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Method: A scalable computational framework for predicting gene expression from candidate cis-regulatory elements
- Qinhu Zhang,
- Siguo Wang,
- Zhipeng Li,
- Wenzheng Bao,
- Wenjian Liu,
- and De-Shuang Huang
Genome Res. February 2026 36: 361-374; Published in Advance January 16, 2026, doi:10.1101/gr.281219.125
....MethodsData preparationCandidate cis-regulatory elementscCREs for Human were downloaded from the SCREEN Registry Version 3 (https://screen.encodeproject.org/). The Registry contains 1,063,878 human cCREs in GRCh38, which are derived from ENCODE data using four types of data including DNase, H3K4me3, H3K27ac, and CTCF...
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Research: Functional genomics analysis of developing zebrafish and human endoderm reveals highly conserved cis-regulatory modules acting during vertebrate organogenesis
- Daniela M Riley,
- Randa Elsayed,
- Mark D Walsh,
- Simaran Johal,
- Ying Lin,
- Harry Walton,
- Till Bretschneider,
- Sascha Ott,
- and Andrew C Nelson
Genome Res. March 4, 2026 gr.280838.125; Published in Advance March 4, 2026, doi:10.1101/gr.280838.125
...1 Functional genomics analysis of developing zebrafish and human endoderm reveals 1 highly conserved cis-regulatory modules acting during vertebrate organogenesis 2 3 Daniela M. Riley1,†, Randa Elsayed1,†, Mark D. Walsh2,†, Simaran Johal2, Ying Lin3,4, Harry 4 Walton1, Till Bretschneider5, Sascha...
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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
...than the Wnt-ON/OFF-only loops, the opposite is observed for promoter–enhancer loops, which were more enriched in the sets of Wnt-ON/OFF-only loops (P-adj ≤ 0.05) (Fig. 4D; Supplemental Fig. S4B). Loop length analysis suggests that Wnt activation or inhibition results in the reorganization of long-range...
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Method: Probabilistic association of differentially expressed genes with cis-regulatory elements
- Brian S. Roberts,
- Ashlyn G. Anderson,
- E. Christopher Partridge,
- Gregory M. Cooper,
- and Richard M. Myers
Genome Res. April 2024 34: 620-632; Published in Advance April 17, 2024, doi:10.1101/gr.278598.123
.... Because DegCre uses rank-order statistics, it can use various types of CRE-associated data, including DNase hypersensitivity, ATAC-seq, and ChIP-seq against either histone marks or TFs. It produces significant associations with a wide range of TSS to CRE distances, up to an upper limit subject only...
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Research: Common cis-regulatory variation modifies the penetrance of pathogenic SHROOM3 variants in craniofacial microsomia
- Hao Zhu,
- Jiao Zhang,
- Soumya Rao,
- Matthew D. Durbin,
- Ying Li,
- Ruirui Lang,
- Jiqiang Liu,
- Baichuan Xiao,
- Hailin Shan,
- Ziqiu Meng,
- Jinmo Wang,
- Xiaokai Tang,
- Zhenni Shi,
- Liza L. Cox,
- Shouqin Zhao,
- Stephanie M. Ware,
- Tiong Y. Tan,
- Michelle de Silva,
- Lyndon Gallacher,
- Ting Liu,
- Jie Mi,
- Changqing Zeng,
- Hou-Feng Zheng,
- Qingguo Zhang,
- Stylianos E. Antonarakis,
- Timothy C. Cox,
- and Yong-Biao Zhang
Genome Res. May 2025 35: 1065-1079; Published in Advance April 15, 2025, doi:10.1101/gr.280047.124
...calculation, which was adjusted according to the respective populations. Additionally, we utilized HaploReg to annotate deleterious-associated variants to identify those potentially affecting SHROOM3 expression. Variants situated in enhancer or promoter regions, as indicated by histone or DNase marks in stem...
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Research: The role of transposon activity in shaping cis-regulatory element evolution after whole-genome duplication
- Øystein Monsen,
- Lars Grønvold,
- Alex Datsomor,
- Thomas Harvey,
- James Kijas,
- Alexander Suh,
- Torgeir R. Hvidsten,
- and Simen Rød Sandve
Genome Res. March 2025 35: 475-488; Published in Advance February 12, 2025, doi:10.1101/gr.278931.124
...The role of transposon activity in shaping cis-regulatory element evolution after whole- duplication Øystein Monsen1,6, Lars Grønvold1,6, Alex Datsomor1, Thomas Harvey1, James Kijas2, Alexander Suh3,4,7, Torgeir R. Hvidsten5 and Simen Rød Sandve1 1Department of Animal and Aquacultural Sciences...
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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
...at different scales.ResultsScreening for factors bound at sites of enriched CRE–CRE interactionsTo quantify interactions between CREs, we merged DNase-accessible ENCODE (Luo et al. 2020) CREs from mESCs within 5 kb of each other and generated observed over expected (O/E) contact frequencies for each CRE pair...
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Research: Regeneration alters open chromatin and cis-regulatory landscape of erythroid precursors
- Yichao Zhou,
- Venkatasai Rahul Dogiparthi,
- Hannah L. Harris,
- Suhita Ray,
- Avik Choudhuri,
- Song Yang,
- Yi Zhou,
- Leonard I. Zon,
- M. Jordan Rowley,
- and Kyle J. Hewitt
Genome Res. July 2025 35: 1518-1529; Published in Advance June 2, 2025, doi:10.1101/gr.279949.124
...a region with changing footprint score and underlying sequence. Candidate cis-regulatory elements (cCREs) were classified by ENCODE (The ENCODE Project Consortium 2012). Red = promoter, orange = proximal enhancer-like signature. (F) ATAC-seq and TOBIAS Footprint scores at the Kif3b locus. Blue line...
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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
...of chromatin accessibility was assigned using a DNase I hypersensitivity analysis (Wilken et al. 2015). Group A sequences are positive for the promoter-associated H3K4me3 epigenetic mark (Vermeulen et al. 2010) and H3K27ac, a mark associated with active CREs (Creyghton et al. 2010), and they are largely...
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Resource: Epigenomic analysis reveals prevalent contribution of transposable elements to cis-regulatory elements, tissue-specific expression, and alternative promoters in zebrafish
- Hyung Joo Lee,
- Yiran Hou,
- Ju Heon Maeng,
- Nakul M. Shah,
- Yujie Chen,
- Heather A. Lawson,
- Hongbo Yang,
- Feng Yue,
- and Ting Wang
Genome Res. July 2022 32: 1424-1436; Published in Advance June 1, 2022, doi:10.1101/gr.276052.121
...also observed similar instances in other tissues and other classes of TE. For example, the DNA2-5_DR element serves as a brain-specific TSS for the gene citb, LTR-10_DR element serves as a kidney-specific TSS for the gene add1, and Polinton-1N1_DR serves as a blood-specific TSS for the gene dnase1l4...
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