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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
...Dynamic barriers modulate cohesin positioning and folding at fixed occupancy Hadi Rahmaninejad, Yao Xiao, Maxime M.C. Tortora and Geoffrey Fudenberg Department of Quantitative and Computational Biology, University of Southern California, Los Angeles, California 90089, USA Corresponding authors...
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Research: GC skew defines distinct RNA polymerase pause sites in CpG island promoters
- Wendy A. Kellner,
- Joshua S.K. Bell,
- and Paula M. Vertino
Genome Res. November 2015 25: 1600-1609; Published in Advance August 14, 2015, doi:10.1101/gr.189068.114
...://hgdownload.soe.ucsc.edu/goldenPath/hg19/database/ cpgIslandExt.txt.gz). Heatmap representations of ChIP-seq, MeDIP-seq, and GRO-seq tag densities were generated by summing the total number of tags in 20-bp bins for 3 kb to either side of the TSS or from the midpoint of the CGI domain and visualized with Java Treeview v.1.1.6. To compare...
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Review: A systematic guide for identifying transcription factors that directly regulate the expression of a gene of interest
- Andrew D. Bates,
- Dawid Grzela,
- Maciej Studzian,
- Louise Brennan,
- Moli Williams,
- Conor Fawcett,
- Beth Hammond,
- Manreen Grewal,
- Marcin Ratajewski,
- Lukasz Pulaski,
- and Urszula L. McClurg
Genome Res. March 2026 36: 433-459; Published in Advance February 17, 2026, doi:10.1101/gr.281154.125
...are available for predicting the presence of CpG islands in DNA sequences. Examples include the CpGplot tool from the European Molecular Biology Open Software Suite (EMBOSS) (Rice et al. 2000), the CpG Island Searcher (Takai and Jones 2003), CpGProD (Ponger and Mouchiroud 2002), and CpGPAP (Chuang et al. 2012...
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Research: ZFX acts as a transcriptional activator in multiple types of human tumors by binding downstream from transcription start sites at the majority of CpG island promoters
- Suhn Kyong Rhie,
- Lijun Yao,
- Zhifei Luo,
- Heather Witt,
- Shannon Schreiner,
- Yu Guo,
- Andrew A. Perez,
- and Peggy J. Farnham
Genome Res. March 2018 28: 310-320; Published in Advance February 2, 2018, doi:10.1101/gr.228809.117
...in MCF-7. (E) A model demonstrating the relationship of ZFX to other components of CpG island promoter structure. ZFX binds at +240 bp in the nucleosome-depleted region of CpG island promoters, between the general transcription preinitiation complex (PIC) and the first nucleosome in the transcribed...
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Research: Transcription and potential functions of a novel XIST isoform in male peripheral glia
- Kevin S. O'Leary,
- Meng-Yen Li,
- Kevyn Jackson,
- Lijie Shi,
- Elena Ezhkova,
- Bernice E. Morrow,
- and Deyou Zheng
Genome Res. February 2026 36: 257-274; Published in Advance December 12, 2025, doi:10.1101/gr.280832.125
..., SOX10, TCF4, ETS1, SREBF1, CEBPB, KLF2, and ETV5) were higher in either skeletal muscle or heart nonmyelinating Schwann cells. Analysis of the transcription regulatory programs by the SCENIC software predicted that FOXO1 (and YY1) could regulate XIST in heart and skeletal muscle Schwann cells...
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Method: Kinetic measurement of gene-specific RNA polymerase II transcription elongation rates
- Haiyue Liu and
- Lea H. Gregersen
Genome Res. November 2025 35: 2550-2562; Published in Advance October 22, 2025, doi:10.1101/gr.280852.125
...of RNAPII complexes. Notably, ZC3H4, a component of the restrictor complex involved in transcription termination of early nonproductive elongation (Estell et al. 2023; Rouvière et al. 2023), showed a negative correlation between its enrichment along the gene body occupancy and RNAPII elongation rates (Fig...
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Research: Distinct contributions of DNA methylation and histone acetylation to the genomic occupancy of transcription factors
- Martin Cusack,
- Hamish W. King,
- Paolo Spingardi,
- Benedikt M. Kessler,
- Robert J. Klose,
- and Skirmantas Kriaucionis
Genome Res. October 2020 30: 1393-1406; Published in Advance September 22, 2020, doi:10.1101/gr.257576.119
...Gs in the are methylated, DNA methylation is absent or reduced in regions bound by transcription factors such as in CpG islands, gene promoters, and distal regulatory elements (Stadler et al. 2011; Hon et al. 2013; Ziller et al. 2013). This observation led to the proposal that DNA methylation may limit transcription...
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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
...of DNA to transcription factors. It is catalyzed by ATP-dependent chromatin remodeling complexes such as the SWI/SNF and NuRD remodelers, both of which bind to numerous common target gene promoters as revealed by the chromatin occupancy profiles of their ATPase subunits (BRG1–SWI/SNF and CHD4–Nu...
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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
...the activation domain of the transcriptional activator Gal4 that binds in their shared promoter (Lohr et al. 1995; Platt and Reece 1998). Accordingly, when we deleted GAL80, we observed a significant gain of TF occupancy at the GAL1-10 promoter and a decrease in nucleosome occupancy in both gene bodies...
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Method: Profiling the quantitative occupancy of myriad transcription factors across conditions by modeling chromatin accessibility data
- Kaixuan Luo,
- Jianling Zhong,
- Alexias Safi,
- Linda K. Hong,
- Alok K. Tewari,
- Lingyun Song,
- Timothy E. Reddy,
- Li Ma,
- Gregory E. Crawford,
- and Alexander J. Hartemink
Genome Res. June 2022 32: 1183-1198; Published in Advance May 24, 2022, doi:10.1101/gr.272203.120
..., North Carolina 27708, USA Corresponding author: amink@cs.duke.eduAbstractOver a thousand different transcription factors (TFs) bind with varying occupancy across the human . Chromatin immunoprecipitation (ChIP) can assay occupancy -wide, but only one TF at a time, limiting our ability to comprehensively...

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