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Research: The impact of SWI/SNF and NuRD inactivation on gene expression is tightly coupled with levels of RNA polymerase II occupancy at promoters
- Sachin Pundhir,
- Jinyu Su,
- Marta Tapia,
- Anne Meldgaard Hansen,
- James Seymour Haile,
- Klaus Hansen,
- and Bo Torben Porse
Genome Res. March 2023 33: 332-345; Published in Advance March 16, 2023, doi:10.1101/gr.277089.122
...closed chromatin states. Our results highlight RNA Pol II occupancy as the key parameter in determining the direction of gene expression changes in response to SWI/SNF and NuRD inactivation at gene promoters in mESCs.Chromatin remodeling is a fundamental process that ensures the proper presentation...
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Research: Contrasting roles of the RSC and ISW1/CHD1 chromatin remodelers in RNA polymerase II elongation and termination
- Josefina Ocampo,
- Răzvan V. Chereji,
- Peter R. Eriksson,
- and David J. Clark
Genome Res. March 2019 29: 407-417; Published in Advance January 25, 2019, doi:10.1101/gr.242032.118
...and Pugh 2009). RSC is an essential SWI/SNF-type complex homologous to human PBAF (Clapier and Cairns 2009). In vitro, RSC can evict, mobilize, or remodel nucleosomes, and create promoter NDRs in reconstituted chromatin (Lorch et al. 2001; Saha et al. 2002; Shukla et al. 2010; Krietenstein et al. 2016...
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Research: Cell-type- and chromosome-specific chromatin landscapes and DNA replication programs of Drosophila testis tumor stem cell–like cells
- Jennifer A. Urban,
- Daniel Ringwalt,
- John M. Urban,
- Wingel Xue,
- Ryan Gleason,
- Keji Zhao,
- and Xin Chen
Genome Res. January 2026 36: 83-101; Published in Advance December 10, 2025, doi:10.1101/gr.280809.125
...-type testis tissue have made it difficult to generate comprehensive cell-type-specific genomic data sets defining their global transcriptional, chromatin, and replication landscapes. To address this, we developed cell-type-specific genomic strategies for testicular stem cells derived from a tumor model...
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Research: Ultraviolet damage and repair maps in Drosophila reveal the impact of domain-specific changes in nucleosome repeat length on repair efficiency
- Benjamin Morledge-Hampton,
- Kathiresan Selvam,
- Manish Chauhan,
- Alan G. Goodman,
- and John J. Wyrick
Genome Res. February 2025 35: 257-267; Published in Advance January 6, 2025, doi:10.1101/gr.279605.124
...susceptible to disruption or repositioning in response to the cellular stress and ongoing repair activity induced by UV damage. For example, a previous study has shown that the SWI/SNF complex can remodel nucleosomes to accommodate the repair of UV damage (Gaillard et al. 2003). Such a mechanism may...
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Research: Genome-wide nucleosome and transcription factor responses to genetic perturbations reveal chromatin-mediated mechanisms of transcriptional regulation
- Kevin Moyung,
- Yulong Li,
- Heather K. MacAlpine,
- Alexander J. Hartemink,
- and David M. MacAlpine
Genome Res. January 2026 36: 115-128; Published in Advance December 9, 2025, doi:10.1101/gr.279637.124
...to explore interactions that involve more than one mutant. For example, SWI4 and SWI6 are key TFs enacting G1/S-specific transcription, and together they form a complex to bind to and regulate genes involved in DNA synthesis and repair (Sidorova and Breeden 1993). The individual deletions of SWI4 (swi4Δ...
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Method: Genome-wide reconstitution of chromatin transactions reveals that RSC preferentially disrupts H2AZ-containing nucleosomes
- Aylin Cakiroglu,
- Cedric R. Clapier,
- Andreas H. Ehrensberger,
- Elodie Darbo,
- Bradley R. Cairns,
- Nicholas M. Luscombe,
- and Jesper Q. Svejstrup
Genome Res. June 2019 29: 988-998; Published in Advance May 16, 2019, doi:10.1101/gr.243139.118
...of chromatin transactions would be very useful.RSC (Remodels the Structure of Chromatin) is a member of the Swi2/Snf2 family of ATP-dependent chromatin remodelers and the most abundant chromatin remodeling factor in yeast (Cairns et al. 1996). It is necessary for transcription by all three nuclear RNA...
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Research: Genomic regulatory landscape underlying the antiviral response of Atlantic salmon
- Shahmir Naseer,
- Thomas C Clark,
- Bertrand Collet,
- Pooran Dewari,
- Damir Baranasic,
- Daniel J Macqueen,
- Pierre Boudinot,
- and Samuel A.M. Martin
Genome Res. October 22, 2025 gr.280579.125; Published in Advance October 22, 2025, doi:10.1101/gr.280579.125
...epigenomic 121 changes in chromatin state following this stimulation and shed light on regulatory elements 122 and TFBSs influencing antiviral transcriptional responses in a complex teleost . 123 Genomic sequencing data and sample metadata 124 Thirty-eight datasets were generated, comprising ATAC-seq (12...
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Research: Global genome nucleotide excision repair is organized into domains that promote efficient DNA repair in chromatin
- Shirong Yu,
- Katie Evans,
- Patrick van Eijk,
- Mark Bennett,
- Richard M. Webster,
- Matthew Leadbitter,
- Yumin Teng,
- Raymond Waters,
- Stephen P. Jackson,
- and Simon H. Reed
Genome Res. October 2016 26: 1376-1387; Published in Advance July 28, 2016, doi:10.1101/gr.209106.116
...throughout the yeast (Yu et al. 2009). The Rad16 protein is a member of the SWI/SNF super-family of chromatin remodeling factors. Proteins in this super-family contain conserved ATPase motifs and are subunits of protein complexeswith chromatin-remodeling activity (Flaus and Owen-Hughes 2011). Since Rad16...
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Research: Nucleosome remodeling at origins of global genome–nucleotide excision repair occurs at the boundaries of higher-order chromatin structure
- Patrick van Eijk,
- Shuvro Prokash Nandi,
- Shirong Yu,
- Mark Bennett,
- Matthew Leadbitter,
- Yumin Teng,
- and Simon H. Reed
Genome Res. January 2019 29: 74-84; Published in Advance December 14, 2018, doi:10.1101/gr.237198.118
...these modifications enhance repair of damage in chromatin remain to be determined.We previously purified a complex of proteins from yeast cells that is uniquely required for GG-NER in this simple eukaryote (Reed et al. 1999). The complex is composed of the SWI/SNF superfamily member, Rad16, the Rad7 protein...
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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
...the complexity of chromatin organization and the nuanced differences in how genomic elements interact within the nucleus (Hyle et al. 2019; Szczepińska et al. 2021; Chakraborty et al. 2023; Spracklin et al. 2023).CTCF/cohesin loopsIn addition to compartments, advancements in -wide chromatin contact mapping have...
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