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Research: Enhancer–silencer transitions in the human genome
- Di Huang and
- Ivan Ovcharenko
Genome Res. March 2022 32: 437-448; Published in Advance February 1, 2022, doi:10.1101/gr.275992.121
...Sharpr-MPRA MaxPos score represents a negative RE. In this study, a genomic sequence was assigned with a MaxPos score only when this sequence hosted the whole corresponding Sharpr-MPRA sequence.Enhancer–silencer transitions during developmentTo identify enhancer–silencer transitions during development...
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Resource: A map of enhancer regions in primary human neural progenitor cells using capture STARR-seq
- Sophia C. Gaynor-Gillett,
- Lijun Cheng,
- Manman Shi,
- Jason Liu,
- Gaoyuan Wang,
- Megan Spector,
- Qiuyu Guo,
- Le Qi,
- Mary Flaherty,
- Martha Wall,
- Ahyeon Hwang,
- Mengting Gu,
- Zhanlin Chen,
- Yuhang Chen,
- PsychENCODE Consortium,
- Jennifer R. Moran,
- Jing Zhang,
- Donghoon Lee,
- Mark Gerstein,
- Daniel Geschwind,
- and Kevin P. White
Genome Res. August 2025 35: 1887-1901; Published in Advance July 11, 2025, doi:10.1101/gr.279584.124
...of candidate selection. (C) The experimental workflow. Sheared genomic DNA was hybridized to probes specific for the candidate enhancer regions. These regions were then cloned into the STARR-seq plasmid and transfected into phNPCs. (D,E) The fold change correlation between the two technical replicates...
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Corrigendum: Corrigendum: Cre-dependent Cas9-expressing pigs enable efficient in vivo genome editing
- Kepin Wang,
- Qin Jin,
- Degong Ruan,
- Yi Yang,
- Qishuai Liu,
- Han Wu,
- Zhiwei Zhou,
- Zhen Ouyang,
- Zhaoming Liu,
- Yu Zhao,
- Bentian Zhao,
- Quanjun Zhang,
- Jiangyun Peng,
- Chengdan Lai,
- Nana Fan,
- Yanhui Liang,
- Ting Lan,
- Nan Li,
- Xiaoshan Wang,
- Xinlu Wang,
- Yong Fan,
- Pieter A. Doevendans,
- Joost P.G. Sluijter,
- Pentao Liu,
- Xiaoping Li,
- and Liangxue Lai
Genome Res. June 2025 35: 1472-2; doi:10.1101/gr.280849.125
...: 10.1101/gr.280849.125 Published by Cold Spring Harbor Laboratory Press Genome Res GENOME Genome Research Genome Res. Genome Res 1088-9051 1549-5469 Cold Spring Harbor Laboratory Press 9509184 10.1101/gr.280849.125 ;35/6/1472-2 ;gr.280849.125 1472-2 gr.280849.125 Corrigendum Corrigendum Corrigenda...
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Corrigendum: Corrigendum: Machine learning identifies activation of RUNX/AP-1 as drivers of mesenchymal and fibrotic regulatory programs in gastric cancer
- Milad Razavi-Mohseni,
- Weitai Huang,
- Yu A. Guo,
- Dustin Shigaki,
- Shamaine Wei Ting Ho,
- Patrick Tan,
- Anders J. Skanderup,
- and Michael A. Beer
Genome Res. February 2026 36: 432; doi:10.1101/gr.281294.125
...Res 1088-9051 1549-5469 Cold Spring Harbor Laboratory Press 9509184 10.1101/gr.281294.125 ;36/2/432 ;gr.281294.125 432 gr.281294.125 Corrigendum Corrigendum Corrigenda Corrigendum Corrigendum Razavi-Mohseni Milad Huang Weitai Guo Yu A. Shigaki Dustin Ho Shamaine Wei Ting Tan Patrick Skanderup Anders J...
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Corrigendum: Corrigendum: Characterization of DNA methylation reader proteins in Arabidopsis thaliana
- Jonathan Cahn,
- James P.B. Lloyd,
- Ino D. Karemaker,
- Pascal W.T.C. Jansen,
- Jahnvi Pflueger,
- Owen Duncan,
- Jakob Petereit,
- Ozren Bogdanovic,
- A. Harvey Millar,
- Michiel Vermeulen,
- and Ryan Lister
Genome Res. June 2025 35: 1472-1; doi:10.1101/gr.280860.125
...by Cold Spring Harbor Laboratory Press Genome Res GENOME Genome Research Genome Res. Genome Res 1088-9051 1549-5469 Cold Spring Harbor Laboratory Press 9509184 10.1101/gr.280860.125 ;35/6/1472-1 ;gr.280860.125 1472-1 gr.280860.125 Corrigendum Corrigendum Corrigenda Corrigendum: Characterization of DNA...
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Corrigendum: Corrigendum: A sheep pangenome reveals the spectrum of structural variations and their effects on tail phenotypes
- Ran Li,
- Mian Gong,
- Xinmiao Zhang,
- Fei Wang,
- Zhenyu Liu,
- Lei Zhang,
- Qimeng Yang,
- Yuan Xu,
- Mengsi Xu,
- Huanhuan Zhang,
- Yunfeng Zhang,
- Xuelei Dai,
- Yuanpeng Gao,
- Zhuangbiao Zhang,
- Wenwen Fang,
- Yuta Yang,
- Weiwei Fu,
- Chunna Cao,
- Peng Yang,
- Zeinab Amiri Ghanatsaman,
- Niloufar Jafarpour Negari,
- Hojjat Asadollahpour Nanaei,
- Xiangpeng Yue,
- Yuxuan Song,
- Xianyong Lan,
- Weidong Deng,
- Xihong Wang,
- Chuanying Pan,
- Ruidong Xiang,
- Eveline M. Ibeagha-Awemu,
- Pat (J.S.) Heslop-Harrison,
- Benjamin D. Rosen,
- Johannes A. Lenstra,
- Shangquan Gan,
- and Yu Jiang
Genome Res. October 2025 35: 2375; doi:10.1101/gr.281340.125
...Genome Research Genome Res. Genome Res 1088-9051 1549-5469 Cold Spring Harbor Laboratory Press 9509184 10.1101/gr.281340.125 ;35/10/2375 ;gr.281340.125 2375 gr.281340.125 Corrigendum Corrigendum Corrigenda Corrigendum: A sheep pan reveals the spectrum of structural variations and their effects on tail...
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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
...is accompanied by the formation of de novo enhancer contacts and activation of MYC, illustrating how structural genomic variants can alter the 3D during oncogenesis. In summary, our findings provide evidence for the loss of organization at multiple scales during breast cancer progression, revealing novel...
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Research: Analyzing super-enhancer temporal dynamics reveals potential critical enhancers and their gene regulatory networks underlying skeletal muscle development
- Song Zhang,
- Chao Wang,
- Shenghua Qin,
- Choulin Chen,
- Yongzhou Bao,
- Yuanyuan Zhang,
- Lingna Xu,
- Qingyou Liu,
- Yunxiang Zhao,
- Kui Li,
- Zhonglin Tang,
- and Yuwen Liu
Genome Res. December 2024 34: 2190-2202; Published in Advance October 21, 2024, doi:10.1101/gr.278344.123
...). Another approach involves integrating population genetics data with functional genomics data. Populations with enhancer DNA variations act as natural genetic screens, shedding light on associations between enhancers and their significant biological functions. Along this line of thinking, several studies...
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Research: Stable genome structures in living fossil fishes
- Cheng Wang,
- Chase D. Brownstein,
- Wenjun Chen,
- Zufa Ding,
- Dan Yu,
- Yu Deng,
- Chenguang Feng,
- Thomas J. Near,
- Shunping He,
- and Liandong Yang
Genome Res. February 2026 36: 318-329; Published in Advance January 13, 2026, doi:10.1101/gr.280800.125
...contributed equally to this work. Corresponding authors: thomas.near@yale.edu, clad@ihb.ac.cn, yangliandong1987@163.comAbstractGenomic evolution can propel and restrict species diversification. Rapid molecular evolution and genomic rearrangement is often associated with increased species diversification...
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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
...distributed across the . Of them, the former represent active genomic elements, and the latter are frequently enriched at distinct genomic locations, where their presence is correlated either positively or negatively with transcriptional activity (Millán-Zambrano et al. 2022). In general, active enhancers...

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