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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
...the binding of transcription factors (TFs) to their target sites with high precision and efficacy. Furthermore, chromosome structural variations can induce chromatin loop reorganization through enhancer hijacking events, leading to severe cancer and primary tumor development (Spielmann et al. 2018; Wang et al...
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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
...with or without RPB1, we saw ULIs in both conditions (Fig. 5F). These results for long-range interactions are similar to the conclusion that inhibition of transcription has a modest global impact on shorter-range promoter–promoter and enhancer–promoter contacts (Hsieh et al. 2020; Jiang et al. 2020; Goel et al...
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Resource: Construction and evaluation of a new rat reference genome assembly, GRCr8, from long reads and long-range scaffolding
- Kai Li,
- Melissa L. Smith,
- J. Chris Blazier,
- Kelli J. Kochan,
- Jonathan M.D. Wood,
- Kerstin Howe,
- Anne E. Kwitek,
- Melinda R. Dwinell,
- Hao Chen,
- Julia L. Ciosek,
- Patrick Masterson,
- Terence D. Murphy,
- Theodore S. Kalbfleisch,
- and Peter A. Doris
Genome Res. November 2024 34: 2081-2093; Published in Advance November 8, 2024, doi:10.1101/gr.279292.124
...Construction and evaluation of a new rat reference assembly, GRCr8, from long reads and long-range scaffolding Kai Li1, Melissa L. Smith2, J. Chris Blazier3, Kelli J. Kochan3, Jonathan M.D. Wood4, Kerstin Howe4, Anne E. Kwitek5, Melinda R. Dwinell5, Hao Chen6, Julia L. Ciosek1, Patrick Masterson7...
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Research: Chromatin loop dynamics during cellular differentiation are associated with changes to both anchor and internal regulatory features
- Marielle L. Bond,
- Eric S. Davis,
- Ivana Y. Quiroga,
- Anubha Dey,
- Manjari Kiran,
- Michael I. Love,
- Hyejung Won,
- and Douglas H. Phanstiel
Genome Res. August 2023 33: 1258-1268; Published in Advance September 12, 2023, doi:10.1101/gr.277397.122
...stimuli (Dixon et al. 2015). Whereas several types of 3D chromatin structures exist, chromatin loops are of particular interest as they are thought to regulate gene expression by bringing distal regulatory elements (e.g., enhancers) into close physical proximity with gene promoters via point to point...
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Research: Sir3 mediates long-range chromosome interactions in budding yeast
- Myriam Ruault,
- Vittore F. Scolari,
- Luciana Lazar-Stefanita,
- Antoine Hocher,
- Isabelle Loïodice,
- Romain Koszul,
- and Angela Taddei
Genome Res. March 2021 31: 411-425; Published in Advance February 12, 2021, doi:10.1101/gr.267872.120
...linked to the formation of heterochromatin in subtelomeric regions through the recruitment of the silencing SIR complex composed of Sir2/3/4. Combining microscopy and Hi-C on strains expressing different alleles of SIR3, we show that the binding of Sir3 directly promotes long-range contacts between...
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Research: A HOTAIR regulatory element modulates glioma cell sensitivity to temozolomide through long-range regulation of multiple target genes
- Lei Zhang,
- Anshun He,
- Bohan Chen,
- Jinfang Bi,
- Jun Chen,
- Dianhao Guo,
- Yuyang Qian,
- Wenbin Wang,
- Tengfei Shi,
- Zhongfang Zhao,
- Jiandang Shi,
- Woojin An,
- Frank Attenello,
- and Wange Lu
Genome Res. February 2020 30: 155-163; Published in Advance January 17, 2020, doi:10.1101/gr.251058.119
...suggests a possible bivalent function.Development of high-order chromosome conformation capture techniques has facilitated analysis of long-range DNA interactions and enabled analysis of regulatory elements that enhance or repress gene expression through long-range interactions (Wei et al. 2013; Liu et al...
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Research: Long-range promoter–enhancer contacts are conserved during evolution and contribute to gene expression robustness
- Alexandre Laverré,
- Eric Tannier,
- and Anamaria Necsulea
Genome Res. February 2022 32: 280-296; Published in Advance December 20, 2021, doi:10.1101/gr.275901.121
...conservation of cis-regulatory landscapes, indicating that selective pressures act to preserve not only regulatory element sequences but also their chromatin contacts with target genes. The extent of evolutionary conservation is remarkable for long-range promoter–enhancer contacts, illustrating how...
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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
.... Deletion of long-range sequences at Sox10 compromises developmental expression in a mouse model of Waardenburg–Shah (WS4) syndrome. Hum Mol Genet 15: 259–271. doi:10.1093/hmg/ddi442 ↵Banani SF, Lee HO, Hyman AA, Rosen MK. 2017. Biomolecular condensates: organizers of cellular biochemistry. Nat Rev Mol Cell...
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Research: Widespread roles of enhancer-like transposable elements in cell identity and long-range genomic interactions
- Yaqiang Cao,
- Guoyu Chen,
- Gang Wu,
- Xiaoli Zhang,
- Joseph McDermott,
- Xingwei Chen,
- Chi Xu,
- Quanlong Jiang,
- Zhaoxiong Chen,
- Yingying Zeng,
- Daosheng Ai,
- Yi Huang,
- and Jing-Dong J. Han
Genome Res. January 2019 29: 40-52; Published in Advance November 19, 2018, doi:10.1101/gr.235747.118
...and L2 elements frequently share long-range intra-chromosomal interactions and binding of physically interacting transcription factors. We validated that eight L2 and nine MIR elements function as enhancers in reporter assays, and among 20 MIR-L2 pairings, one MIR repressed and one boosted the enhancer...
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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
...IP-seq and chromatin looping data suggest that R3, M3, and C3 likely function as enhancers and are active in the heart.To further investigate the developmental role of these individual enhancers, we analyzed ATAC-seq and histone ChIP-seq data from the heart during mouse fetal development (e10.5 to e16.5) and after...
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