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Method: Inhibition of transcription leads to rewiring of locus-specific chromatin proteomes
- Deepani W. Poramba-Liyanage,
- Tessy Korthout,
- Christine E. Cucinotta,
- Ila van Kruijsbergen,
- Tibor van Welsem,
- Dris El Atmioui,
- Huib Ovaa,
- Toshio Tsukiyama,
- and Fred van Leeuwen
Genome Res. April 2020 30: 635-646; Published in Advance March 18, 2020, doi:10.1101/gr.256255.119
...correlates with loss of Rpb3, one of the subunits of Pol II (McKnight et al. 2015; Young et al. 2017).To systematically interrogate the chromatin changes at a transcriptionally active locus upon inhibition of transcription, we used Epi-Decoder, a tag–chromatin immunoprecipitation (ChIP)–barcode (BC...
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Research: An optogenetic switch for the Set2 methyltransferase provides evidence for transcription-dependent and -independent dynamics of H3K36 methylation
- Andrew M. Lerner,
- Austin J. Hepperla,
- Gregory R. Keele,
- Hashem A. Meriesh,
- Hayretin Yumerefendi,
- David Restrepo,
- Seth Zimmerman,
- James E. Bear,
- Brian Kuhlman,
- Ian J. Davis,
- and Brian D. Strahl
Genome Res. November 2020 30: 1605-1617; Published in Advance October 5, 2020, doi:10.1101/gr.264283.120
...by the methyltransferase Set2 (Wagner and Carpenter 2012; McDaniel and Strahl 2017). As the sole H3K36 methyltransferase in Saccharomyces cerevisiae (S. cerevisiae), Set2 cotranscriptionally deposits up to three methyl groups, resulting in mono-, di-, or trimethylated H3K36 (H3K36me1, H3K36me2, and H3K36me3, respectively...
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Methods: Discovering functional transcription-factor combinations in the human cell cycle
- Zhou Zhu,
- Jay Shendure,
- and George M. Church
Genome Res. June 2005 15: 848-855; doi:10.1101/gr.3394405
...regulation by transcription factors Oct-1 and NF-Y. Oncogene 22 : 7762 -7773. ↵ Hughes, J.D., Estep, P.W., Tavazoie, S., and Church, G.M. 2000 . Computational identification of cis -regulatory elements associated with groups of functionally related genes in Saccharomyces cerevisiae . J. Mol. Biol. 296 : 1205...
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Methods: Discovery, validation, and genetic dissection of transcription factor binding sites by comparative and functional genomics
- Jason Gertz,
- Linda Riles,
- Peter Turnbaugh,
- Su-Wen Ho,
- and Barak A. Cohen
Genome Res. August 2005 15: 1145-1152; doi:10.1101/gr.3859605
.... Sci. 45 : 18 –29. ↵ Sudarsanam, P., Pilpel, Y., and Church, G.M. 2002 . Genome-wide co-occurrence of promoter elements reveals a cis -regulatory cassette of rRNA transcription motifs in Saccharomyces cerevisiae. Genome Res. 12 : 1723 –1731. ↵ Tavazoie, S., Hughes, J.D., Campbell, M.J., Cho, R...
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Research: Noise in gene expression is coupled to growth rate
- Leeat Keren,
- David van Dijk,
- Shira Weingarten-Gabbay,
- Dan Davidi,
- Ghil Jona,
- Adina Weinberger,
- Ron Milo,
- and Eran Segal
Genome Res. December 2015 25: 1893-1902; Published in Advance September 9, 2015, doi:10.1101/gr.191635.115
...variability are not known. Here, we measure the single-cell expression distributions of approximately 900 Saccharomyces cerevisiae promoters across four environmental conditions using flow cytometry, and find that gene expression noise is tightly coupled to the environment and is generally higher at lower...
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ARTICLE: Identification of Target Sites of the α2–Mcm1 Repressor Complex in the Yeast Genome
- Hualin Zhong,
- Ron McCord,
- and Andrew K. Vershon
Genome Res. November 1, 1999 9: 1040-1047; doi:10.1101/gr.9.11.1040
...control in Saccharomyces cerevisiae : Implications for regulation of alpha-specific and a-specific genes. Mol. Cell. Biol. 8 : 309 – 320 . ↵ Johnson A. Yamamoto K.R. , McKnight S.L. ( 1992 ) A combinatorial regulatory circuit in budding yeast. in Transcriptional regulation , eds Yamamoto K.R. , McKnight S...
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PERSPECTIVE: Large-Scale Gene Expression Data Analysis: A New Challenge to Computational Biologists
- Michael Q. Zhang
Genome Res. August 1, 1999 9: 681-688; doi:10.1101/gr.9.8.681
..., tissue specificity, hormonal communication, or cellular stress responses. Gene expression is largely controlled at the transcriptional level, and transcriptional regulatory elements are located primarily in the upstream promoter region of each gene; however, the lack of quality upstream experimental data...
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Research: Local nucleosome dynamics and eviction following a double-strand break are reversible by NHEJ-mediated repair in the absence of DNA replication
- Vinay Tripuraneni,
- Gonen Memisoglu,
- Heather K. MacAlpine,
- Trung Q. Tran,
- Wei Zhu,
- Alexander J. Hartemink,
- James E. Haber,
- and David M. MacAlpine
Genome Res. May 2021 31: 775-788; Published in Advance April 2, 2021, doi:10.1101/gr.271155.120
.... 2015; Polo 2015). However, chromatin remodelers may exhibit pleiotropic activities such as regulation of cell-cycle dependent gene expression and may not directly influence the chromatin environment surrounding a DSB. Thus, despite a critical role for ATP-dependent chromatin remodeling complexes in DSB...
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Research: Expanding heterochromatin reveals discrete subtelomeric domains delimited by chromatin landscape transitions
- Antoine Hocher,
- Myriam Ruault,
- Petra Kaferle,
- Marc Descrimes,
- Mickaël Garnier,
- Antonin Morillon,
- and Angela Taddei
Genome Res. December 2018 28: 1867-1881; Published in Advance October 24, 2018, doi:10.1101/gr.236554.118
...Corresponding author: angela.taddei@curie.frAbstractThe eukaryotic is divided into chromosomal domains of heterochromatin and euchromatin. Transcriptionally silent heterochromatin is found at subtelomeric regions, leading to the telomeric position effect (TPE) in yeast, fly, and human. Heterochromatin generally...
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Research: Cell cycle arrest explains the observed bulk 3D genomic alterations in response to long-term heat shock in K562 cells
- Bingxiang Xu,
- Xiaomeng Gao,
- Xiaoli Li,
- Yan Jia,
- Feifei Li,
- and Zhihua Zhang
Genome Res. July 2022 32: 1285-1297; Published in Advance July 14, 2022, doi:10.1101/gr.276554.122
...the accessibility of two classes of the most important regulatory elements, promoters and distal transcription regulatory elements (dTREs), using the coverage depths of short ATAC-seq fragments. The accessible levels of both promoters and dTREs were globally maintained, even after LHS, with larger variability for d...

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