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Research: Estrogen-induced chromatin looping changes identify a subset of functional regulatory elements
- Hosiana Abewe,
- Alexandra Richey,
- Jeffery M. Vahrenkamp,
- Matthew Ginley-Hidinger,
- Craig M. Rush,
- Noel Kitchen,
- Xiaoyang Zhang,
- and Jason Gertz
Genome Res. March 2025 35: 393-403; Published in Advance March 3, 2025, doi:10.1101/gr.279699.124
...of effects on the transcriptional response to estrogen. However, these effects are only subtly and not significantly stronger for ERBSs in differential chromatin loops. In addition, we observed an enrichment of 3D interactions between the promoters of estrogen-upregulated genes and found that looped...
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Research: Cohesin organizes 3D DNA contacts surrounding active enhancers in C. elegans
- Jun Kim,
- Haoyu Wang,
- and Sevinç Ercan
Genome Res. May 2025 35: 1108-1123; Published in Advance April 10, 2025, doi:10.1101/gr.279365.124
...that most enhancers are located ∼2 kb from promoters, but some enhancers can be up to ∼12 kb away (Shi et al. 2009).In humans, somatic cohesin is composed of four subunits, SMC1, SMC3, RAD21, and STAG (Hassler et al. 2018). The STAG subunit has two isoforms, STAG1 and STAG2, that form cohesin in a mutually...
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Research: Dynamic barriers modulate cohesin positioning and genome folding at fixed occupancy
- Hadi Rahmaninejad,
- Yao Xiao,
- Maxime M.C. Tortora,
- and Geoffrey Fudenberg
Genome Res. August 2025 35: 1745-1757; Published in Advance July 8, 2025, doi:10.1101/gr.280108.124
...chromatin loops between convergent CTCF sites (van Ruiten and Rowland 2021). The genomic positions of boundaries and dots anchor all display enrichment for cohesin by ChIP-seq. Acute depletion of CTCF leads to -wide loss of TADs and dots in Hi-C contact maps as well as a loss of cohesin ChIP-seq enrichment...
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Resource: Isoform- and pathway-specific regulation of post-transcriptional RNA processing in human cells
- Ishwarya Venkata Narayanan,
- Karan Bedi,
- Brian Magnuson,
- Ariel McShane,
- Mario Ashaka,
- Michelle Paulsen,
- Thomas E Wilson,
- and Mats Ljungman
Genome Res. March 26, 2026 gr.280892.125; Published in Advance March 26, 2026, doi:10.1101/gr.280892.125
...activating or repressive transcription factors (The ENCODE Project Consortium et al. 41 2020). Epigenetic regulation to compact chromatin restricts transcription and we 42 recently reported that only about 20% of the in human cells is actively 43 producing measurable amounts of RNA (McShane et al. 2024...
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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
...@cs.duke.eduAbstractEpigenetic mechanisms contribute to gene regulation by altering chromatin accessibility through changes in transcription factor (TF) and nucleosome occupancy across the . Despite numerous studies focusing on changes in gene expression, the intricate chromatin-mediated regulatory code remains largely uncharted...
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Method: Statistically rigorous and computationally efficient chromatin stripe detection with Quagga
- Fan Feng,
- Sean Moran,
- Anders S. Hansen,
- Xiaotian Zhang,
- and Jie Liu
Genome Res. January 2026 36: 159-168; Published in Advance November 12, 2025, doi:10.1101/gr.280132.124
...(stripe anchor) and a continuum of genomic regions (Banigan et al. 2020). For example, chromatin stripes may be based on CTCF/cohesin loops, in which multiple genomic sites that lie far apart linearly are brought into spatial proximity to a distal single locus by loop extrusion. At the bulk...
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Method: Simultaneous modeling of chromatin conformation changes from multiple single-cell interaction maps with ChromMovie
- Krzysztof H. Banecki,
- Haoxi Chai,
- Yijun Ruan,
- and Dariusz Plewczynski
Genome Res. April 8, 2026 ; Published in Advance April 8, 2026, doi:10.1101/gr.280985.125
...to validate chromatin structural models (Cheng et al. 2020). DNA tracing data sets were also successfully used for the studying of loop architecture (Beckwith et al. 2025b), as well asmitotic chromosome formation (Beckwith et al. 2025a). These methods have led to a diverse range of computational strategies...
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Research: Cohesin and CTCF do not assemble TADs in Xenopus sperm and male pronuclei
- Gregor Jessberger,
- Csilla Várnai,
- Roman R. Stocsits,
- Wen Tang,
- Georg Stary,
- and Jan-Michael Peters
Genome Res. December 2023 33: 2094-2107; Published in Advance December 21, 2023, doi:10.1101/gr.277865.123
...experiments, the cohesin subunits Smc3 and Stag1 could be detected on sperm chromatin at levels that were higher than those on XL-177 chromatin (as judged by comparison to the levels of histone H3) (Fig. 3H), indicating that the number of cohesin complexes on sperm chromatin would principally be sufficient...
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Research: Intergenic accumulation of RNA polymerase II maintains the potential for swift transcriptional restart upon release from quiescence
- Manuela Baquero Pérez,
- Gertjan Laenen,
- Isabelle Loïodice,
- Mickaël Garnier,
- Ugo Szachnowski,
- Antonin Morillon,
- Myriam Ruault,
- and Angela Taddei
Genome Res. October 2025 35: 2226-2239; Published in Advance August 12, 2025, doi:10.1101/gr.279874.124
...and understand its functional relationship with telomere hypercluster formation. We mapped the -wide transcription machinery occupancy by quantitative chromatin-immunoprecipitation of the Rpb3 subunit fused to a FLAG tag (Methods). In parallel, using the same strain, we followed the subnuclear distribution...
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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
...-mediated (blue) chromatin extrusion forms loops between CTCF (red) sites. This could bring promoters and enhancers into 3D contact to facilitate transcription. NIPBL may also help with BRD4 (purple). The NIPBL variant disrupts BRD4 occupancy and cohesin loading, likely impacting extrusion, CTCF looping, and E...
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