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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
...techniques have been developed that monitor transcription as it occurs. Pioneering work introduced methods such as global run-on sequencing (GRO-seq) (Core and Lis 2008) and precision nuclear run-on sequencing (PRO-seq) (Kwak et al. 2013), which measure the location and activity of engaged RNA polymerase II...
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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
...European Molecular Biology Laboratory (EMBL), Structural and Computational Biology Unit, D-69117 Heidelberg, Germany; 3Collaboration for Joint PhD Degree between EMBL and Heidelberg University, Faculty of Biosciences, D-69117 Heidelberg, Germany; 4Aix Marseille Univ, INSERM, TAGC, 13009 Marseille, France...
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Method: Profiling the quantitative occupancy of myriad transcription factors across conditions by modeling chromatin accessibility data
- Kaixuan Luo,
- Jianling Zhong,
- Alexias Safi,
- Linda K. Hong,
- Alok K. Tewari,
- Lingyun Song,
- Timothy E. Reddy,
- Li Ma,
- Gregory E. Crawford,
- and Alexander J. Hartemink
Genome Res. June 2022 32: 1183-1198; Published in Advance May 24, 2022, doi:10.1101/gr.272203.120
...traits are located in noncoding genomic regions (Hindorff et al. 2009), suggesting roles in transcriptional regulation. To elucidate this, it is imperative that we continue to identify genetic variants affecting TF occupancy and chromatin dynamics. To examine whether TOP is capable of sensitively...
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Method: Pooled analysis of radiation hybrids identifies loci for growth and drug action in mammalian cells
- Arshad H. Khan,
- Andy Lin,
- Richard T. Wang,
- Joshua S. Bloom,
- Kenneth Lange,
- and Desmond J. Smith
Genome Res. October 2020 30: 1458-1467; Published in Advance September 2, 2020, doi:10.1101/gr.262204.120
...yet to be performed in mammalian cells (Yang et al. 2011; Arnoldo et al. 2014). In addition, cDNA screens typically omit novel isoforms, whose number exceeds that of known transcripts (Škalamera et al. 2011; Eksi et al. 2013; Li et al. 2014), as well as noncoding genes (Derrien et al. 2012; Kozomara...
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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
...Yuning Zhang1,2, Tiffany D. Ho1,3, Nicolas E. Buchler4 and Raluca Gordân1,3,5 1Center for Genomic and Computational Biology, Duke University, Durham, North Carolina 27708, USA; 2Program in Computational Biology and Bioinformatics, Duke University, Durham, North Carolina 27708, USA; 3Department...
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Method: Locating protein-coding sequences under selection for additional, overlapping functions in 29 mammalian genomes
- Michael F. Lin,
- Pouya Kheradpour,
- Stefan Washietl,
- Brian J. Parker,
- Jakob S. Pedersen,
- and Manolis Kellis
Genome Res. November 2011 21: 1916-1928; Published in Advance October 12, 2011, doi:10.1101/gr.108753.110
...Locating protein-coding sequences under selection for additional, overlapping functions in 29 mammalian genomes Michael F. Lin 1 , 2 , Pouya Kheradpour 1 , 2 , Stefan Washietl 2 , Brian J. Parker 3 , Jakob S. Pedersen 3 , 5...
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Method: Simple and efficient profiling of transcription initiation and transcript levels with STRIPE-seq
- Robert A. Policastro,
- R. Taylor Raborn,
- Volker P. Brendel,
- and Gabriel E. Zentner
Genome Res. June 2020 30: 910-923; Published in Advance July 6, 2020, doi:10.1101/gr.261545.120
..., current protocols for -wide TSS profiling are laborious and/or expensive. We present Survey of TRanscription Initiation at Promoter Elements with high-throughput sequencing (STRIPE-seq), a simple, rapid, and cost-effective protocol for sequencing capped RNA 5′ ends from as little as 50 ng total RNA...
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Resource: Integration of high-resolution promoter profiling assays reveals novel, cell type–specific transcription start sites across 115 human cell and tissue types
- Jill E. Moore,
- Xiao-Ou Zhang,
- Shaimae I. Elhajjajy,
- Kaili Fan,
- Henry E. Pratt,
- Fairlie Reese,
- Ali Mortazavi,
- and Zhiping Weng
Genome Res. February 2022 32: 389-402; Published in Advance December 23, 2021, doi:10.1101/gr.275723.121
...biochemically and transcriptionally active in the evaluated cell types, GENCODE TSSs correspond to transcripts expressed in other cell types that have not been surveyed by the RAMPAGE assay. Therefore, for cell type–agnostic data analyses, we suggest users supplement GENCODE TSS annotations with RAMPAGE...
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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
...of candidate CRE regions The genomic locations of CREs can be predicted by the patterns of phylogenetic conservation, the occurrence of transcription factor binding sites, and the presence of various chromatin features (Levo and Segal 2014; Shlyueva et al. 2014). DNase I hypersensitive (DHS) sites, which...
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Research: Divergence of a conserved elongation factor and transcription regulation in budding and fission yeast
- Gregory T. Booth,
- Isabel X. Wang,
- Vivian G. Cheung,
- and John T. Lis
Genome Res. June 2016 26: 799-811; Published in Advance May 12, 2016, doi:10.1101/gr.204578.116
...cerevisiae (Hahn and Young 2011; Pelechano and Steinmetz 2013). However, although location and production of genomic RNA has been investigated in fission yeast (Wilhelm et al. 2008; DeGennaro et al. 2013), various aspects of the transcriptional landscape of Schizosaccharomyces pombe remain more vague...

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