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Research: Loss of multilevel 3D genome organization during breast cancer progression
- Roberto Rossini,
- Saleh Oshaghi,
- Maxim Nekrasov,
- Aurélie Bellanger,
- Renae Domaschenz,
- Yasmin Dijkwel,
- Mohamed Abdelhalim,
- Rahul Agrawal,
- Marit Ledsaak,
- Philippe Collas,
- Ragnhild Eskeland,
- David Tremethick,
- and Jonas Paulsen
Genome Res. January 2026 36: 20-37; Published in Advance October 9, 2025, doi:10.1101/gr.280791.125
...relationships between 3D structure and oncogenic processes.The mammalian is folded into large-scale dynamic three-dimensional (3D) chromatin conformations that provide a framework for regulated gene expression. In the interphase nucleus, chromosomes exist as territories (Cremer and Cremer 2010; Rowley...
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Research: Suv39h-catalyzed H3K9me3 is critical for euchromatic genome organization and the maintenance of gene transcription
- Christine R. Keenan,
- Hannah D. Coughlan,
- Nadia Iannarella,
- Andres Tapia del Fierro,
- Andrew Keniry,
- Timothy M. Johanson,
- Wing Fuk Chan,
- Alexandra L. Garnham,
- Lachlan W. Whitehead,
- Marnie E. Blewitt,
- Gordon K. Smyth,
- and Rhys S. Allan
Genome Res. April 2024 34: 556-571; Published in Advance May 6, 2024, doi:10.1101/gr.279119.124
...in weakened DI anchors, including that of CCCTC-binding factor (CTCF), the canonical regulator (together with cohesin complex) of chromatin architecture (Fig. 3F; Ong and Corces 2014; Rao et al. 2014; Tang et al. 2015). To explore whether CTCF occupancy affects which regions alter structure in the Suv39DKO...
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Research: Wnt signaling activation induces CTCF binding and loop formation at cis-regulatory elements of target genes
- Anna Nordin,
- Chaitali Chakraborty,
- Mattias Jonasson,
- Orgena Dano,
- Gianluca Zambanini,
- Pierfrancesco Pagella,
- Silvia Remeseiro,
- and Claudio Cantù
Genome Res. August 2025 35: 1701-1716; Published in Advance June 23, 2025, doi:10.1101/gr.279684.124
...how Wnt signaling influences CTCF and cohesin, key regulators of 3D organization. We identify a series of novel CTCF binding sites that emerge upon Wnt stimulation: CTCF Redistributions Under Wnt (RUW). RUW sites are characterized by CTCF, cohesin, and TCF/LEF occupancy, and are dependent on beta...
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Research: Mitotic chromosomes harbor cell type– and species-specific structural features within a universal loop array conformation
- Marlies E. Oomen,
- A. Nicole Fox,
- Inma Gonzalez,
- Amandine Molliex,
- Thaleia Papadopoulou,
- Pablo Navarro,
- and Job Dekker
Genome Res. August 2025 35: 1733-1744; Published in Advance June 6, 2025, doi:10.1101/gr.280648.125
...are folded as helical loop arrays mediated by condensin I and II, which are not positioned at any specific genomic locations (Belmont 2006; Gibcus et al. 2018; Batty and Gerlich 2019). This results in the observation of a generally smooth and -wide inverse relationship between genomic distance...
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Research: Distinct classes of lamina-associated domains are defined by differential patterns of repressive histone methylation
- Caden J. Martin,
- Elizabeth A. Oser,
- Prabakaran Nagarajan,
- Liudmila V. Popova,
- Benjamin D. Sunkel,
- Benjamin Z. Stanton,
- and Mark R. Parthun
Genome Res. September 2025 35: 1959-1974; Published in Advance August 5, 2025, doi:10.1101/gr.280380.124
...3K27me3, H3K14ac, H3K27ac, and H3K9ac in MEF cell lines derived from the same mouse colony, and cluster LADs based on the abundance and distribution of these features across LADs. We find that LADs fall into three groups, each enriched in a unique set of histone modifications and genomic features...
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Research: YY1 and CTCF orchestrate a 3D chromatin looping switch during early neural lineage commitment
- Jonathan A. Beagan,
- Michael T. Duong,
- Katelyn R. Titus,
- Linda Zhou,
- Zhendong Cao,
- Jingjing Ma,
- Caroline V. Lachanski,
- Daniel R. Gillis,
- and Jennifer E. Phillips-Cremins
Genome Res. July 2017 27: 1139-1152; Published in Advance May 23, 2017, doi:10.1101/gr.215160.116
...long-range looping interactions (de Wit et al. 2015; Guo et al. 2015). Given the large number of CTCF peaks that are dynamic across development, we sought to investigate how chromatin folding is altered as a function of occupancy during each cell fate transition. We generated fine-scale chromatin...
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Research: Chromatin architecture transitions from zebrafish sperm through early embryogenesis
- Candice L. Wike,
- Yixuan Guo,
- Mengyao Tan,
- Ryohei Nakamura,
- Dana Klatt Shaw,
- Noelia Díaz,
- Aneasha F. Whittaker-Tademy,
- Neva C. Durand,
- Erez Lieberman Aiden,
- Juan M. Vaquerizas,
- David Grunwald,
- Hiroyuki Takeda,
- and Bradley R. Cairns
Genome Res. June 2021 31: 981-994; Published in Advance May 18, 2021, doi:10.1101/gr.269860.120
...(red) indicates increased contacts, and negative insulation (blue) indicates a lack of contacts. (C) Comparisons of chromatin factor and attribute occupancy at enhancers. Metaplot of log2 fold enrichment of histone H3K27ac ChIP-seq (Zhang et al. 2018), RNA Pol II ChIP-seq, Rad21-cohesin ChIP-seq, ATAC...
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Letter: A positive but complex association between meiotic double-strand break hotspots and open chromatin in Saccharomyces cerevisiae
- Luke E. Berchowitz,
- Sean E. Hanlon,
- Jason D. Lieb,
- and Gregory P. Copenhaver
Genome Res. December 2009 19: 2245-2257; Published in Advance October 2, 2009, doi:10.1101/gr.096297.109
.... Predictive value is expressed with respect to two DSB hotspot datasets (Blitzblau et al. 2007; Buhler et al. 2007). Because this analysis is probe based, multiple true-positives may be derived from a single DSB hotspot. Nucleosome occupancy in meiosis Genome Research 2251 www..org time points in relation...
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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
...to regulate transcription initiation and elongation at CGIs is not well understood. Genome-wide studies of RNA polymerase (Pol) II occupancy and nascent transcription have demonstrated that a significant component of transcriptional regulation occurs at post-initiation steps in the transcription cycle...

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