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Research: Genomic regulatory landscape underlying the antiviral response of Atlantic salmon
- Shahmir Naseer,
- Thomas C Clark,
- Bertrand Collet,
- Pooran Dewari,
- Damir Baranasic,
- Daniel J Macqueen,
- Pierre Boudinot,
- and Samuel A.M. Martin
Genome Res. October 22, 2025 gr.280579.125; Published in Advance October 22, 2025, doi:10.1101/gr.280579.125
...used to map 51 open chromatin and histone modifications across the , enabling the identification of 52 putative regulatory elements. While these assays are powerful, they have limitations, 53 including the potential for false positives (regions that are accessible but not functionally 54 active...
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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
...). Compartments consist of multiple subcompartments that differ in their chromosomal contact frequencies, enrichment in histone modifications, and chromatin-binding proteins (Spracklin et al. 2023). At a resolution ranging from ∼10–800 kbp, topologically associated domains (TADs) emerge as local, highly...
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Research: Genome-wide profiles of H3K9me3, H3K27me3 modifications, and DNA methylation during diapause of Asian corn borer (Ostrinia furnacalis)
- Pengfei Lv,
- Xingzhuo Yang,
- Xianguo Zhao,
- Zhangwu Zhao,
- and Juan Du
Genome Res. May 2024 34: 725-739; Published in Advance June 12, 2024, doi:10.1101/gr.278661.123
...in Drosophila. However, the genomic distribution of these DNA and histone modifications at different stages of diapause and the dynamic changes of the distributions need to be identified to better understand the mechanism of these epigenetic modifications.To gain a deeper understanding of the epigenetic control...
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Method: Profiling single-cell histone modifications using indexing chromatin immunocleavage sequencing
- Wai Lim Ku,
- Lixia Pan,
- Yaqiang Cao,
- Weiwu Gao,
- and Keji Zhao
Genome Res. October 2021 31: 1831-1842; Published in Advance April 14, 2021, doi:10.1101/gr.260893.120
...-cell immunocleavage sequencing (iscChIC-seq), a multiplex indexing method based on TdT terminal transferase and T4 DNA ligase-mediated barcoding strategy and single-cell ChIC-seq, which is capable of readily analyzing histone modifications across tens of thousands of single cells in one experiment. Application of isc...
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Resource: Charting the regulatory landscape of TP53 on transposable elements in cancer
- Xuan Qu,
- Yonghao Liang,
- Colin McCornack,
- Xiaoyun Xing,
- Heather Schmidt,
- Chad Tomlinson,
- Catrina Fronick,
- Edward A. Belter, Jr.,
- Juan F. Macias-Velasco,
- and Ting Wang
Genome Res. June 2025 35: 1456-1471; Published in Advance May 13, 2025, doi:10.1101/gr.279398.124
...Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, Missouri 63110, USA; 3McDonnell Genome Institute, Washington University School of Medicine, St. Louis, Missouri 63108, USA ↵4 These authors contributed equally to this work. Corresponding...
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Research: Variation in histone configurations correlates with gene expression across nine inbred strains of mice
- Anna L Tyler,
- Catrina Spruce,
- Romy Kursawe,
- Annat Haber,
- Robyn L Ball,
- Wendy A Pitman,
- Alexander D Fine,
- Narayanan Raghupathy,
- Michael Walker,
- Vivek M Philip,
- Christopher L Baker,
- J. Matthew Mahoney,
- Gary A. Churchill,
- Jennifer J Trowbridge,
- Michael L Stitzel,
- Kenneth Paigen,
- Petko M Petkov,
- and Gregory W Carter
Genome Res. May 22, 2023 gr.277467.122; Published in Advance May 22, 2023, doi:10.1101/gr.277467.122
...modifications20 (H3K4me1, H3K4me3, H3K27me3, and H3K27ac), and DNA methylation. We used ChromHMM to21 identify 14 chromatin states, each of which represented a distinct combination of the four histone22 modifications. We found that the epigenetic landscape was highly variable across the DO founders23...
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Research: H3K36 dimethylation shapes the epigenetic interaction landscape by directing repressive chromatin modifications in embryonic stem cells
- Haifen Chen,
- Bo Hu,
- Cynthia Horth,
- Eric Bareke,
- Phillip Rosenbaum,
- Sin Young Kwon,
- Jacinthe Sirois,
- Daniel N. Weinberg,
- Faith M. Robison,
- Benjamin A. Garcia,
- Chao Lu,
- William A. Pastor,
- and Jacek Majewski
Genome Res. May 2022 32: 825-837; Published in Advance April 8, 2022, doi:10.1101/gr.276383.121
...'s epigenetic landscape are tightly interwoven (Strahl and Allis 2000; Janssen and Lorincz 2022). Steric changes introduced by modifications to some histone residues affect the probability of altering nearby or interacting residues. Chromatin modifying enzymes can be either recruited by or antagonized...
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Research: H3K27 and H3K9 methylation mask potential CTCF binding sites to maintain 3D genome integrity
- Kei Fukuda,
- Chikako Shimura,
- and Yoichi Shinkai
Genome Res. October 2025 35: 2199-2210; Published in Advance August 5, 2025, doi:10.1101/gr.280732.125
...CTCF binding at distinct genomic regions, and their simultaneous loss induces drastic changes in CTCF binding. These changes are associated with alterations in 3D architecture and gene expression, suggesting that repressive chromatin modifications preserve proper chromatin organization by preventing...
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Method: Defining the separation landscape of topological domains for decoding consensus domain organization of the 3D genome
- Dachang Dang,
- Shao-Wu Zhang,
- Ran Duan,
- and Shihua Zhang
Genome Res. March 2023 33: 386-400; Published in Advance March 9, 2023, doi:10.1101/gr.277187.122
...the upstream and downstream regions versus that across them (Fig. 3A). Next, three kinds of operations are performed to modify the boundary score profile and construct the TAD separation landscape based on the contrast P-value (Methods). Through these refinements, we can filter out some unreliable bins...
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Method: Allele-specific RNA N⁶-methyladenosine modifications reveal functional genetic variants in human tissues
- Shuo Cao,
- Haoran Zhu,
- Jinru Cui,
- Sun Liu,
- Yuhe Li,
- Junfang Shi,
- Junyuan Mo,
- Zihan Wang,
- Hailan Wang,
- Jiaxin Hu,
- Lizhi Chen,
- Yuan Li,
- Laixin Xia,
- and Shan Xiao
Genome Res. August 2023 33: 1369-1380; Published in Advance September 15, 2023, doi:10.1101/gr.277704.123
..., histone modification, gene expression, and post-transcriptional splicing (McDaniell et al. 2010; Shoemaker et al. 2010; The ENCODE Project Consortium 2012; McVicker et al. 2013; Leung et al. 2015; Roadmap Epigenomics Consortium et al. 2015; Schultz et al. 2015; GTEx Consortium 2017; Gate et al. 2018; Yang...

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