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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
...are superficially diverse, they share key commonalities in terms of 23 overall morphology, and organ configuration and function. Maintenance of these traits during 24 evolution is partially explained by conservation of critical genes governing embryonic 25 development. However, for conserved genes to deliver...
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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
...@eitech.edu.cnAbstractDeciphering the relationships between cis-regulatory elements (CREs) and target gene expression has been a long-standing unsolved problem in molecular biology, and the dynamics of CREs in different cell types make this problem more challenging. To address this challenge, we propose a scalable computational framework...
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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
...). For RAD21, 17,387 peaks (44%) were common between the two conditions, and 9462 and 12,706 unique to Wnt-OFF and Wnt-ON (Fig. 1C, bottom). Using PePr (Zhang et al. 2014), we found a subset of the peaks for CTCF and RAD21 for which the differential enrichment fulfills FC > 2 and P < 0.01 (hereafter referred...
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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
.... 2016. The allelic landscape of human blood cell trait variation and links to common complex disease. Cell 167: 1415–1429.e19. doi:10.1016/j.cell.2016.10.042 ↵Bennett LF, Liao C, Quickel MD, Yeoh BS, Vijay-Kumar M, Hankey-Giblin P, Prabhu KS, Paulson RF. 2019. Inflammation induces stress erythropoiesis...
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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
...per bin that pass FDR less than 0.05. The bottom panel displays the per bin DegCre association probability. The common x-axis shows for each bin the association distance from TSS to CRE. Each bin comprises a range of distances with the upper bound of that range plotted here. The black line indicates...
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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: 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
...that gained or lost activity and found none that were strongly associated with a specific pattern of response to the mutant genotypes. This suggests that changes in activity common to subsets of enhancers are not defined by the presence or absence of common motifs but instead by a more complex cis-regulatory...
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Research: Integrating genetic variation with deep learning provides context for variants impacting transcription factor binding during embryogenesis
- Olga M. Sigalova,
- Mattia Forneris,
- Frosina Stojanovska,
- Bingqing Zhao,
- Rebecca R. Viales,
- Adam Rabinowitz,
- Fayrouz Hammal,
- Benoît Ballester,
- Judith B. Zaugg,
- and Eileen E.M. Furlong
Genome Res. May 2025 35: 1138-1153; Published in Advance April 15, 2025, doi:10.1101/gr.279652.124
...genetic variation impacts transcription factor (TF) binding remains a major challenge, limiting our ability to model disease-associated variants. Here, we used a highly controlled system of F1 crosses with extensive genetic diversity to profile allele-specific binding of four TFs at several time points...
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Research: HDAC9 structural variants disrupting TWIST1 transcriptional regulation lead to craniofacial and limb malformations
- Naama Hirsch,
- Idit Dahan,
- Eva D'haene,
- Matan Avni,
- Sarah Vergult,
- Marta Vidal-García,
- Pamela Magini,
- Claudio Graziano,
- Giulia Severi,
- Elena Bonora,
- Anna Maria Nardone,
- Francesco Brancati,
- Alberto Fernández-Jaén,
- Olson J. Rory,
- Benedikt Hallgrímsson,
- and Ramon Y. Birnbaum
Genome Res. July 2022 32: 1242-1253; Published in Advance June 16, 2022, doi:10.1101/gr.276196.121
...in HDAC9. Blue lines represent CTCF sites involved in chromatin looping in the HDAC9-TWIST1 locus. Red lines represent TWIST1 enhancers located in introns or exons of the HDAC9 sequence and intergenic regions. (B) Human Phenotype Ontology heat map of patients’ common clinical features. Gray boxes...
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Research: Modeling alternative translation initiation sites in plants reveals evolutionarily conserved cis-regulatory codes in eukaryotes
- Ting-Ying Wu,
- Ya-Ru Li,
- Kai-Jyun Chang,
- Jhen-Cheng Fang,
- Daisuke Urano,
- and Ming-Jung Liu
Genome Res. February 2024 34: 272-285; Published in Advance March 13, 2024, doi:10.1101/gr.278100.123
...ribosomes recognize different types of TISs along mRNA sequences, including those initiated at both canonical AUG and nonAUG codons, and explored uncharacterized TIS-initiated ORFs in the tomato. We built ML models using TIS-flanking mRNA sequence and TIS codon usage and characterized common or species...
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