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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
...FANTOM5 (Kawaji et al. 2014) or DBTSS (Suzuki et al. 2015). However, for genes expressed at a low level, whole- experiments might not have enough coverage to reliably pinpoint TSS(s).Several databases provide comprehensive DNA methylation data derived from high-throughput sequencing, including single...
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Methods: High-throughput biochemical analysis of in vivo location data reveals novel distinct classes of POU5F1(Oct4)/DNA complexes
- Dean Tantin,
- Matthew Gemberling,
- Catherine Callister,
- and William Fairbrother
Genome Res. April 2008 18: 631-639; Published in Advance January 22, 2008, doi:10.1101/gr.072942.107
...information into a motif finding algorithm. In addition to further refining location studies for transcription factors, this method holds promise for the high-throughput screening of promoters, SNP regions, and epigenetic modifications for factor binding. Gene expression is mediated by the interaction...
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Methods: A novel, high-performance random array platform for quantitative gene expression profiling
- Kenneth Kuhn,
- Shawn C. Baker,
- Eugene Chudin,
- Minh-Ha Lieu,
- Steffen Oeser,
- Holly Bennett,
- Philippe Rigault,
- David Barker,
- Timothy K. McDaniel,
- and Mark S. Chee
Genome Res. November 2004 14: 2347-2356; doi:10.1101/gr.2739104
.... ↵ Fan, J.B., Yeakley, J.M., Bibikova, M., Chudin, E., Wickham, E., Chen, J., Doucet, D., Rigault, P., Zhang, B., Shen, R., et al. 2004 . A versatile assay for high-throughput gene expression profiling on universal array matrices. Genome Res. 14 : 878 -885. ↵ Fingeroth, J.D. 1990 . Comparative structure...
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Research: Wnt signaling activation induces CTCF binding and loop formation at cis-regulatory elements of target genes
- Anna Nordin,
- Chaitali Chakraborty,
- Mattias Jonasson,
- Orgena Dano,
- Gianluca Zambanini,
- Pierfrancesco Pagella,
- Silvia Remeseiro,
- and Claudio Cantù
Genome Res. August 2025 35: 1701-1716; Published in Advance June 23, 2025, doi:10.1101/gr.279684.124
...of differentially expressed genes (Log2FC > 0.5, adj. P < 0.05) in Wnt-ON versus Wnt-OFF.CTCF and beta-catenin come into physical proximity upon Wnt activationA comparison of beta-catenin and LEF1 data (Zambanini et al. 2022) and CTCF -wide binding profiles revealed—as the motifs indicated—that RUW sites could also...
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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
..., Zibo Zhao5, Avani P. Shah5, Katherine Novitzky6, Eileen McAnarney6, Michael-C. Keogh6, Ali Shilatifard5, Uttiya Basu4, Martha L. Bulyk3,7 and B. Franklin Pugh1,2 1Center for Eukaryotic Gene Regulation, Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park...
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Research: Combinatorial binding of transcription factors in the pluripotency control regions of the genome
- Luciana Ferraris,
- Allan P. Stewart,
- Jinsuk Kang,
- Alec M. DeSimone,
- Matthew Gemberling,
- Dean Tantin,
- and William G. Fairbrother
Genome Res. July 2011 21: 1055-1064; Published in Advance April 28, 2011, doi:10.1101/gr.115824.110
...binding assay. Both genomic regions contain equally strong matches to the octamer site (ATGCA[A/T]AT, 4C!T inboth regions) and two FOXO1binding sites (TTGTTT) (Fig. 5A). These oligonucleotides map to in vivo regions of POU5F1 binding and are located upstream of ERMN and RAB5A genes. We performed a series...
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Research: Genetic analysis of complex traits in the emerging Collaborative Cross
- David L. Aylor,
- William Valdar,
- Wendy Foulds-Mathes,
- Ryan J. Buus,
- Ricardo A. Verdugo,
- Ralph S. Baric,
- Martin T. Ferris,
- Jeff A. Frelinger,
- Mark Heise,
- Matt B. Frieman,
- Lisa E. Gralinski,
- Timothy A. Bell,
- John D. Didion,
- Kunjie Hua,
- Derrick L. Nehrenberg,
- Christine L. Powell,
- Jill Steigerwalt,
- Yuying Xie,
- Samir N.P. Kelada,
- Francis S. Collins,
- Ivana V. Yang,
- David A. Schwartz,
- Lisa A. Branstetter,
- Elissa J. Chesler,
- Darla R. Miller,
- Jason Spence,
- Eric Yi Liu,
- Leonard McMillan,
- Abhishek Sarkar,
- Jeremy Wang,
- Wei Wang,
- Qi Zhang,
- Karl W. Broman,
- Ron Korstanje,
- Caroline Durrant,
- Richard Mott,
- Fuad A. Iraqi,
- Daniel Pomp,
- David Threadgill,
- Fernando Pardo-Manuel de Villena,
- and Gary A. Churchill
Genome Res. August 2011 21: 1213-1222; Published in Advance March 15, 2011, doi:10.1101/gr.111310.110
...) for characterization of innate immune response and to The Jackson Laboratory ( JAX) for gene expression analysis. In addition to these four study arms, phenotyping efforts were also performed using different sets of mice at the ORNL and Tel Aviv University (TAU) breeding facilities. Here we present the first genetic...
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Research: CRX ChIP-seq reveals the cis-regulatory architecture of mouse photoreceptors
- Joseph C. Corbo,
- Karen A. Lawrence,
- Marcus Karlstetter,
- Connie A. Myers,
- Musa Abdelaziz,
- William Dirkes,
- Karin Weigelt,
- Martin Seifert,
- Vladimir Benes,
- Lars G. Fritsche,
- Bernhard H.F. Weber,
- and Thomas Langmann
Genome Res. November 2010 20: 1512-1525; Published in Advance August 6, 2010, doi:10.1101/gr.109405.110
...and assayed their activity in electroporated retinas. A minimal basal promoter including the first 35 bp upstream of the TATA box of the bovine Rho gene and containing a single CRX site fails to drive any expression in electroporated mouse retinas (Supplemental Fig. S6D). Addition of a synthetic 50-bp DNA...
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Research: Dynamic evolution of satellite DNAs drastically differentiates the genomes of Tribolium sibling species
- Damira Veseljak,
- Evelin Despot-Slade,
- Marin Volarić,
- Lucija Horvat,
- Tanja Vojvoda Zeljko,
- Nevenka Meštrović,
- and Brankica Mravinac
Genome Res. November 2025 35: 2445-2460; Published in Advance September 16, 2025, doi:10.1101/gr.280516.125
...-occurring (Fig. 1C), but similar average distances (4–5 kb) between satDNA arrays and the closest annotated element were observed for all three addressed sequence types (genes, satDNAs, TEs) (Supplemental Table S7).Having obtained a general overview of the T. freemani satellitome, we next focused on the in...
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Methods: Chromosome Conformation Capture Carbon Copy (5C): A massively parallel solution for mapping interactions between genomic elements
- Josée Dostie,
- Todd A. Richmond,
- Ramy A. Arnaout,
- Rebecca R. Selzer,
- William L. Lee,
- Tracey A. Honan,
- Eric D. Rubio,
- Anton Krumm,
- Justin Lamb,
- Chad Nusbaum,
- Roland D. Green,
- and Job Dekker
Genome Res. October 2006 16: 1299-1309; Published in Advance September 5, 2006, doi:10.1101/gr.5571506
...individually by PCR. Here we present a high-throughput 3C approach, 3C-Carbon Copy (5C), that employs microarrays or quantitative DNA sequencing using 454-technology as detection methods. We applied 5C to analyze a 400-kb region containing the human β-globin locus and a 100-kb conserved gene desert region. We...

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