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Research: Genome-wide chromatin interaction profiling reveals a vital role of super-enhancers and rearrangements in host enhancer contacts during BmNPV infection
- Shudi Zhao,
- Yuedong Li,
- Guanping Chen,
- Xingyang Wang,
- Nan Chen,
- and Xiaofeng Wu
Genome Res. November 2023 33: 1958-1974; Published in Advance October 23, 2023, doi:10.1101/gr.277931.123
...directly rearranges the enhancer contacts. Such a rearrangement disturbs the intrinsic enhancer–gene connections in several antiviral genes, resulting in reduced expression of these genes, which accelerates viral infection. Overall, our results reveal the regulatory role of super-enhancers and shed new...
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Research: Multi-species analysis of inflammatory response elements reveals ancient and lineage-specific contributions of transposable elements to NF-kB binding
- Liangxi Wang,
- Tiegh Taylor,
- Kumaragurubaran Rathnakumar,
- Nadiya Khyzha,
- Minggao Liang,
- Azad Alizada,
- Laura F. Campitelli,
- Sara E. Pour,
- Zain M. Patel,
- Lina Antounians,
- Ian C. Tobias,
- Huayun Hou,
- Timothy R. Hughes,
- Sushmita Roy,
- Jennifer A. Mitchell,
- Jason E. Fish,
- and Michael D. Wilson
Genome Res. July 2025 35: 1544-1559; Published in Advance June 6, 2025, doi:10.1101/gr.280357.124
...-kB in three mammalian lineages. Our comparative analyses of RELA binding, together with epigenetic and transcriptional profiles, revealed conserved and lineage-specific TE subfamilies that are likely to participate in mammalian NF-kB regulatory networks. Given the active enhancer features and proximity...
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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
...-catenin. Beta-catenin and CTCF colocalize upon pathway activation, and disruption of selected binding sites perturbs target gene regulation. Moreover, Wnt signaling reorganizes the 3D as evidenced by -wide alterations in CTCF-bound loops. This work reveals a previously unexplored role for CTCF in the regulation...
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Research: GC-biased gene conversion drives accelerated evolution of ultraconserved elements in mammalian and avian genomes
- Anguo Liu,
- Nini Wang,
- Guoxiang Xie,
- Yang Li,
- Xixi Yan,
- Xinmei Li,
- Zhenliang Zhu,
- Zhuohui Li,
- Jing Yang,
- Fanxin Meng,
- Mingle Dou,
- Weihuang Chen,
- Nange Ma,
- Yu Jiang,
- Yuanpeng Gao,
- and Yu Wang
Genome Res. October 2023 33: 1673-1689; Published in Advance October 26, 2023, doi:10.1101/gr.277784.123
...These authors contributed equally to this work. Corresponding authors: wang_yu@nwafu.edu.cn, gaoyuanpeng1990@163.comAbstractUltraconserved elements (UCEs) are the most conserved regions among the s of evolutionarily distant species and are thought to play critical biological functions. However, some UCEs...
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Research: Ultra-long-range interactions between active regulatory elements
- Elias T. Friman,
- Ilya M. Flyamer,
- Davide Marenduzzo,
- Shelagh Boyle,
- and Wendy A. Bickmore
Genome Res. August 2023 33: 1269-1283; Published in Advance July 14, 2023, doi:10.1101/gr.277567.122
...of DNA-binding factors for binding at regions of enriched contacts. This analysis revealed enriched contacts at sites bound by many factors associated with active transcription. We show that active regulatory elements, independent of cohesin and polycomb, interact with each other across distances of tens...
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Research: Acute TNF-induced repression of cell identity genes is mediated by NFκB-directed redistribution of cofactors from super-enhancers
- Søren Fisker Schmidt,
- Bjørk Ditlev Larsen,
- Anne Loft,
- Ronni Nielsen,
- Jesper Grud Skat Madsen,
- and Susanne Mandrup
Genome Res. September 2015 25: 1281-1294; Published in Advance June 25, 2015, doi:10.1101/gr.188300.114
...Skat, Madsen Nielsen, R Schmidt Jesper Madsen genome;gr.188300.114 1549-5469 10.1101/gr.188300.114 1088-9051 Acute TNF-induced repression of cell identity genes is mediated by NFκB-directed redistribution of cofactors from super-enhancers Schmidt et al. Gene repression by cofactor redistribution Acute...
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Research: A DNA methylation haplotype block landscape in human tissues and preimplantation embryos reveals regulatory elements defined by comethylation patterns
- Yan Feng,
- Zhiqiang Zhang,
- Yuyang Hong,
- Yi Ding,
- Leiqin Liu,
- Siqi Gao,
- Hai Fang,
- and Jiantao Shi
Genome Res. December 2023 33: 2041-2052; Published in Advance November 8, 2023, doi:10.1101/gr.278146.123
...of regulatory element characterized by comethylation patterns rather than mean methylation levels. We show the enrichment of MHBs in open chromatin regions, tissue-specific histone marks, and enhancers, including super-enhancers. Moreover, we find that MHBs tend to localize near tissue-specific genes and show...
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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
...of CCND1-driven PB. We identified PB-specific enhancers and super-enhancers, and found that in some cases, the accessible dynamics precede transcriptomic changes, a characteristic that is underexplored in tumor progression. During progression of PB, newly acquired open chromatin regions lacking H3K27ac...
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Research: Enhancers and super-enhancers have an equivalent regulatory role in embryonic stem cells through regulation of single or multiple genes
- Sakthi D. Moorthy,
- Scott Davidson,
- Virlana M. Shchuka,
- Gurdeep Singh,
- Nakisa Malek-Gilani,
- Lida Langroudi,
- Alexandre Martchenko,
- Vincent So,
- Neil N. Macpherson,
- and Jennifer A. Mitchell
Genome Res. February 2017 27: 246-258; Published in Advance November 28, 2016, doi:10.1101/gr.210930.116
...enhancer deletion data, which revealed an equivalent regulatory role for enhancers compared to super-enhancers, are supported by recent computational analyses. Finucane et al. (2015) investigated links between classes of functional elements and the heritability of complex diseases and observed enrichment...
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Resource: RefSeq Functional Elements as experimentally assayed nongenic reference standards and functional interactions in human and mouse
- Catherine M. Farrell,
- Tamara Goldfarb,
- Sanjida H. Rangwala,
- Alexander Astashyn,
- Olga D. Ermolaeva,
- Vichet Hem,
- Kenneth S. Katz,
- Vamsi K. Kodali,
- Frank Ludwig,
- Craig L. Wallin,
- Kim D. Pruitt,
- and Terence D. Murphy
Genome Res. January 2022 32: 175-188; Published in Advance December 7, 2021, doi:10.1101/gr.275819.121
...selected just a sampling of those for comparison, namely, ENCODE candidate cis-regulatory elements (cCREs) (The ENCODE Project Consortium et al. 2020), Ensembl Regulation (Zerbino et al. 2016), FANTOM5 enhancers (Andersson et al. 2014), VISTA enhancers (Visel et al. 2007), and dbSUPER super-enhancers (Khan...

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