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Research: Ligand-induced native G-quadruplex stabilization impairs transcription initiation
- Conghui Li,
- Honghong Wang,
- Zhinang Yin,
- Pingping Fang,
- Ruijing Xiao,
- Ying Xiang,
- Wen Wang,
- Qiuzi Li,
- Beili Huang,
- Jian Huang,
- and Kaiwei Liang
Genome Res. September 2021 31: 1546-1560; Published in Advance August 16, 2021, doi:10.1101/gr.275431.121
...RNA 3′ ends and maps transcriptionally engaged Pol II. G4 signals overlapped with the TSSs and Pol II pausing sites at promoter regions (Fig. 1I,J), indicating that G4s may participate in the early stages of transcription.Because G4-CUT&Tag could detect the G4 signals at enhancers (Fig. 1E), we...
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Research: Genome-wide variability in recombination activity is associated with meiotic chromatin organization
- Xiaofan Jin,
- Geoff Fudenberg,
- and Katherine S. Pollard
Genome Res. September 2021 31: 1561-1572; Published in Advance July 23, 2021, doi:10.1101/gr.275358.121
...of meiotic folding are linked to recombination activity. We apply an integrative bioinformatics approach to analyze how three-dimensional (3D) chromosomal organization during meiosis relates to rates of double-strand-break (DSB) and crossover (CO) formation at PRDM9 binding peaks. We show that active...
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Research: Genome-wide profiling reveals functional interplay of DNA sequence composition, transcriptional activity, and nucleosome positioning in driving DNA supercoiling and helix destabilization in C. elegans
- Kristina Krassovsky,
- Rajarshi P. Ghosh,
- and Barbara J. Meyer
Genome Res. July 2021 31: 1187-1202; Published in Advance June 24, 2021, doi:10.1101/gr.270082.120
...-strandedness, which is most pronounced at transcript end sites, is dependent on high AT content and symmetrically positioned nucleosomes. We propose that sharp transitions in sequence composition at functional genomic elements constitute a common regulatory code and that DNA structure and propagation of torsional...
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Research: CTCF sites display cell cycle–dependent dynamics in factor binding and nucleosome positioning
- Marlies E. Oomen,
- Anders S. Hansen,
- Yu Liu,
- Xavier Darzacq,
- and Job Dekker
Genome Res. February 2019 29: 236-249; Published in Advance January 17, 2019, doi:10.1101/gr.241547.118
...contribute to the observed loss of TADs and CTCF loops during mitosis and reveals that CTCF sites, key architectural cis-elements, display cell cycle stage–dependent dynamics in factor binding and nucleosome positioning.Several studies have observed a key role of CCCTC-binding factor (CTCF) in organizing...
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Research: Study of mitotic chromatin supports a model of bookmarking by histone modifications and reveals nucleosome deposition patterns
- Elisheva Javasky,
- Inbal Shamir,
- Shashi Gandhi,
- Shawn Egri,
- Oded Sandler,
- Scott B. Rothbart,
- Noam Kaplan,
- Jacob D. Jaffe,
- Alon Goren,
- and Itamar Simon
Genome Res. October 2018 28: 1455-1466; Published in Advance August 30, 2018, doi:10.1101/gr.230300.117
...understand the role of mitotic histone modifications and nucleosome de-positioning, we investigated the global dynamics and genomic organization of histone modifications in mitosis and in interphase. Using HeLa-S3 cells as a model system, our study incorporated a synchronization approach that enables...
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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
...with independent observations in a mouse blood progenitor cell line, in which the retained CTCF binding has been implicated in faster transcription reactivation, when involving promoters, and more generally in fast restoration of 3D contacts after mitosis (Zhang et al. 2019). Together, these reports suggest...
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Research: Nucleosomal signatures impose nucleosome positioning in coding and noncoding sequences in the genome
- Sara González,
- Alicia García,
- Enrique Vázquez,
- Rebeca Serrano,
- Mar Sánchez,
- Luis Quintales,
- and Francisco Antequera
Genome Res. November 2016 26: 1532-1543; Published in Advance September 23, 2016, doi:10.1101/gr.207241.116
...1 in Saccharomyces cerevisiae (Gkikopoulos et al. 2011), results in gross -wide alteration of their nucleosomal patterns. Transcription factors contribute to chromatin organization through the recruitment of remodelers to promoters (Yudkovsky et al. 1999; Korber et al. 2004) and also through...
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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
...) leads to rapid loss of transcription in yeast. This has, for example, enabled the determination of mRNA half-lives and establishing the role of Pol II activity in nucleosome positioning (Adams and Gross 1991; Grigull et al. 2004; Sun et al. 2013; Hsieh et al. 2015; Vasseur et al. 2016; Lauinger et al...
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Research: Genome accessibility is widely preserved and locally modulated during mitosis
- Chris C.-S. Hsiung,
- Christapher S. Morrissey,
- Maheshi Udugama,
- Christopher L. Frank,
- Cheryl A. Keller,
- Songjoon Baek,
- Belinda Giardine,
- Gregory E. Crawford,
- Myong-Hee Sung,
- Ross C. Hardison,
- and Gerd A. Blobel
Genome Res. February 2015 25: 213-225; Published in Advance November 4, 2014, doi:10.1101/gr.180646.114
...Mitosis entails global alterations to chromosome structure and nuclear architecture, concomitant with transient silencing of transcription. How cells transmit transcriptional states through mitosis remains incompletely understood. While many nuclear factors dissociate from mitotic chromosomes...
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Mini-Review: Revisiting models of enhancer–promoter communication in gene regulation
- Gilad Barshad and
- Charles G. Danko
Genome Res. June 2025 35: 1277-1286; doi:10.1101/gr.278389.123
...they communicate.Enhancers: functional elements characterized by a stereotyped chromatin architectureEnhancers are one variety of cis-regulatory element encoded in Metazoan s. They are characterized by a stereotyped pattern of transcription factor binding, transcription initiation, and chromatin organization (Fig...

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