; 8(1): 315–330. Published online 2017 Nov 20. doi: 10.1534/g3.117.300415

PMCID:: PMC5765359

Abstract Article PDF–2.2M

Select item 566188518.

A global interaction network maps a wiring diagram of cellular function

Michael Costanzo, Benjamin VanderSluis, Elizabeth N. Koch, Anastasia Baryshnikova, Carles Pons, Guihong Tan, Wen Wang, Matej Usaj, Julia Hanchard, Susan D. Lee, Vicent Pelechano, Erin B. Styles, Maximilian Billmann, Jolanda van Leeuwen, Nydia van Dyk, Zhen-Yuan Lin, Elena Kuzmin, Justin Nelson, Jeff S. Piotrowski, Tharan Srikumar, Sondra Bahr, Yiqun Chen, Raamesh Deshpande, Christoph F. Kurat, Sheena C. Li, Zhijian Li, Mojca Mattiazzi Usaj, Hiroki Okada, Natasha Pascoe, Bryan-Joseph San Luis, Sara Sharifpoor, Emira Shuteriqi, Scott W. Simpkins, Jamie Snider, Harsha Garadi Suresh, Yizhao Tan, Hongwei Zhu, Noel Malod-Dognin, Vuk Janjic, Natasa Przulj, Olga G. Troyanskaya, Igor Stagljar, Tian Xia, Yoshikazu Ohya, Anne-Claude Gingras, Brian Raught, Michael Boutros, Lars M. Steinmetz, Claire L. Moore, Adam P. Rosebrock, Amy A. Caudy, Chad L. Myers, Brenda Andrews, Charles Boone

Science. Author manuscript; available in PMC 2017 Oct 30.

Published in final edited form as: Science. 2016 Sep 23; 353(6306): aaf1420. doi: 10.1126/science.aaf1420

PMCID:: PMC5661885

Abstract Article PDF–2.6M

Select item 564803219.

Architecture and dynamics of overlapped RNA regulatory networks

Christopher P. Lapointe, Melanie A. Preston, Daniel Wilinski, Harriet A.J. Saunders, Zachary T. Campbell, Marvin Wickens

RNA. 2017 Nov; 23(11): 1636–1647. doi: 10.1261/rna.062687.117

PMCID:: PMC5648032

Abstract Article PDF–6.6M

Select item 560192020.

P-body proteins regulate transcriptional rewiring to promote DNA replication stress resistance

Raphael Loll-Krippleber, Grant W. Brown

Nat Commun. 2017; 8: 558. Published online 2017 Sep 15. doi: 10.1038/s41467-017-00632-2

PMCID:: PMC5601920

Abstract Article PDF–3.8M

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