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Research: Mediator dynamics during heat shock in budding yeast
- Debasish Sarkar,
- Z. Iris Zhu,
- Elizabeth R. Knoll,
- Emily Paul,
- David Landsman,
- and Randall H. Morse
Genome Res. January 2022 32: 111-123; Published in Advance November 16, 2021, doi:10.1101/gr.275750.121
...to transcription by RNA polymerase II (Pol II) in eukaryotes. In budding yeast (Saccharomyces cerevisiae), Mediator is recruited by activators and associates with core promoter regions, where it facilitates preinitiation complex (PIC) assembly, only transiently before Pol II escape. Interruption...
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Method: Absolute nucleosome occupancy map for the Saccharomyces cerevisiae genome
- Elisa Oberbeckmann,
- Michael Wolff,
- Nils Krietenstein,
- Mark Heron,
- Jessica L. Ellins,
- Andrea Schmid,
- Stefan Krebs,
- Helmut Blum,
- Ulrich Gerland,
- and Philipp Korber
Genome Res. December 2019 29: 1996-2009; Published in Advance November 6, 2019, doi:10.1101/gr.253419.119
..., United Kingdom; 7Laboratory of Functional Genome Analysis (LAFUGA), Gene Center, Faculty of Chemistry and Pharmacy, Ludwig-Maximilians-Universität München, 81377 Munich, Germany ↵8 These authors contributed equally to the work. Corresponding author: pkorber@lmu.deAbstractMapping of nucleosomes, the basic...
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Research: Evolutionary expansion of DNA hypomethylation in the mammalian germline genome
- Jianghan Qu,
- Emily Hodges,
- Antoine Molaro,
- Pascal Gagneux,
- Matthew D. Dean,
- Gregory J. Hannon,
- and Andrew D. Smith
Genome Res. February 2018 28: 145-158; Published in Advance December 19, 2017, doi:10.1101/gr.225896.117
...Chase, Maryland 20815, USA; 7Cancer Research UK Cambridge Institute, Li Ka Shing Centre, University of Cambridge, Cambridge CB2 0RE, United Kingdom; 8The New York Genome Center, New York, New York 10013, USA Corresponding author: andrewds@usc.eduAbstractDNA methylation in the germline is among the most...
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Research: Pou5f3, SoxB1, and Nanog remodel chromatin on high nucleosome affinity regions at zygotic genome activation
- Marina Veil,
- Lev Y. Yampolsky,
- Björn Grüning,
- and Daria Onichtchouk
Genome Res. March 2019 29: 383-395; Published in Advance January 23, 2019, doi:10.1101/gr.240572.118
...: post-ZGA nucleosome depletion by synergistic action of Pou5f3 and Nanog in the presence of SoxB1We detected widespread alignment of nucleosomes on their DNA-encoded nucleosome positioning signals from pre- to post-ZGA (Fig. 4C, black arrows). Increase of nucleosome positioning strength was previously...
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LETTER: The extensive and condition-dependent nature of epistasis among whole-genome duplicates in yeast
- Gabriel Musso,
- Michael Costanzo,
- ManQin Huangfu,
- Andrew M. Smith,
- Jadine Paw,
- Bryan-Joseph San Luis,
- Charles Boone,
- Guri Giaever,
- Corey Nislow,
- Andrew Emili,
- and Zhaolei Zhang
Genome Res. July 2008 18: 1092-1099; Published in Advance May 7, 2008, doi:10.1101/gr.076174.108
...lost. However, in budding yeast, experimental evidence collected for duplicated metabolic enzymes and in global physical interaction surveys had suggested widespread functional overlap between paralogs. While maintained functional overlap is thought to confer robustness against genetic mutation...
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Method: Genome-wide determination of RNA stability reveals hundreds of short-lived noncoding transcripts in mammals
- Hidenori Tani,
- Rena Mizutani,
- Kazi Abdus Salam,
- Keiko Tano,
- Kenichi Ijiri,
- Ai Wakamatsu,
- Takao Isogai,
- Yutaka Suzuki,
- and Nobuyoshi Akimitsu
Genome Res. May 2012 22: 947-956; Published in Advance February 27, 2012, doi:10.1101/gr.130559.111
...Genome-wide determination of RNA stability reveals hundreds of short-lived noncoding transcripts in mammals Hidenori Tani 1 , Rena Mizutani 1 , Kazi Abdus Salam 1 , Keiko Tano 1 , Kenichi Ijiri 1 , Ai Wakamatsu 2 , Takao Isogai...
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Mini-Review: The chromatin tapestry as a framework for neurodevelopment
- Ben Nolan,
- Timothy E. Reznicek,
- Christopher T. Cummings,
- and M. Jordan Rowley
Genome Res. October 2024 34: 1477-1486; doi:10.1101/gr.278408.123
...and MeCP2 function was further highlighted in a model of Rett syndrome that uses loss-of-function point mutations in MeCP2 within human interneurons (Xiang et al. 2020). In this system, loss of MeCP2 function was associated with an increase in E–P interactions (as measured by Hi-C) as well as widespread...
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RESEARCH: Multiplex Sequencing of 1.5 Mb of the Mycobacterium leprae Genome
- Douglas R. Smith,
- Peter Richterich,
- Marc Rubenfield,
- Philip W. Rice,
- Carol Butler,
- Hong-Mei Lee,
- Susan Kirst,
- Kristin Gundersen,
- Kari Abendschan,
- Qinxue Xu,
- Maria Chung,
- Craig Deloughery,
- Tyler Aldredge,
- James Maher,
- Ronald Lundstrom,
- Craig Tulig,
- Kathleen Falls,
- Joan Imrich,
- Dana Torrey,
- Marcy Engelstein,
- Gary Breton,
- Deepika Madan,
- Raymond Nietupski,
- Bruce Seitz,
- Steven Connelly,
- Steven McDougall,
- Hershel Safer,
- Rene Gibson,
- Lynn Doucette-Stamm,
- Karin Eiglmeier,
- Staffan Bergh,
- Stewart T. Cole,
- Keith Robison,
- Laura Richterich,
- Jason Johnson,
- George M. Church,
- and Jen-i Mao
Genome Res. August 1, 1997 7: 802-819; doi:10.1101/gr.7.8.802
..., convergent. A similar observation of widespread scrambling but consistent clustering is seen in comparison of large operons in S. typhimurium and Pseudomonas denitrificans ( Roth et al. 1993 ). The clustering of genes in adjacent operons may reveal selective pressures to maintain proximity, for example...
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Method: Single-molecule long-read sequencing reveals the chromatin basis of gene expression
- Yunhao Wang,
- Anqi Wang,
- Zujun Liu,
- Andrew L. Thurman,
- Linda S. Powers,
- Meng Zou,
- Yue Zhao,
- Adam Hefel,
- Yunyi Li,
- Joseph Zabner,
- and Kin Fai Au
Genome Res. August 2019 29: 1329-1342; Published in Advance June 14, 2019, doi:10.1101/gr.251116.119
...the cell wall that serves as a barrier against methyltransferase treatment of genomic DNA: Yeast cells were treated with Zymolyase to generate spheroplasts (Fig. 1). After the subsequent methyltransferase treatment, extracted genomic DNA without any PCR amplification was directly submitted to library...
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Research: Linking the dynamics of chromatin occupancy and transcription with predictive models
- Trung Q. Tran,
- Heather K. MacAlpine,
- Vinay Tripuraneni,
- Sneha Mitra,
- David M. MacAlpine,
- and Alexander J. Hartemink
Genome Res. June 2021 31: 1035-1046; Published in Advance April 23, 2021, doi:10.1101/gr.267237.120
...dynamics associated with transcription during cadmium stressWe sought to precisely characterize the dynamics of chromatin organization in yeast cells responding to cadmium stress, while simultaneously monitoring the large-scale changes to their transcriptional program. A nucleotide-resolution view...

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