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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
...model argues that CTCF barrier bound times effectively approach those of cohesin extruder lifetimes. Together, we demonstrate how models that are informed by biophysically measured protein dynamics broaden our understanding of folding.Genome-wide chromosome conformation capture (Hi-C) reveals multiple...
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Method: A fast and adaptive detection framework for genome-wide chromatin loop mapping from Hi-C data
- Siyuan Chen,
- Jiuming Wang,
- Inkyung Jung,
- Zhaowen Qiu,
- Xin Gao,
- and Yu Li
Genome Res. August 2024 34: 1174-1184; Published in Advance August 13, 2024, doi:10.1101/gr.279274.124
...@cse.cuhk.edu.hk, xin.gao@kaust.edu.saAbstractChromatin loop identification plays an important role in molecular biology and 3D genomics research, as it constitutes a fundamental process in transcription and gene regulation. Such precise chromatin structures can be identified across -wide interaction matrices via Hi...
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Research: Transcription factor activity and nucleosome organization in mitosis
- Nicola Festuccia,
- Nick Owens,
- Thaleia Papadopoulou,
- Inma Gonzalez,
- Alexandra Tachtsidi,
- Sandrine Vandoermel-Pournin,
- Elena Gallego,
- Nancy Gutierrez,
- Agnès Dubois,
- Michel Cohen-Tannoudji,
- and Pablo Navarro
Genome Res. February 2019 29: 250-260; Published in Advance January 17, 2019, doi:10.1101/gr.243048.118
...on the chromosomes or locally at gene regulatory regions during mitosis. We subsequently use this information to correlate TF binding with chromatin accessibility and nucleosome positioning and stability in interphase and mitosis.ResultsThe global localization of ESRRB to mitotic chromosomes is preserved upon DSG...
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Research: Ancestral aneuploidy and stable chromosomal duplication resulting in differential genome structure and gene expression control in trypanosomatid parasites
- João L. Reis-Cunha,
- Samuel A. Pimenta-Carvalho,
- Laila V. Almeida,
- Anderson Coqueiro-dos-Santos,
- Catarina A. Marques,
- Jennifer A. Black,
- Jeziel Damasceno,
- Richard McCulloch,
- Daniella C. Bartholomeu,
- and Daniel C. Jeffares
Genome Res. March 2024 34: 441-453; Published in Advance April 11, 2024, doi:10.1101/gr.278550.123
...contributed equally to this work. ↵6 These authors contributed equally to this work. Corresponding author: joao.cunha@york.ac.uk AbstractAneuploidy is widely observed in both unicellular and multicellular eukaryotes, usually associated with adaptation to stress conditions. Chromosomal duplication stability...
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Research: Somatic structural variant formation is guided by and influences genome architecture
- Nikos Sidiropoulos,
- Balca R. Mardin,
- F. Germán Rodríguez-González,
- Ivan D. Bochkov,
- Shilpa Garg,
- Adrian M. Stütz,
- Jan O. Korbel,
- Erez Lieberman Aiden,
- and Joachim Weischenfeldt
Genome Res. April 2022 32: 643-655; Published in Advance February 17, 2022, doi:10.1101/gr.275790.121
...genomic rearrangements in a single cell cycle (Mardin et al. 2015). Dox, a widely used chemotherapeutic, traps Topoisomerase II (TOP2) on DNA and acts as a poison for TOP2 cleavage complexes by inhibiting DNA religation, causing TOP2-linked double-strand breaks (DSBs), which can result in the formation...
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Research: The organization of genome duplication is a critical determinant of the landscape of genome maintenance
- Blanca Gómez-Escoda and
- Pei-Yun Jenny Wu
Genome Res. August 2018 28: 1179-1192; Published in Advance June 22, 2018, doi:10.1101/gr.224527.117
...-compromised cells.View larger version: In this window In a new window Figure 4. The profile of origin de-regulation delineates the profiles of RPA and Rad52 binding in replication stress. (A) Genome-wide comparisons of origin de-regulation and instability. This analysis takes into account all 876 identified origins...
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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
...overwind or underwind DNA, creating DNA supercoils (Kouzine and Levens 2007). Supercoils can, in turn, induce formation of single-stranded DNA (ssDNA, hereafter SS DNA) or other non-B DNA structures.Genome-wide mapping of alternative DNA structures in cell lines and computational predictions in s suggested...
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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
...that there is a relationship between the longest genomic q-arm length and the level of mitotic chromosome compaction through -wide modulation of mitotic loop size, as shown using both genomics and microscopy techniques. We propose that this ensures that even the longest arms are sufficiently compacted to ensure...
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Research: Characterization of the distribution and dynamics of chromatin states in the C. elegans germline reveals substantial H3K4me3 remodeling during oogenesis
- Mariateresa Mazzetto,
- Lauren E. Gonzalez,
- Nancy Sanchez,
- and Valerie Reinke
Genome Res. January 2024 34: 57-69; Published in Advance December 26, 2023, doi:10.1101/gr.278247.123
...me3 across the gene body. Genomic regions in state 10 show high levels of H3K36me3 and H3K4me3 on gene bodies without high H3K27ac and are named “active transcription.” Finally, states 11 and 12 have both H3K4me3 and H3K36me3 and either low or highly accessible chromatin and are called “euchromatin 1...
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Research: A gene regulatory element modulates myosin expression and controls cardiomyocyte response to stress
- Taylor Anglen,
- Irene M. Kaplow,
- Baekgyu Choi,
- Enya Dewars,
- Robin M. Perelli,
- Kevin T. Hagy,
- Duc Tran,
- Megan E. Ramaker,
- Svati H. Shah,
- Inkyung Jung,
- Andrew P. Landstrom,
- Ravi Karra,
- Yarui Diao,
- and Charles A. Gersbach
Genome Res. November 2025 35: 2418-2432; Published in Advance October 22, 2025, doi:10.1101/gr.280825.125
...samples. See also Supplemental Figures S3–S7.The genomic composition surrounding MYH6 and MYH7 is preserved between humans and mice (Fig. 2A; Supplemental Fig. S5A). We identified three noncoding regions (R1–R3, M3, and C3) that interact with MYH6 and likely influence MYH6 expression (Fig. 2A...
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