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Research: Multi-species analysis of inflammatory response elements reveals ancient and lineage-specific contributions of transposable elements to NF-kB binding
- Liangxi Wang,
- Tiegh Taylor,
- Kumaragurubaran Rathnakumar,
- Nadiya Khyzha,
- Minggao Liang,
- Azad Alizada,
- Laura F. Campitelli,
- Sara E. Pour,
- Zain M. Patel,
- Lina Antounians,
- Ian C. Tobias,
- Huayun Hou,
- Timothy R. Hughes,
- Sushmita Roy,
- Jennifer A. Mitchell,
- Jason E. Fish,
- and Michael D. Wilson
Genome Res. July 2025 35: 1544-1559; Published in Advance June 6, 2025, doi:10.1101/gr.280357.124
...) play a role in shaping gene regulation by serving as a source of novel cis-regulatory elements (CREs) (Chuong et al. 2017; Pontis et al. 2019; Sundaram and Wysocka 2020; Hermant and Torres‐Padilla 2021; Senft and Macfarlan 2021; Fueyo et al. 2022).Identifying which TFs interact with TEs and under what...
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Research: Transposable elements drive the evolution of metazoan zinc finger genes
- Jonathan N. Wells,
- Ni-Chen Chang,
- John McCormick,
- Caitlyn Coleman,
- Nathalie Ramos,
- Bozhou Jin,
- and Cédric Feschotte
Genome Res. August 2023 33: 1325-1339; Published in Advance September 15, 2023, doi:10.1101/gr.277966.123
...repressing TEs, KZNFs play an important role in their domestication by taming their cis-regulatory activities and facilitating their integration into existing gene regulatory networks (Ecco et al. 2017; Bruno et al. 2019; Pontis et al. 2019). Under this model, KZNFs act as tolerogenic agents promoting...
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Method: Massively parallel cis-regulatory analysis in the mammalian central nervous system
- Susan Q. Shen,
- Connie A. Myers,
- Andrew E.O. Hughes,
- Leah C. Byrne,
- John G. Flannery,
- and Joseph C. Corbo
Genome Res. February 2016 26: 238-255; Published in Advance November 17, 2015, doi:10.1101/gr.193789.115
..., California 94720, USA Cis-regulatory elements (CREs, e.g., promoters and enhancers) regulate gene expression, and variants within CREs can modulate disease risk. Next-generation sequencing has enabled the rapid generation of genomic data that predict the locations of CREs, but a bottleneck lies...
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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
...and functions of different cell types are determined by the expression of distinctive sets of genes in each. This differential gene expression is regulated by the interplay of transcription factors (TFs) binding to cis-regulatory elements (CREs) in the genomic DNA, such as promoters and enhancers, forging...
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Resource: A temporal in vivo catalog of chromatin accessibility and expression profiles in pineoblastoma reveals a prevalent role for repressor elements
- Salam Idriss,
- Mohammad Hallal,
- Abdullah El-Kurdi,
- Hasan Zalzali,
- Inaam El-Rassi,
- Erik A. Ehli,
- Christel M. Davis,
- Philip E.D. Chung,
- Deena M.A. Gendoo,
- Eldad Zacksenhaus,
- Raya Saab,
- and Pierre Khoueiry
Genome Res. February 2023 33: 269-282; Published in Advance January 17, 2023, doi:10.1101/gr.277037.122
...of heterochromatin by rendering it more accessible (Wu et al. 2009).Only 6% of P10 → P90−GO or P49 → P90−GO overlapped with ENCODE candidate cis-regulatory elements (cCREs) that are identified by either histone modifications (H3K4me3 and H3K27ac) or CTCF-binding data. This percentage ranged between 48% and 77...
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Perspective: Applications of single-cell genomics and computational strategies to study common disease and population-level variation
- Benjamin J. Auerbach,
- Jian Hu,
- Muredach P. Reilly,
- and Mingyao Li
Genome Res. October 2021 31: 1728-1741; doi:10.1101/gr.275430.121
...to be a promising approach toward modeling the role of genomic variants in cis regulatory logic. In particular, CNNs have already shown great promise in modeling the contribution of promoter genetic variation on mean gene expression levels. Agarwal and Shendure (2020) first introduced their algorithm, Xpresso...
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Perspective: Functional genomics bridges the gap between quantitative genetics and molecular biology
- Tuuli Lappalainen
Genome Res. October 2015 25: 1427-1431; doi:10.1101/gr.190983.115
.... Nature 452: 423–428. The ENCODE Project Consortium. 2012. An integrated encyclopedia of DNA elements in the human . Nature 489: 57–74. The FANTOM Consortium and the RIKEN PMI and CLST (DGT). 2014. A promoter-level mammalian expression atlas. Nature 507: 462–470. Farh KK, Marson A, Zhu J, Kleinewietfeld M...
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LETTER: Pseudogenes in the ENCODE regions: Consensus annotation, analysis of transcription, and evolution
- Deyou Zheng,
- Adam Frankish,
- Robert Baertsch,
- Philipp Kapranov,
- Alexandre Reymond,
- Siew Woh Choo,
- Yontao Lu,
- France Denoeud,
- Stylianos E. Antonarakis,
- Michael Snyder,
- Yijun Ruan,
- Chia-Lin Wei,
- Thomas R. Gingeras,
- Roderic Guigó,
- Jennifer Harrow,
- and Mark B. Gerstein
Genome Res. June 2007 17: 839-851; doi:10.1101/gr.5586307
...genomics, and is also critical for obtaining an accurate picture of a ’s structure and function. However, no consensus computational scheme for defining and detecting pseudogenes has been developed thus far. As part of the ENCyclopedia Of DNA Elements (ENCODE) project, we have compared several distinct...
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ARTICLE: Evolutionarily conserved elements in vertebrate, insect, worm, and yeast genomes
- Adam Siepel,
- Gill Bejerano,
- Jakob S. Pedersen,
- Angie S. Hinrichs,
- Minmei Hou,
- Kate Rosenbloom,
- Hiram Clawson,
- John Spieth,
- LaDeana W. Hillier,
- Stephen Richards,
- George M. Weinstock,
- Richard K. Wilson,
- Richard A. Gibbs,
- W. James Kent,
- Webb Miller,
- and David Haussler
Genome Res. August 2005 15: 1034-1050; Published in Advance July 15, 2005, doi:10.1101/gr.3715005
...for local RNA secondary structure, indicating that many may encode functional RNAs. In vertebrates, intergenic HCEs are strongly enriched (nearly fivefold) in stable gene deserts, suggesting that many of them may act as distal cis -regulatory elements for precisely regulated genes ( Ovcharenko et al. 2005b...
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Resource: Single-nucleus multiomic profiling of the aging mouse substantia nigra reveals conserved gene alterations linked to Parkinson's disease
- Kangli Wang,
- Weikun Xia,
- Yingli Gu,
- Songpeng Zu,
- Qian Yang,
- Maria Luisa Amaral,
- Yaozhi Wang,
- Allen Wang,
- Xiang-Dong Fu,
- William C. Mobley,
- and Bing Ren
Genome Res. April 2026 36: 849-864; Published in Advance March 4, 2026, doi:10.1101/gr.281113.125
...transcriptional programs. Gene expression is regulated by cis-regulatory elements (CREs) in a spatiotemporal manner through precise gene regulatory networks (Lee and Young 2013; Levine et al. 2014; Long et al. 2016). Understanding these regulatory mechanisms beyond transcription may reveal critical aspects of how...
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