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Research: Transcription and potential functions of a novel XIST isoform in male peripheral glia
- Kevin S. O'Leary,
- Meng-Yen Li,
- Kevyn Jackson,
- Lijie Shi,
- Elena Ezhkova,
- Bernice E. Morrow,
- and Deyou Zheng
Genome Res. February 2026 36: 257-274; Published in Advance December 12, 2025, doi:10.1101/gr.280832.125
...cells, the optic nerve, and skeletal muscle), with the sample metadata indicating 32% males, 32% females, and 36% as other/NA (Supplemental Fig. S4A; Noguchi et al. 2017). Additionally, the binding sites for a variety of transcription factors (TFs), such as FOXD3 and REST, are found in this region...
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Research: Unraveling undiagnosed rare disease cases by HiFi long-read genome sequencing
- Wouter Steyaert,
- Lydia Sagath,
- German Demidov,
- Vicente A. Yépez,
- Anna Esteve-Codina,
- Julien Gagneur,
- Kornelia Ellwanger,
- Ronny Derks,
- Marjan Weiss,
- Amber den Ouden,
- Simone van den Heuvel,
- Hilde Swinkels,
- Nick Zomer,
- Marloes Steehouwer,
- Luke O'Gorman,
- Galuh Astuti,
- Kornelia Neveling,
- Rebecca Schüle,
- Jishu Xu,
- Matthis Synofzik,
- Danique Beijer,
- Holger Hengel,
- Ludger Schöls,
- Kristl G. Claeys,
- Jonathan Baets,
- Liedewei Van de Vondel,
- Alessandra Ferlini,
- Rita Selvatici,
- Heba Morsy,
- Marwa Saeed Abd Elmaksoud,
- Volker Straub,
- Juliane Müller,
- Veronica Pini,
- Luke Perry,
- Anna Sarkozy,
- Irina Zaharieva,
- Francesco Muntoni,
- Enrico Bugiardini,
- Kiran Polavarapu,
- Rita Horvath,
- Evan Reid,
- Hanns Lochmüller,
- Marco Spinazzi,
- Marco Savarese,
- Solve-RD DITF-ITHACA, Solve-RD DITF-Euro-NMD, Solve-RD DITF-RND, Solve-RD DITF-EpiCARE,
- Leslie Matalonga,
- Steven Laurie,
- Han G. Brunner,
- Holm Graessner,
- Sergi Beltran,
- Stephan Ossowski,
- Lisenka E.L.M. Vissers,
- Christian Gilissen,
- Alexander Hoischen,
- and on behalf of the Solve-RD consortium
Genome Res. April 2025 35: 755-768; Published in Advance March 26, 2025, doi:10.1101/gr.279414.124
...Unraveling undiagnosed rare disease cases by HiFi long-read sequencing Wouter Steyaert1,36, Lydia Sagath1,36, German Demidov2, Vicente A. Yépez3, Anna Esteve-Codina4,5, Julien Gagneur3,6,7, Kornelia Ellwanger2,8, Ronny Derks1, Marjan Weiss1, Amber den Ouden1, Simone van den Heuvel1, Hilde Swinkels1...
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Method: Unraveling the palindromic and nonpalindromic motifs of retroviral integration site sequences by statistical mixture models
- Dalibor Miklík,
- Jiří Grim,
- Daniel Elleder,
- and Jiří Hejnar
Genome Res. August 2023 33: 1395-1408; Published in Advance July 18, 2023, doi:10.1101/gr.277694.123
...; Linheiro and Bergman 2008; Gangadharan et al. 2010; Mularoni et al. 2012; Riggs et al. 2021) and is a marker of binding sites of some transcription factors (Datta and Rister 2022).View larger version: In this window In a new window Figure 1. Origin of palindrome consensus motifs at sites of retroviral...
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Corrigendum: Corrigendum: Unraveling determinants of transcription factor binding outside the core binding site
- Michal Levo,
- Einat Zalckvar,
- Eilon Sharon,
- Ana Carolina Dantas Machado,
- Yael Kalma,
- Maya Lotan-Pompan,
- Adina Weinberger,
- Zohar Yakhini,
- Remo Rohs,
- and Eran Segal
Genome Res. September 2015 25: 1410.2
...: Unraveling determinants of transcription factor binding outside the core binding site Genome Research 25: 655–666 (2015) Corrigendum: Extensive microRNA-mediated crosstalk between lncRNAs and mRNAs in mouse embryonic stem cells Jennifer Y. Tan, Tamara Sirey, Frantisek Honti, Bryony Graham, Allison Piovesan...
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Research: Evolution of transcription factor binding through sequence variations and turnover of binding sites
- Gat Krieger,
- Offir Lupo,
- Patricia Wittkopp,
- and Naama Barkai
Genome Res. June 2022 32: 1099-1111; Published in Advance May 26, 2022, doi:10.1101/gr.276715.122
...(27%), and a small fraction (7%) shows compensation through binding-site turnover, likely indicating functional conservation despite sequence divergence.DiscussionUnderstanding the sequence determinants of transcription factor binding in living cells is a major challenge. In this study, we profiled...
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Research: The origin and evolution of a distinct mechanism of transcription initiation in yeasts
- Zhaolian Lu and
- Zhenguo Lin
Genome Res. January 2021 31: 51-63; Published in Advance November 20, 2020, doi:10.1101/gr.264325.120
...the conversion of genetic codes from the DNA into functional products. A crucial step of transcriptional regulation occurs at the level of transcription initiation, as it determines not only the number of transcripts produced but also the locations of the transcription start site (TSS). Therefore, transcription...
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Method: SelexGLM differentiates androgen and glucocorticoid receptor DNA-binding preference over an extended binding site
- Liyang Zhang,
- Gabriella D. Martini,
- H. Tomas Rube,
- Judith F. Kribelbauer,
- Chaitanya Rastogi,
- Vincent D. FitzPatrick,
- Jon C. Houtman,
- Harmen J. Bussemaker,
- and Miles A. Pufall
Genome Res. January 2018 28: 111-121; Published in Advance December 1, 2017, doi:10.1101/gr.222844.117
...site by iteratively fitting a feature-based generalized linear model to SELEX probe counts. This analysis revealed that the DNA-binding preferences of AR and GR homodimers differ significantly, both within and outside the 15-bp core binding site. The relative preference between the two factors can...
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Research: Core promoter sequence in yeast is a major determinant of expression level
- Shai Lubliner,
- Ifat Regev,
- Maya Lotan-Pompan,
- Sarit Edelheit,
- Adina Weinberger,
- and Eran Segal
Genome Res. July 2015 25: 1008-1017; Published in Advance May 12, 2015, doi:10.1101/gr.188193.114
...) (Fieldet al. 2008; Kaplan et al. 2009). In the study of regulatory sequences and their effects on expression, core promoter sequences remain relatively understudied, asmost efforts are directed at transcription factor (TF) binding sites and their role in determining regulatory logic and expression levels...
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Method: High-throughput characterization of genetic effects on DNA–protein binding and gene transcription
- Cynthia A. Kalita,
- Christopher D. Brown,
- Andrew Freiman,
- Jenna Isherwood,
- Xiaoquan Wen,
- Roger Pique-Regi,
- and Francesca Luca
Genome Res. November 2018 28: 1701-1708; Published in Advance September 25, 2018, doi:10.1101/gr.237354.118
.... Pediatr Int 57: 1149–1153. ↵Levo M, Zalckvar E, Sharon E, Dantas Machado AC, Kalma Y, Lotam-Pompan M, Weinberger A, Yakhini Z, Rohs R, Segal E. 2015. Unraveling determinants of transcription factor binding outside the core binding site. Genome Res 25: 1018–1029. ↵Li Q, Verma IM. 2002. NF-κB regulation...
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Research: Relationship between histone modifications and transcription factor binding is protein family specific
- Beibei Xin and
- Remo Rohs
Genome Res. March 2018 28: 321-333; Published in Advance January 11, 2018, doi:10.1101/gr.220079.116
...transcriptional regulation. The relatively short core-binding motifs of TFs can appear numerous times in a , but only a very small fraction of these putative binding sites is functional (Landolin et al. 2010; Spitz and Furlong 2012). TFs can precisely identify their functional binding sites from among the other...
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