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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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Method: Unraveling determinants of transcription factor binding outside the core binding site
- Michal Levo,
- Einat Zalckvar,
- Eilon Sharon,
- Ana Carolina Dantas Machado,
- Yael Kalma,
- Maya Lotam-Pompan,
- Adina Weinberger,
- Zohar Yakhini,
- Remo Rohs,
- and Eran Segal
Genome Res. July 2015 25: 1018-1029; Published in Advance March 11, 2015, doi:10.1101/gr.185033.114
...Unraveling determinants of transcription factor binding outside the core binding site Michal Levo 1 , 2 , 6 , Einat Zalckvar 1 , 2 , 6 , Eilon Sharon 1 , Ana Carolina Dantas Machado 3 , Yael Kalma 2 , Maya Lotam-Pompan 2...
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Perspective: Unraveling the hidden complexity of cancer through long-read sequencing
- Qiuhui Li,
- Ayse G. Keskus,
- Justin Wagner,
- Michal B. Izydorczyk,
- Winston Timp,
- Fritz J. Sedlazeck,
- Alison P. Klein,
- Justin M. Zook,
- Mikhail Kolmogorov,
- and Michael C. Schatz
Genome Res. April 2025 35: 599-620; Published in Advance March 20, 2025, doi:10.1101/gr.280041.124
...haplotype, meaning they often cannot conclusively determine if there has been a complete loss of function in genes from compound heterozygous mutations (Sedlazeck et al. 2018). In addition to these limitations for detecting DNA variations and mutations, short-reads also face related challenges resolving...
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Research: Genome-wide nucleosome and transcription factor responses to genetic perturbations reveal chromatin-mediated mechanisms of transcriptional regulation
- Kevin Moyung,
- Yulong Li,
- Heather K. MacAlpine,
- Alexander J. Hartemink,
- and David M. MacAlpine
Genome Res. January 2026 36: 115-128; Published in Advance December 9, 2025, doi:10.1101/gr.279637.124
...@cs.duke.eduAbstractEpigenetic mechanisms contribute to gene regulation by altering chromatin accessibility through changes in transcription factor (TF) and nucleosome occupancy across the . Despite numerous studies focusing on changes in gene expression, the intricate chromatin-mediated regulatory code remains largely uncharted...
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Review: A systematic guide for identifying transcription factors that directly regulate the expression of a gene of interest
- Andrew D. Bates,
- Dawid Grzela,
- Maciej Studzian,
- Louise Brennan,
- Moli Williams,
- Conor Fawcett,
- Beth Hammond,
- Manreen Grewal,
- Marcin Ratajewski,
- Lukasz Pulaski,
- and Urszula L. McClurg
Genome Res. March 2026 36: 433-459; Published in Advance February 17, 2026, doi:10.1101/gr.281154.125
...sitesA eukaryotic gene typically consists of regulatory elements such as distal enhancers, which can act over long distances; a proximal promoter containing key TF binding sites; a core promoter surrounding the transcription start site (TSS) where the preinitiation complex assembles, followed...
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Method: Kinetic measurement of gene-specific RNA polymerase II transcription elongation rates
- Haiyue Liu and
- Lea H. Gregersen
Genome Res. November 2025 35: 2550-2562; Published in Advance October 22, 2025, doi:10.1101/gr.280852.125
...and proceeds along the gene body to transcribe RNA (Jonkers and Lis 2015; Core and Adelman 2019; Noe Gonzalez et al. 2021; Aoi and Shilatifard 2023). As with all steps in the transcription process, elongation is tightly regulated to ensure that RNAPII travels along the gene at a proper speed (i.e., elongation...
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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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Research: Autism spectrum disorder risk genes have convergent effects on transcription and neuronal firing patterns in primary neurons
- Alekh Paranjapye,
- Rili Ahmad,
- Steven Su,
- Abraham J. Waldman,
- Jennifer E. Phillips-Cremins,
- Shuo Zhang,
- and Erica Korb
Genome Res. November 2025 35: 2433-2444; Published in Advance October 20, 2025, doi:10.1101/gr.280698.125
...) and overlapping (ASH1L, SETD5) histone sites, histone remodelers from two different complexes (CHD8, MED13L), a DNA modifying enzyme (DNMT3A), a transcription factor (TBR1), and a noncatalytic chromatin-complex protein (MBD5) (Table 1). Additional criteria included that all are high-confidence ASD genes (scored...

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