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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
..., hinging on the precise binding of transcription factors (TFs) and cofactors to gene regulatory elements such as promoters and enhancers. Although it is relatively routine to profile -wide DNA binding landscapes of proteins, identifying the specific proteins that bind to, and regulate the transcription of...
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RECOMB 2022 Special/Methods: Learning probabilistic protein–DNA recognition codes from DNA-binding specificities using structural mappings
- Joshua L. Wetzel,
- Kaiqian Zhang,
- and Mona Singh
Genome Res. September 2022 32: 1776-1786; Published in Advance September 19, 2022, doi:10.1101/gr.276606.122
...are expressed in each spatiotemporal context, mutations—within either TFs themselves or the particular genomic regions that they are intended to interact with—can alter gene expression programs and lead to disease phenotypes (for review, see Lee and Young 2013). Because of the central importance of TF...
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Research: A novel quantitative trait locus implicates Msh3 in the propensity for genome-wide short tandem repeat expansions in mice
- Mikhail O. Maksimov,
- Cynthia Wu,
- David G. Ashbrook,
- Flavia Villani,
- Vincenza Colonna,
- Nima Mousavi,
- Nichole Ma,
- Lu Lu,
- Jonathan K. Pritchard,
- Alon Goren,
- Robert W. Williams,
- Abraham A. Palmer,
- and Melissa Gymrek
Genome Res. May 2023 33: 689-702; Published in Advance May 1, 2023, doi:10.1101/gr.277576.122
...opportunity to map genetic determinants of these “mutator phenotypes.” Here, we performed QTL mapping for three quantitative STR mutator phenotypes and identified a robust QTL on Chr 13 for expansion propensity in mice. The QTL region encompasses dozens of protein-coding genes, including Msh3, an important...
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Method: Quantitative insertion-site sequencing (QIseq) for high throughput phenotyping of transposon mutants
- Iraad F. Bronner,
- Thomas D. Otto,
- Min Zhang,
- Kenneth Udenze,
- Chengqi Wang,
- Michael A. Quail,
- Rays H.Y. Jiang,
- John H. Adams,
- and Julian C. Rayner
Genome Res. July 2016 26: 980-989; Published in Advance May 10, 2016, doi:10.1101/gr.200279.115
..., whereas the late phenotypes (>Cycle 12) also reflect within-system growth competition advantages (neutral mutations) and disadvantages (deleterious mutations). When GO term analysis was performed on the different phenotypes, the genes in the ‘losing’ groupwere enriched for genes more likely to be critical...
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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
...Suv39h-catalyzed H3K9me3 is critical for euchromatic organization and the maintenance of gene transcription Christine R. Keenan1,2,4,6, Hannah D. Coughlan1,2,4, Nadia Iannarella1, Andres Tapia del Fierro1,2, Andrew Keniry1,2, Timothy M. Johanson1,2, Wing Fuk Chan1,2,7, Alexandra L. Garnham1...
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Research: tRNA-derived small RNAs are embedded in the gene regulatory network instructing Drosophila metamorphosis
- Junling Shi,
- Jiaqi Xu,
- Jun Ma,
- and Feng He
Genome Res. December 2023 33: 2119-2132; Published in Advance November 16, 2023, doi:10.1101/gr.278128.123
...” and “cuticle development” (adjusted P = 10−7 and 10−14, respectively; Fig. 3B). Therefore, the pupa-accumulated 5′-tsRNA in our test could suppress specific gene activities that are crucial for pupal development.The actions of tsRNAs on gene expression could depend on their recognition sites in targeted m...
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Method: Genome-scale identification of cellular pathways required for cell surface recognition
- Sumana Sharma,
- S. Josefin Bartholdson,
- Amalie C.M. Couch,
- Kosuke Yusa,
- and Gavin J. Wright
Genome Res. September 2018 28: 1372-1382; Published in Advance June 18, 2018, doi:10.1101/gr.231183.117
..., and by selecting those cells with a phenotype of interest, the gene products involved can be identified (Ma et al. 2015; Parnas et al. 2015; Zhang et al. 2016). Here, we use -scale, cell-based CRISPR knockout (KO) screens to determine the molecular basis of cell surface recognition events made by mAbs, secreted...
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Method: Predicting transfer RNA gene activity from sequence and genome context
- Bryan P. Thornlow,
- Joel Armstrong,
- Andrew D. Holmes,
- Jonathan M. Howard,
- Russell B. Corbett-Detig,
- and Todd M. Lowe
Genome Res. January 2020 30: 85-94; Published in Advance December 19, 2019, doi:10.1101/gr.256164.119
...study detected occupancy by RNA Polymerase III (Pol III) for only 224 of 417 high-confidence tRNA genes in human liver, with other mammals showing similar patterns (Kutter et al. 2011).tRNA gene expression may coevolve with phenotypic differences between species. Data from previous studies suggest...
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Research: Blood-derived mitochondrial DNA copy number is associated with gene expression across multiple tissues and is predictive for incident neurodegenerative disease
- Stephanie Y. Yang,
- Christina A. Castellani,
- Ryan J. Longchamps,
- Vamsee K. Pillalamarri,
- Brian O'Rourke,
- Eliseo Guallar,
- and Dan E. Arking
Genome Res. March 2021 31: 349-358; Published in Advance January 13, 2021, doi:10.1101/gr.269381.120
...-Tissue Expression Project, we interrogated relationships between mtDNA-CN measured in whole blood and gene expression from whole blood and 47 additional tissues in 419 individuals. mtDNA-CN was significantly associated with expression of 700 genes in whole blood, including nuclear genes required for mt...
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Research: Conserved microRNA targeting reveals preexisting gene dosage sensitivities that shaped amniote sex chromosome evolution
- Sahin Naqvi,
- Daniel W. Bellott,
- Kathy S. Lin,
- and David C. Page
Genome Res. April 2018 28: 474-483; Published in Advance February 15, 2018, doi:10.1101/gr.230433.117
...obtained from a variety of publicly available data sets. Further details are provided in Supplemental Methods in the section titled “Gene expression profiling and crosslinking datasets.” All fold-changes and CLIP targets are provided in Supplemental Table S6.Software availabilityA custom Python (RRID...
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