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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
...modulating enhancer activity. (8) Validate the role of candidate critical enhancers in myogenic differentiation using CRISPR–Cas9-mediated enhancer knockout in C2C12 cells.ResultsDynamic H3K27ac landscape across prenatal and postnatal stages of PSMTo investigate the enhancer landscape during myofiber...
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Method: A versatile type VI CRISPR-based approach for targeted m⁶A demethylation in mRNAs
- Panagiotis G. Adamopoulos,
- Konstantina Athanasopoulou,
- and Andreas Scorilas
Genome Res. January 2026 36: 169-182; Published in Advance December 11, 2025, doi:10.1101/gr.280476.125
...and disease pathogenesis (Terns 2018; Pickar-Oliver and Gersbach 2019). The discovery of Cas13, a class 2 type VI CRISPR-Cas RNA endonuclease, has opened new avenues for targeting the dynamics of endogenous RNA transcripts and has already been used for both cleavage and subsequent degradation of RNA...
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Method: CRISPR-Cas9-mediated pinpoint microbial genome editing aided by target-mismatched sgRNAs
- Ho Joung Lee,
- Hyun Ju Kim,
- and Sang Jun Lee
Genome Res. May 2020 30: 768-775; Published in Advance April 23, 2020, doi:10.1101/gr.257493.119
...: 380–389. doi:10.1080/15476286.2019.1582974 ↵Liang X, Potter J, Kumar S, Ravinder N, Chesnut JD. 2017. Enhanced CRISPR/Cas9-mediated precise editing by improved design and delivery of gRNA, Cas9 nuclease, and donor DNA. J Biotechnol 241: 136–146. doi:10.1016/j.jbiotec.2016.11.011 ↵Lin YN, Cradick TJ...
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Method: A high-throughput screening method for selecting feature SNPs to evaluate breed diversity and infer ancestry
- Meilin Zhang,
- Heng Du,
- Yu Zhang,
- Yue Zhuo,
- Zhen Liu,
- Yahui Xue,
- Lei Zhou,
- Sixuan Zhou,
- Wanying Li,
- and Jian-Feng Liu
Genome Res. August 2025 35: 1875-1886; Published in Advance July 15, 2025, doi:10.1101/gr.280176.124
...for efficient and accurate discovery of the breed diversities of species and ancestries of populations are needed.Breed diversity can be evaluated through genetic or phenotypic analyses, each offering unique insights (Reist-Marti et al. 2003). Traditionally, genetic diversity assessments relied on pedigree...
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Research: A low-abundance class of Dicer-dependent siRNAs produced from a variety of features in C. elegans
- Thiago L. Knittel,
- Brooke E. Montgomery,
- Alex J. Tate,
- Ennis W. Deihl,
- Anastasia S. Nawrocki,
- Frederic J. Hoerndli,
- and Taiowa A. Montgomery
Genome Res. December 2024 34: 2203-2216; Published in Advance December 2, 2024, doi:10.1101/gr.279083.124
...notably transposons, suggesting a common role for siRNAs in silencing foreign elements (Chung et al. 2008; Czech et al. 2008; Ghildiyal et al. 2008; Okamura et al. 2008a,b; Tam et al. 2008; Watanabe et al. 2008).C. elegans contains multiple distinct classes of endogenous small RNAs but canonical si...
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Research: Active enhancers strengthen insulation by RNA-mediated CTCF binding at chromatin domain boundaries
- Zubairul Islam,
- Bharath Saravanan,
- Kaivalya Walavalkar,
- Umer Farooq,
- Anurag Kumar Singh,
- Sabarinathan Radhakrishnan,
- Jitendra Thakur,
- Awadhesh Pandit,
- Steven Henikoff,
- and Dimple Notani
Genome Res. January 2023 33: 1-17; Published in Advance January 17, 2023, doi:10.1101/gr.276643.122
...by the Student's unpaired two-tailed t-test. qRT-PCR primers are listed in Supplemental Table S1.CRISPR-Cas9-mediated deletiongRNAs were designed with the crispr.mit.edu tool. gRNAs were selected based on the highest score and the least number of off-targets. gRNAs were cloned in a pgRNA humanized vector...
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Method: Predicted protein 3D structures provide essential insights into the genetic architecture underlying phenotypic diversity in maize
- Shuai Wang,
- Merritt Khaipho-Burch,
- Lynn C. Johnson,
- Zachary R. Miller,
- Peter J. Bradbury,
- Doug Speed,
- William J. Allen,
- M. Cinta Romay,
- Jiquan Xue,
- Edward S. Buckler,
- Guillaume P. Ramstein,
- and Baoxing Song
Genome Res. January 2026 36: 214-225; Published in Advance October 31, 2025, doi:10.1101/gr.280514.125
...a pioneering exploration of how predicted protein 3D structural diversity can enhance our understanding of phenotypic variation.Prediction of protein structure requires high-quality sequence and annotationPrediction of protein structure heavily depends on high-quality protein sequences, as the 3D conformation...
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Research: Pathogenic variants in CRX have distinct cis-regulatory effects on enhancers and silencers in photoreceptors
- James L. Shepherdson,
- Ryan Z. Friedman,
- Yiqiao Zheng,
- Chi Sun,
- Inez Y. Oh,
- David M. Granas,
- Barak A. Cohen,
- Shiming Chen,
- and Michael A. White
Genome Res. February 2024 34: 243-255; Published in Advance February 14, 2024, doi:10.1101/gr.278133.123
...corresponds with their phenotypic severity. The two variants affect similar sets of enhancers, and p.E168d2 has distinct effects on silencers. Cis-regulatory elements (CREs) near cone photoreceptor genes are enriched for silencers that are derepressed in the presence of p.E168d2. Chromatin environments of CRX...
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Research: Comprehensive functional annotation of ESR1-driven enhancers in breast cancer reveals hierarchical activity independent of genomic and epigenomic contexts
- Yanis Zekri,
- Sebastian Gregoricchio,
- Elif Yapıcı,
- Chia-Chi Flora Huang,
- Tunç Morova,
- Umut Berkay Altıntaş,
- Gozde Korkmaz,
- Nathan A. Lack,
- and Wilbert Zwart
Genome Res. July 2025 35: 1530-1543; Published in Advance June 10, 2025, doi:10.1101/gr.280320.124
...of a similar model for ESR1. Supporting this, we found that 30% of ESR1-linked genes were associated with multiple ERBS classes, suggesting that all three enhancer types may participate in gene regulation in a context-dependent manner.Beyond validating our ERBS annotation through orthogonal in vitro data sets...
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Method: Highly efficient CRISPR/Cas9-mediated knock-in in zebrafish by homology-independent DNA repair
- Thomas O. Auer,
- Karine Duroure,
- Anne De Cian,
- Jean-Paul Concordet,
- and Filippo Del Bene
Genome Res. January 2014 24: 142-153; Published in Advance October 31, 2013, doi:10.1101/gr.161638.113
...the widespread application of gene targeting by HR because screening a large number of animals may be required to isolate founders carrying the mutation of interest. Here we report highly efficient CRISPR/Cas9-mediated knock-in of >5.7-kb-long DNA cassettes into the zebrafish based on homology-independent DSB...

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