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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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Research: Suv39h-catalyzed H3K9me3 is critical for euchromatic genome organization and the maintenance of gene transcription
- Christine R. Keenan,
- Hannah D. Coughlan,
- Nadia Iannarella,
- Andres Tapia del Fierro,
- Andrew Keniry,
- Timothy M. Johanson,
- Wing Fuk Chan,
- Alexandra L. Garnham,
- Lachlan W. Whitehead,
- Marnie E. Blewitt,
- Gordon K. Smyth,
- and Rhys S. Allan
Genome Res. April 2024 34: 556-571; Published in Advance May 6, 2024, doi:10.1101/gr.279119.124
...by HOMER. (H) Example tracks of the region surrounding the promoter of a down-regulated DE gene (Itga4) showing ATAC-seq, ChIP-seq (H3K4me3, H3K27ac, H3K27me3, H3K9me3, IgG), and RNA-seq data. (I) Plots of mean coverage from 3 kb upstream of the transcription start site (TSS) to 3 kb downstream...
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Method: Evidence of widespread, independent sequence signature for transcription factor cobinding
- Manqi Zhou,
- Hongyang Li,
- Xueqing Wang,
- and Yuanfang Guan
Genome Res. February 2021 31: 265-278; Published in Advance December 10, 2020, doi:10.1101/gr.267310.120
...Roadmap Projects have provided invaluable resources of the in vivo biochemical signatures, including chromatin accessibility and TF binding. Many exciting computational approaches have been developed to predict transcription factor binding sites (TFBSs) and to study what controls the binding patterns...
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Method: Discovery of an unusually high number of de novo mutations in sperm of older men using duplex sequencing
- Renato Salazar,
- Barbara Arbeithuber,
- Maja Ivankovic,
- Monika Heinzl,
- Sofia Moura,
- Ingrid Hartl,
- Theresa Mair,
- Angelika Lahnsteiner,
- Thomas Ebner,
- Omar Shebl,
- Johannes Pröll,
- and Irene Tiemann-Boege
Genome Res. March 2022 32: 499-511; Published in Advance February 24, 2022, doi:10.1101/gr.275695.121
...Renato Salazar1, Barbara Arbeithuber1,4, Maja Ivankovic1, Monika Heinzl1, Sofia Moura1, Ingrid Hartl1, Theresa Mair1, Angelika Lahnsteiner1,5, Thomas Ebner2, Omar Shebl2, Johannes Pröll3 and Irene Tiemann-Boege1 1Institute of Biophysics, Johannes Kepler University, Linz, Austria 4020; 2Department...
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Research: Competition for DNA binding between paralogous transcription factors determines their genomic occupancy and regulatory functions
- Yuning Zhang,
- Tiffany D. Ho,
- Nicolas E. Buchler,
- and Raluca Gordân
Genome Res. July 2021 31: 1216-1229; Published in Advance May 11, 2021, doi:10.1101/gr.275145.120
...by competing for their common putative genomic binding sites. The competition is different at different genomic sites, as dictated by the TFs’ expression levels and their divergence in DNA-binding specificity and affinity. Analyses of ChIP-seq data show that the biophysical rules that dictate the competitive...
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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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Research: Ranking noncanonical 5′ splice site usage by genome-wide RNA-seq analysis and splicing reporter assays
- Steffen Erkelenz,
- Stephan Theiss,
- Wolfgang Kaisers,
- Johannes Ptok,
- Lara Walotka,
- Lisa Müller,
- Frank Hillebrand,
- Anna-Lena Brillen,
- Michael Sladek,
- and Heiner Schaal
Genome Res. December 2018 28: 1826-1840; Published in Advance October 24, 2018, doi:10.1101/gr.235861.118
...site carries 10% GNR, and the neighboring GT sites at position −1 have only 2% GNR. This difference in GNR may be due to nonsense-mediated decay (NMD) consistent with out-of-frame transcript removal, since the difference of splice site positions is no multiple of three. In all these cases, noncanonical...
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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
...): View larger version: In this window In a new window Figure 2. SelexGLM shows differences in DNA recognition between AR and GR throughout their binding sites. (A–D) Energy logos for AR-DBD (top) and GR-DBD (bottom), obtained by fitting biophysical models for protein–DNA interaction to the SELEX read...
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Research: Replication timing networks reveal a link between transcription regulatory circuits and replication timing control
- Juan Carlos Rivera-Mulia,
- Sebo Kim,
- Haitham Gabr,
- Abhijit Chakraborty,
- Ferhat Ay,
- Tamer Kahveci,
- and David M. Gilbert
Genome Res. September 2019 29: 1415-1428; Published in Advance August 21, 2019, doi:10.1101/gr.247049.118
...transcription factors were found to bind cooperatively to sites in the affected replication domains, providing provocative evidence that they constitute biologically significant directional interactions. Our findings suggest a regulatory link between the establishment of cell-type–specific TRNs and RT control...
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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
...fraction of putative binding sites (BSs) that are occupied by transcription factors (TFs) in vivo can be highly variable across different cell types. This observation has been partly attributed to changes in chromatin accessibility and histone modification (HM) patterns surrounding BSs. Previous studies...
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