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Resource: The SynMall resource for characterizing the functional impact of synonymous variation
- Chen Ye,
- Xiaoyan Li,
- Na Cheng,
- Yansen Su,
- and Junfeng Xia
Genome Res. February 2026 36: 421-431; Published in Advance December 17, 2025, doi:10.1101/gr.281257.125
...of the cancer : aberrations in regulatory elements, untranslated regions, splice sites, non-coding RNA and synonymous mutations. EMBO Mol Med 8: 442–457. doi:10.15252/emmm.201506055 ↵Gao H, Hamp T, Ede J, Schraiber JG, McRae J, Singer-Berk M, Yang Y, Dietrich ASD, Fiziev PP, Kuderna LFK, et al. 2023...
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Research: Evidence for compensatory evolution within pleiotropic regulatory elements
- Zane Kliesmete,
- Peter Orchard,
- Victor Yan Kin Lee,
- Johanna Geuder,
- Simon M. Krauß,
- Mari Ohnuki,
- Jessica Jocher,
- Beate Vieth,
- Wolfgang Enard,
- and Ines Hellmann
Genome Res. October 2024 34: 1528-1539; Published in Advance September 10, 2024, doi:10.1101/gr.279001.124
...of the best predictors for protein sequence and expression conservation. In this study, we investigated its effect on the evolution of cis-regulatory elements (CREs). To this end, we carefully reanalyzed the Epigenomics Roadmap data for nine fetal tissues, assigning a measure of pleiotropic degree to nearly...
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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
.... 2013). This variability is attributed to a multitude of factors, including but not limited to genetic modifiers, environmental conditions, and epigenetic modifications. Variants in regulatory elements that impact gene expression, otherwise known as expression quantitative trait loci (eQTLs), serve...
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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
...variants occur in the noncoding (Edwards et al. 2013; Buniello et al. 2019) and likely affect gene regulation (Claringbould and Zaugg 2021). One mechanism by which mutations impact transcriptional programs is through the disruption of transcription factor (TF) binding sites within regulatory elements...
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Resource: Interspecies regulatory landscapes and elements revealed by novel joint systematic integration of human and mouse blood cell epigenomes
- Guanjue Xiang,
- Xi He,
- Belinda M. Giardine,
- Kathryn J. Isaac,
- Dylan J. Taylor,
- Rajiv C. McCoy,
- Camden Jansen,
- Cheryl A. Keller,
- Alexander Q. Wixom,
- April Cockburn,
- Amber Miller,
- Qian Qi,
- Yanghua He,
- Yichao Li,
- Jens Lichtenberg,
- Elisabeth F. Heuston,
- Stacie M. Anderson,
- Jing Luan,
- Marit W. Vermunt,
- Feng Yue,
- Michael E.G. Sauria,
- Michael C. Schatz,
- James Taylor,
- Berthold Göttgens,
- Jim R. Hughes,
- Douglas R. Higgs,
- Mitchell J. Weiss,
- Yong Cheng,
- Gerd A. Blobel,
- David M. Bodine,
- Yu Zhang,
- Qunhua Li,
- Shaun Mahony,
- and Ross C. Hardison
Genome Res. July 2024 34: 1089-1105; Published in Advance July 1, 2024, doi:10.1101/gr.277950.123
...of the cCRE catalogs by conservation of sequence and inferred function revealed informative categories that differed both in evolutionary trajectories and in types of functional enrichment.Conservation of noncoding genomic DNA sequences among species has been used extensively to predict regulatory elements...
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Research: GC-biased gene conversion drives accelerated evolution of ultraconserved elements in mammalian and avian genomes
- Anguo Liu,
- Nini Wang,
- Guoxiang Xie,
- Yang Li,
- Xixi Yan,
- Xinmei Li,
- Zhenliang Zhu,
- Zhuohui Li,
- Jing Yang,
- Fanxin Meng,
- Mingle Dou,
- Weihuang Chen,
- Nange Ma,
- Yu Jiang,
- Yuanpeng Gao,
- and Yu Wang
Genome Res. October 2023 33: 1673-1689; Published in Advance October 26, 2023, doi:10.1101/gr.277784.123
...BGC.gBGC promotes parallel alterations in genes and the proximal conserved elementsStrong gBGC can lead to severe W → S substitutions in both coding and flanking noncoding regions (Ratnakumar et al. 2010). Therefore, a conspicuous GC-biased substitution pattern in proximal conserved elements may be a potential...
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Research: Ancient exapted transposable elements promote nuclear enrichment of human long noncoding RNAs
- Joana Carlevaro-Fita,
- Taisia Polidori,
- Monalisa Das,
- Carmen Navarro,
- Tatjana I. Zoller,
- and Rory Johnson
Genome Res. February 2019 29: 208-222; Published in Advance December 26, 2018, doi:10.1101/gr.229922.117
...author: rory.johnson@dbmr.unibe.chAbstractThe sequence domains underlying long noncoding RNA (lncRNA) activities, including their characteristic nuclear enrichment, remain largely unknown. It has been proposed that these domains can originate from neofunctionalized fragments of transposable elements (TEs...
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Research: Functional noncoding SNPs in human endothelial cells fine-map vascular trait associations
- Anu Toropainen,
- Lindsey K. Stolze,
- Tiit Örd,
- Michael B. Whalen,
- Paula Martí Torrell,
- Verena M. Link,
- Minna U. Kaikkonen,
- and Casey E. Romanoski
Genome Res. March 2022 32: 409-424; Published in Advance February 22, 2022, doi:10.1101/gr.276064.121
...Diseases, National Institutes of Health, Bethesda, Maryland 20892, USA ↵5 These authors are co-first authors and contributed equally to this work. Corresponding authors: cromanoski@arizona.edu, minna.kaikkonen@uef.fiAbstractFunctional consequences of genetic variation in the noncoding human are difficult...
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Research: Dynamic modulation of genomic enhancer elements in the suprachiasmatic nucleus, the site of the mammalian circadian clock
- Akanksha Bafna,
- Gareth Banks,
- Michael H. Hastings,
- and Patrick M. Nolan
Genome Res. May 2023 33: 673-688; Published in Advance May 8, 2023, doi:10.1101/gr.277581.122
...if genetic variation within any of these regulatory elements presents a threat to the well-orchestrated circadian timekeeping mechanism directed by the SCN. This could potentially constitute starting points to understand the association between aberrant gene-regulatory regions and the human disease...
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Perspective: Decrypting noncoding RNA interactions, structures, and functional networks
- Muller Fabbri,
- Leonard Girnita,
- Gabriele Varani,
- and George A. Calin
Genome Res. September 2019 29: 1377-1388; Published in Advance August 21, 2019, doi:10.1101/gr.247239.118
...grammar and the ncRNA structure grammar. (A) The elements of the ncRNA language grammar. A schematic view of IEs, SEs, structural domains of a ncRNA, and the noncoding RNA interactor network (NIN) composed by the ncRNA, interactor RNAs (such as miRNAs), interactor proteins (such as P1), interactor DNA...
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