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Select item 114236781.

An APEX2-based proximity-dependent biotinylation assay with temporal specificity to study protein interactions during autophagy in the yeast Saccharomyces cerevisiae

Yasmina Filali-Mouncef, Alexandre Leytens, Prado Vargas Duarte, Mattia Zampieri, Jörn Dengjel, Fulvio Reggiori

Autophagy. 2024; 20(10): 2323–2337. Published online 2024 Jul 3. doi: 10.1080/15548627.2024.2366749

PMCID:: PMC11423678

Abstract Article PDF–1.7M

Select item 111820082.

The Prp19C/NTC subunit Syf2 and the Prp19C/NTC-associated protein Cwc15 function in TREX occupancy and transcription elongation

Laura Henke-Schulz, Rashmi Minocha, Nils Holger Maier, Katja Sträßer

RNA. 2024 Jul; 30(7): 854–865. doi: 10.1261/rna.079944.124

PMCID:: PMC11182008

Abstract Article PDF–1.0M

Select item 110241853.

The DEAD-box ATPase Dbp10/DDX54 initiates peptidyl transferase center formation during 60S ribosome biogenesis

Victor E. Cruz, Christine S. Weirich, Nagesh Peddada, Jan P. Erzberger

Nat Commun. 2024; 15: 3296. Published online 2024 Apr 17. doi: 10.1038/s41467-024-47616-7

PMCID:: PMC11024185

Abstract Article PDF–7.4M

Select item 108724774.

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 108687275.

Adaptive preservation of orphan ribosomal proteins in chaperone-dispersed condensates

Asif Ali, Rania Garde, Olivia C. Schaffer, Jared A. M. Bard, Kabir Husain, Samantha Keyport Kik, Kathleen A. Davis, Sofia Luengo-Woods, Maya G. Igarashi, D. Allan Drummond, Allison H. Squires, David Pincus

Nat Cell Biol. Author manuscript; available in PMC 2024 Feb 15.

Published in final edited form as: Nat Cell Biol. 2023 Nov; 25(11): 1691–1703. Published online 2023 Oct 16. doi: 10.1038/s41556-023-01253-2

PMCID:: PMC10868727

Abstract Article PDF–7.0M

Select item 108477206.

Mutations in yeast Pcf11, a conserved protein essential for mRNA 3′ end processing and transcription termination, elicit the Environmental Stress Response

Joel H Graber, Derick Hoskinson, Huiyun Liu, Katarzyna Kaczmarek Michaels, Peter S Benson, Nathaniel J Maki, Christian L Wilson, Caleb McGrath, Franco Puleo, Erika Pearson, Jason N Kuehner, Claire Moore

Genetics. 2024 Feb; 226(2): iyad199. Published online 2023 Nov 15. doi: 10.1093/genetics/iyad199

PMCID:: PMC10847720

Abstract Article PDF–14M

Select item 108018617.

Elf1 promotes Rad26’s interaction with lesion-arrested Pol II for transcription-coupled repair

Reta D. Sarsam, Jun Xu, Indrajit Lahiri, Wenzhi Gong, Qingrong Li, Juntaek Oh, Zhen Zhou, Peini Hou, Jenny Chong, Nan Hao, Shisheng Li, Dong Wang, Andres E. Leschziner

Proc Natl Acad Sci U S A. 2024 Jan 16; 121(3): e2314245121. Published online 2024 Jan 9. doi: 10.1073/pnas.2314245121

PMCID:: PMC10801861

Abstract Article PDF–3.3M

Select item 107988588.

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 107787139.

RNA Pol II Assembly Affects ncRNA Expression

Ana I. Garrido-Godino, Ishaan Gupta, Vicent Pelechano, Francisco Navarro

Int J Mol Sci. 2024 Jan; 25(1): 507. Published online 2023 Dec 29. doi: 10.3390/ijms25010507

PMCID:: PMC10778713

Abstract Article PDF–1.5M

Select item 1070013810.

The social and structural architecture of the yeast protein interactome

André C. Michaelis, Andreas-David Brunner, Maximilian Zwiebel, Florian Meier, Maximilian T. Strauss, Isabell Bludau, Matthias Mann

Nature. 2023; 624(7990): 192–200. Published online 2023 Nov 15. doi: 10.1038/s41586-023-06739-5

PMCID:: PMC10700138

Abstract Article PDF–20M

Select item 1059874311.

Elongation rate of RNA polymerase II affects pausing patterns across 3′ UTRs

Alexandra Khitun, Christian Brion, Zarmik Moqtaderi, Joseph V. Geisberg, L. Stirling Churchman, Kevin Struhl

J Biol Chem. 2023 Nov; 299(11): 105289. Published online 2023 Sep 24. doi: 10.1016/j.jbc.2023.105289

PMCID:: PMC10598743

Abstract Article PDF–2.9M

Select item 1025024612.

Spt6 directly interacts with Cdc73 and is required for Paf1 complex occupancy at active genes in Saccharomyces cerevisiae

Mitchell A Ellison, Sanchirmaa Namjilsuren, Margaret K Shirra, Matthew S Blacksmith, Rachel A Schusteff, Eleanor M Kerr, Fei Fang, Yufei Xiang, Yi Shi, Karen M Arndt

Nucleic Acids Res. 2023 Jun 9; 51(10): 4814–4830. Published online 2023 Mar 17. doi: 10.1093/nar/gkad180

PMCID:: PMC10250246

Abstract Article PDF–3.6M

Select item 993539613.

Structures of transcription preinitiation complex engaged with the +1 nucleosome

Haibo Wang, Sandra Schilbach, Momchil Ninov, Henning Urlaub, Patrick Cramer

Nat Struct Mol Biol. 2023; 30(2): 226–232. Published online 2022 Nov 21. doi: 10.1038/s41594-022-00865-w

PMCID:: PMC9935396

Abstract Article PDF–15M

Select item 982918014.

The RNA export and RNA decay complexes THO and TRAMP prevent transcription-replication conflicts, DNA breaks, and CAG repeat contractions

Rebecca E. Brown, Xiaofeng A. Su, Stacey Fair, Katherine Wu, Lauren Verra, Robyn Jong, Kristin Andrykovich, Catherine H. Freudenreich

PLoS Biol. 2022 Dec; 20(12): e3001940. Published online 2022 Dec 27. doi: 10.1371/journal.pbio.3001940

PMCID:: PMC9829180

Abstract Article PDF–2.5M

Select item 963802815.

Yeast Smy2 and its human homologs GIGYF1 and -2 regulate Cdc48/VCP function during transcription stress

Michelle Harreman Lehner, Jane Walker, Kotryna Temcinaite, Anna Herlihy, Michael Taschner, Adam C. Berger, Anita H. Corbett, A. Barbara Dirac Svejstrup, Jesper Q. Svejstrup

Cell Rep. 2022 Oct 25; 41(4): 111536. Published online 2022 Oct 25. doi: 10.1016/j.celrep.2022.111536

PMCID:: PMC9638028

Abstract Article

Select item 954653216.

The Paf1 complex is required for RNA polymerase II removal in response to DNA damage

Feilong Chen, Beibei Liu, Hao Zhou, Jiafu Long

Proc Natl Acad Sci U S A. 2022 Oct 4; 119(40): e2207332119. Published online 2022 Sep 26. doi: 10.1073/pnas.2207332119

PMCID:: PMC9546532

Abstract Article PDF–2.1M

Select item 947892817.

Transcriptional regulator Taf14 binds DNA and is required for the function of transcription factor TFIID in the absence of histone H2A.Z

Kadri Peil, Signe Värv, Ivar Ilves, Kersti Kristjuhan, Henel Jürgens, Arnold Kristjuhan

J Biol Chem. 2022 Sep; 298(9): 102369. Published online 2022 Aug 13. doi: 10.1016/j.jbc.2022.102369

PMCID:: PMC9478928

Abstract Article PDF–1.0M

Select item 927885818.

An integrated model for termination of RNA polymerase III transcription

Juanjuan Xie, Umberto Aiello, Yves Clement, Nouhou Haidara, Mathias Girbig, Jana Schmitzova, Vladimir Pena, Christoph W. Müller, Domenico Libri, Odil Porrua

Sci Adv. 2022 Jul; 8(28): eabm9875. Published online 2022 Jul 13. doi: 10.1126/sciadv.abm9875

PMCID:: PMC9278858

Abstract Article PDF–3.3M

Select item 920981119.

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