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Research: Historical RNA expression profiles from the extinct Tasmanian tiger
- Emilio Mármol-Sánchez,
- Bastian Fromm,
- Nikolay Oskolkov,
- Zoé Pochon,
- Panagiotis Kalogeropoulos,
- Eli Eriksson,
- Inna Biryukova,
- Vaishnovi Sekar,
- Erik Ersmark,
- Björn Andersson,
- Love Dalén,
- and Marc R. Friedländer
Genome Res. August 2023 33: 1299-1316; Published in Advance July 18, 2023, doi:10.1101/gr.277663.123
...into the modern era. They belonged to the order Dasyuromorphia and were closely related to the extant families Dasyuridae (including Tasmanian devils, quolls, phascogales, and dunnarts, among others) and Myrmecobiidae (numbats) (Miller et al. 2009; Feigin et al. 2018). These apex marsupials were once widespread...
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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
...cis-regulatory elements. Here, CTCF binds in tandem with beta-catenin and TCF/LEF to increase cohesin stalling and induce the formation of chromatin loops that contribute to the upregulation of a subset of Wnt target genes (Fig. 7). This, to our knowledge, represents a previously unknown mechanism...
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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
...in the significant CFM-associated variants (Supplemental Fig. 5B). Furthermore, on deeper examination, conditioning on all rare variants within a 1 kb region of all cis-regulatory (cis-reg) elements and the 11 presumptively pathogenic variants, a considerable number of variants remained significantly associated...
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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: 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. April 2026 36: 695-712; Published in Advance March 4, 2026, doi:10.1101/gr.280838.125
...and to associated organs including the liver and pancreas. We used functional genomic approaches to identify highly conserved endodermal cis-regulatory modules (CRMs) functioning across the 400 million years of evolution separating zebrafish and humans. Our analyses suggest that there are few endoderm-specific CRMs...
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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: Ancient dog introgression into the Iberian wolf genome may have facilitated adaptation to human-dominated landscapes
- Diana Lobo,
- Hernán E. Morales,
- Cock Van Oosterhout,
- José Vicente López-Bao,
- Pedro Silva,
- Luis Llaneza,
- Carolina Pacheco,
- Diana Castro,
- Germán Hernández-Alonso,
- George Pacheco,
- John Archer,
- M. Thomas P. Gilbert,
- Nuno Ferrand,
- and Raquel Godinho
Genome Res. March 2025 35: 432-445; Published in Advance February 14, 2025, doi:10.1101/gr.279093.124
...Peninsula (Portugal and Spain), has uniquely persisted in human-dominated landscapes, unlike many other wolf populations that faced widespread extinction across Europe during the twentieth century. In this study, we conducted a comprehensive -wide analysis of 145 historical and contemporary Iberian wolf...
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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
...-rod homeobox (CRX) are linked with human blinding diseases that vary in their severity and age of onset. How different variants in this single TF alter its function in ways that lead to a range of phenotypes is unclear. We characterized the effects of human disease-causing variants on CRX cis-regulatory...
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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
...progenitors and precursors temporarily rewire their transcriptome, up- and downregulating hundreds of genes to accelerate the production of mature RBCs. Effective regeneration requires communication between critical cytokine signals (e.g., BMP4) and cis-regulatory elements on chromatin which coordinate...
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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
...Corresponding authors: gcooper@hudsonalpha.org, rmyers@hudsonalpha.orgAbstractDifferential gene expression in response to perturbations is mediated at least in part by changes in binding of transcription factors (TFs) and other proteins at specific genomic regions. Association of these cis-regulatory elements...

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