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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
...of 15 chromatin states annotated by ChromHMM (Ernst and Kellis 2012) in three types of boundary regions, we observe that the WBs are enriched with active TSS, strong transcription, and other chromatin states associated with active gene transcription, and NSBs show stronger enrichment of bivalent...
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Resource: A temporal in vivo catalog of chromatin accessibility and expression profiles in pineoblastoma reveals a prevalent role for repressor elements
- Salam Idriss,
- Mohammad Hallal,
- Abdullah El-Kurdi,
- Hasan Zalzali,
- Inaam El-Rassi,
- Erik A. Ehli,
- Christel M. Davis,
- Philip E.D. Chung,
- Deena M.A. Gendoo,
- Eldad Zacksenhaus,
- Raya Saab,
- and Pierre Khoueiry
Genome Res. February 2023 33: 269-282; Published in Advance January 17, 2023, doi:10.1101/gr.277037.122
..., the role of epigenetic deregulation and cis-regulatory regions in PB pathogenesis and progression is largely unknown. Here, we generated -wide gene expression, chromatin accessibility, and H3K27ac profiles covering key time points of PB initiation and progression from pineal tissues of a mouse model...
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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
..., Quebec H3A 1B1, Canada; 2McGill University Genome Centre, Montreal, Quebec H3A 0G1, Canada; 3Department of Biochemistry, McGill University, Montreal, Quebec H3G 1Y6, Canada; 4The Rosalind & Morris Goodman Cancer Institute, McGill University, Montreal, Quebec H3A 1A3, Canada; 5Laboratory of Chromatin...
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Method: Multicondition and multimodal temporal profile inference during mouse embryonic development
- Ran Zhang,
- Chengxiang Qiu,
- Galina N. Filippova,
- Gang Li,
- Jay Shendure,
- Jean-Philippe Vert,
- Xinxian Deng,
- William Stafford Noble,
- and Christine M. Disteche
Genome Res. October 2025 35: 2339-2351; Published in Advance August 14, 2025, doi:10.1101/gr.279997.124
...profiles, we can couple encoders of, for example, gene expression (scRNA-seq) with decoders of chromatin accessibility (scATAC-seq) to enable the prediction of missing scATAC-seq profiles across time (Fig. 1C).Sunbear can predict a cell's transcriptional profile at missing time points and missing...
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Method: k-mer cross-species profiling reveals taxon-specific TE expansions accompanied by KZFP co-option and functional impacts in ruminants
- Pengju Zhao,
- Jiayi He,
- Chen Peng,
- Yuelang Zhang,
- Chong Wang,
- Dongyou Yu,
- Lingzhao Fang,
- and Zhengguang Wang
Genome Res. March 23, 2026 gr.281289.125; Published in Advance March 23, 2026, doi:10.1101/gr.281289.125
...states were decoded through 594 combinatorial patterns of these epigenetic signals. Promoter-associated chromatin states into 595 three subtypes: TssA (active promoters with strong transcription), TssAHet (flanking active 596 transcription start sites lacking ATAC-seq signal), and TssBiv (bivalent...
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Research: Identification of a transcriptional signature found in multiple models of ASD and related disorders
- Samuel Thudium,
- Katherine Palozola,
- Éloïse L'Her,
- and Erica Korb
Genome Res. September 2022 32: 1642-1654; Published in Advance September 14, 2022, doi:10.1101/gr.276591.122
.... We examined the functions of genes within the transcriptional signatures and found an enrichment in many neurotransmitter transport genes and activity-dependent genes. In addition, these genes are enriched for specific chromatin features such as bivalent domains that allow for highly dynamic...
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Research: Distal regulation, silencers, and a shared combinatorial syntax are hallmarks of animal embryogenesis
- Paola Cornejo-Páramo,
- Kathrein Roper,
- Sandie M. Degnan,
- Bernard M. Degnan,
- and Emily S. Wong
Genome Res. March 2022 32: 474-487; Published in Advance January 19, 2022, doi:10.1101/gr.275864.121
...Sciences, University of Queensland, Brisbane 4072, Australia; 4School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney 2033, Australia Corresponding authors: b.degan@uq.edu.au, e.wong@victorchang.edu.auAbstractThe chromatin environment plays a central role in regulating...
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Research: Active retrotransposons help maintain pericentromeric heterochromatin required for faithful cell division
- Yajing Hao,
- Dongpeng Wang,
- Shuheng Wu,
- Xiao Li,
- Changwei Shao,
- Peng Zhang,
- Jia-Yu Chen,
- Do-Hwan Lim,
- Xiang-Dong Fu,
- Runsheng Chen,
- and Shunmin He
Genome Res. November 2020 30: 1570-1582; Published in Advance October 15, 2020, doi:10.1101/gr.256131.119
..., 100101, China; 2University of Chinese Academy of Sciences, Beijing, 100049, China; 3Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, California 92093-0651, USA; 4Guangdong Geneway Decoding Bio-Tech Corporation Limited, Foshan 528316, China ↵5 These authors...
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Perspective: Epigenomics and the structure of the living genome
- Nir Friedman and
- Oliver J. Rando
Genome Res. October 2015 25: 1482-1490; doi:10.1101/gr.190165.115
...and RNA in Gene Regulation” to N.F. References Bernstein BE, Mikkelsen TS, Xie X, Kamal M, Huebert DJ, Cuff J, Fry B, Meissner A, Wernig M, Plath K, et al. 2006. A bivalent chromatin structure marks key developmental genes in embryonic stem cells. Cell 125: 315–326. Brogaard K, Xi L, Wang JP, Widom J...
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Research: DNA methylation epitypes highlight underlying developmental and disease pathways in acute myeloid leukemia
- Brian Giacopelli,
- Min Wang,
- Ada Cleary,
- Yue-Zhong Wu,
- Anna Reister Schultz,
- Maximilian Schmutz,
- James S. Blachly,
- Ann-Kathrin Eisfeld,
- Bethany Mundy-Bosse,
- Sebastian Vosberg,
- Philipp A. Greif,
- Rainer Claus,
- Lars Bullinger,
- Ramiro Garzon,
- Kevin R. Coombes,
- Clara D. Bloomfield,
- Brian J. Druker,
- Jeffrey W. Tyner,
- John C. Byrd,
- and Christopher C. Oakes
Genome Res. May 2021 31: 747-761; Published in Advance March 11, 2021, doi:10.1101/gr.269233.120
...on the study design (Bullinger et al. 2010; Figueroa et al. 2010; Melnick 2010; Glass et al. 2017). Many of these subgroups showed associations with genetic aberrations but others represented novel subgroups. Decoding altered -wide DNA methylation patterns can provide insight into novel disease...
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