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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
..., and cell state–dependent protein dynamics. In this review, we dissect the strengths, limitations, and biological relevance of current approaches for studying direct protein–DNA interactions, distinguishing between protein-centric and DNA-centric methodologies. We introduce a conceptual matrix of biological...
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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
...to explore interactions that involve more than one mutant. For example, SWI4 and SWI6 are key TFs enacting G1/S-specific transcription, and together they form a complex to bind to and regulate genes involved in DNA synthesis and repair (Sidorova and Breeden 1993). The individual deletions of SWI4 (swi4Δ...
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Research: Characterization of human transcription factor function and patterns of gene regulation in HepG2 cells
- Belle A. Moyers,
- E. Christopher Partridge,
- Mark Mackiewicz,
- Michael J. Betti,
- Roshan Darji,
- Sarah K. Meadows,
- Kimberly M. Newberry,
- Laurel A. Brandsmeier,
- Barbara J. Wold,
- Eric M. Mendenhall,
- and Richard M. Myers
Genome Res. November 2023 33: 1879-1892; Published in Advance October 18, 2023, doi:10.1101/gr.278205.123
...of the human cell line HepG2 and show the usefulness of large genomic analyses for elucidation of individual TF functions.Gene expression is regulated and modulated by the association, either direct or indirect, of various classes of proteins to DNA, including RNA polymerase and transcription...
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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
...was correlated with the degree of DNase depletion at the motif (Supplemental Fig. S8). For TFs with higher prediction accuracy, like NRF1 and ATF1, we observed clear profiles of depletion within motif regions and elevation at nearby flanking regions (Supplemental Fig. S9), suggesting direct TF–DNA contact. Many...
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Research: Sir3 mediates long-range chromosome interactions in budding yeast
- Myriam Ruault,
- Vittore F. Scolari,
- Luciana Lazar-Stefanita,
- Antoine Hocher,
- Isabelle Loïodice,
- Romain Koszul,
- and Angela Taddei
Genome Res. March 2021 31: 411-425; Published in Advance February 12, 2021, doi:10.1101/gr.267872.120
...on several DNA mechanisms, including genetic regulation, the maintenance of chromosomal stability, or also compaction and folding throughout the cell cycle. Chromatin tethering or colocalization involves a variety of direct or indirect molecular mechanisms, such as cohesin-mediated loop formation (Nasmyth...
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Method: MEDEA: analysis of transcription factor binding motifs in accessible chromatin
- Luca Mariani,
- Kathryn Weinand,
- Stephen S. Gisselbrecht,
- and Martha L. Bulyk
Genome Res. May 2020 30: 736-748; Published in Advance May 18, 2020, doi:10.1101/gr.260877.120
...-factor-binding-site-prediction-challenge/).To identify TFBSs, DNase-seq data are often mined for digital footprints (DFPs), which are short (∼10 bp) sharp decreases of accessibility within open chromatin regions, suggesting the presence of bound proteins (i.e., TFs) that locally protect the DNA from DNase I cleavage (Hesselberth et al. 2009; Pique...
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Resource: A ChIP-exo screen of 887 Protein Capture Reagents Program transcription factor antibodies in human cells
- William K.M. Lai,
- Luca Mariani,
- Gerson Rothschild,
- Edwin R. Smith,
- Bryan J. Venters,
- Thomas R. Blanda,
- Prashant K. Kuntala,
- Kylie Bocklund,
- Joshua Mairose,
- Sarah N. Dweikat,
- Katelyn Mistretta,
- Matthew J. Rossi,
- Daniela James,
- James T. Anderson,
- Sabrina K. Phanor,
- Wanwei Zhang,
- Zibo Zhao,
- Avani P. Shah,
- Katherine Novitzky,
- Eileen McAnarney,
- Michael-C. Keogh,
- Ali Shilatifard,
- Uttiya Basu,
- Martha L. Bulyk,
- and B. Franklin Pugh
Genome Res. September 2021 31: 1663-1679; Published in Advance August 23, 2021, doi:10.1101/gr.275472.121
...component of a wide variety of biochemical assays. They serve as protein-specific affinity-capture and detection reagents, useful in vivo and in vitro. Example assays include chromatin immunoprecipitation (ChIP) of protein–DNA interactions, immunofluorescence, immunoblotting, ELISA, purification of cells...
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Method: Anchor: trans-cell type prediction of transcription factor binding sites
- Hongyang Li,
- Daniel Quang,
- and Yuanfang Guan
Genome Res. February 2019 29: 281-292; Published in Advance December 19, 2018, doi:10.1101/gr.237156.118
...be applied to the remaining missing pairs. A major challenge is that TF binding sites are cell-type–specific, which can be attributed to cellular contexts such as chromatin accessibility. Meanwhile, indirect TF-DNA binding and interactions between TFs complicate this regulatory process. Technical issues...
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Research: Noncoding transcription influences the replication initiation program through chromatin regulation
- Julien Soudet,
- Jatinder Kaur Gill,
- and Françoise Stutz
Genome Res. December 2018 28: 1882-1893; Published in Advance November 6, 2018, doi:10.1101/gr.239582.118
.... Bottom panel shows a zoom around ARS1320 of the RNA Pol II PAR-CLIP in the Nrd1-AA strain (Schaughency et al. 2014). Transcriptional readthrough is indicated by an arrow. (E) Plot depicting the mean coverage of BrdU nascent DNA in a 5-kb window around ACS in −Rap versus +Rap. The 17 red dots and 19...
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Method: Inhibition of transcription leads to rewiring of locus-specific chromatin proteomes
- Deepani W. Poramba-Liyanage,
- Tessy Korthout,
- Christine E. Cucinotta,
- Ila van Kruijsbergen,
- Tibor van Welsem,
- Dris El Atmioui,
- Huib Ovaa,
- Toshio Tsukiyama,
- and Fred van Leeuwen
Genome Res. April 2020 30: 635-646; Published in Advance March 18, 2020, doi:10.1101/gr.256255.119
...that Ctr9 has a transcription elongation–independent mechanism to bind to DNA, perhaps mediated by its known interactions with DNA and nucleosomes (Musso et al. 2000; Deng et al. 2018; Vos et al. 2018). These binding activities may be responsible for anchoring Ctr9 to PH-perturbed chromatin in the absence...
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