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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
...-base resolution methylation levels for individual CpG sites across the . These resources also annotate hypomethylated regions commonly linked to gene promoters, as well as allele-specific methylation patterns relevant to genomic imprinting. Notable examples include MethBase (Song et al. 2013), MethBank (Zhang et...
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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
...successfully identified differential CTCF occupancy between individuals across CEU and YRI families (Fig. 6A) and was sensitive enough to capture quantitative differences in CTCF occupancy between allele genotypes at allele-specific sites within CEU and YRI families (Fig. 6B).View larger version...
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Method: A powerful and flexible statistical framework for testing hypotheses of allele-specific gene expression from RNA-seq data
- Daniel A. Skelly,
- Marnie Johansson,
- Jennifer Madeoy,
- Jon Wakefield,
- and Joshua M. Akey
Genome Res. October 2011 21: 1728-1737; Published in Advance August 26, 2011, doi:10.1101/gr.119784.110
...loci that show unusual and biologically interesting patterns of ASE, including allele-specific alternative splicing and transcription termination sites. Our methodology provides a rigorous, quantitative, and high-resolution tool for profiling ASE across whole genomes. Footnotes ↵ 3...
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Research: Massive variation of short tandem repeats with functional consequences across strains of Arabidopsis thaliana
- Maximilian O. Press,
- Rajiv C. McCoy,
- Ashley N. Hall,
- Joshua M. Akey,
- and Christine Queitsch
Genome Res. August 2018 28: 1169-1178; Published in Advance July 3, 2018, doi:10.1101/gr.231753.117
...allele-specific mRNA species were formed (Supplemental Fig. S6; Supplemental Text). The MEE36 STR expansion alleles were associated with dramatically reduced MEE36 transcript levels (Fig. 2F), possibly due to the STR expansion altering transcript processing (Jackson 1993). Although due to numerous other...
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Resource: Multitissue single-nucleus RNA-seq reveals cell type–specific regulatory patterns of alternative polyadenylation in pigs
- Qiuhan Wen,
- Zhen Wang,
- Qi Bao,
- Tianli Ding,
- Haihan Zhang,
- Jianbo Li,
- Zhuang Liu,
- Jieping Huang,
- and Guoqiang Yi
Genome Res. September 2025 35: 2116-2129; Published in Advance June 16, 2025, doi:10.1101/gr.280095.124
.... 4G).Enrichment of eQTLs and sQTLs in the 3′ UTRs of different cell typesTo explore the functional relationship between 3′ UTR length, gene expression, and splice site regulation across various tissues and cell types, we first retrieved eQTL and sQTL data from the PigGTEx database (Teng et al. 2024...
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Research: Diverse environmental perturbations reveal the evolution and context-dependency of genetic effects on gene expression levels
- Amanda J. Lea,
- Julie Peng,
- and Julien F. Ayroles
Genome Res. October 2022 32: 1826-1839; Published in Advance October 13, 2022, doi:10.1101/gr.276430.121
..., and 786452).To validate and contextualize the eQTLs we identified, we performed two follow-up analyses: (1) we tested for an expected mechanistic pattern, namely, enrichment of eQTLs within accessible chromatin regions and active regulatory regions, and (2) we tested for overlap between our eQTL...
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Research: Sex differences in human adipose tissue gene expression and genetic regulation involve adipogenesis
- Warren D. Anderson,
- Joon Yuhl Soh,
- Sarah E. Innis,
- Alexis Dimanche,
- Lijiang Ma,
- Carl D. Langefeld,
- Mary E. Comeau,
- Swapan K. Das,
- Eric E. Schadt,
- Johan L.M. Björkegren,
- and Mete Civelek
Genome Res. October 2020 30: 1379-1392; Published in Advance September 23, 2020, doi:10.1101/gr.264614.120
.... Approximately 30% of the eQTL SNPs were within transcription start sites, enhancers, or transcribed regions.Based on data showing that females exhibit a higher degree of heritability for cardiometabolic traits (Pulit et al. 2017), we evaluated the SNP-based narrow-sense heritability of gene expression in a sex...
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Perspective: Applications of single-cell genomics and computational strategies to study common disease and population-level variation
- Benjamin J. Auerbach,
- Jian Hu,
- Muredach P. Reilly,
- and Mingyao Li
Genome Res. October 2021 31: 1728-1741; doi:10.1101/gr.275430.121
..., and coexpression between cells, are genetically heritable and are masked when examining whole-tissue expression across cells. Later studies by Jiang et al. (2017) and Larsson et al. (2019) further provided evidence of genetically determined bursting kinetics. In particular, through -wide analysis of allele-specific...
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