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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
...hypersensitivity), high nucleosomal turnover (e.g., high levels of rapid-turnover histones H2A.Z and H3.3), specific epigenetic markers (e.g., high ratio of H3K4me1 and H3K4me2 to H3K4me3, high ratio of 5hmC to 5mC, enrichment of H3K27ac), chromatin loops in direct contact with the core promoter (enrichment...
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Method: Identification of human silencers by correlating cross-tissue epigenetic profiles and gene expression
- Di Huang,
- Hanna M. Petrykowska,
- Brendan F. Miller,
- Laura Elnitski,
- and Ivan Ovcharenko
Genome Res. April 2019 29: 657-667; Published in Advance March 18, 2019, doi:10.1101/gr.247007.118
...of putative TFBSs along its DNA sequence (as detailed below), the signal intensity of several histone modifications (including H3K4me1, H3K4me2, H3K4me3, H3K27ac, H3K79me1, H3K9ac, H3K9me3, H2A.Z, and H3K36me3), as well as the maximum and minimum of the expressions of proximal genes. The values of each...
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Research: Disclosing the crosstalk among DNA methylation, transcription factors, and histone marks in human pluripotent cells through discovery of DNA methylation motifs
- Phuc-Loi Luu,
- Hans R. Schöler,
- and Marcos J. Araúzo-Bravo
Genome Res. December 2013 23: 2013-2029; Published in Advance October 22, 2013, doi:10.1101/gr.155960.113
...cell to FBs (Fig. 5C). The last type is formed by the active transcription marks (H3K4me2, H3K79me2, H3K4me3) (Sims and Reinberg 2006; Koch et al. 2007; Steger et al. 2008) that have the highest correlation with CpGMM targets, independently of the cell or the CpGMM type. To clarify the distinctive role...
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Research: EHMT2 directs DNA methylation for efficient gene silencing in mouse embryos
- Ghislain Auclair,
- Julie Borgel,
- Lionel A. Sanz,
- Judith Vallet,
- Sylvain Guibert,
- Michael Dumas,
- Patricia Cavelier,
- Michael Girardot,
- Thierry Forné,
- Robert Feil,
- and Michael Weber
Genome Res. February 2016 26: 192-202; Published in Advance November 17, 2015, doi:10.1101/gr.198291.115
...) (Liu et al. 2015), H3K4me2 in ESCs (GEO accession no. GSE30203) (Stadler et al. 2011), and H3K9me2 in E8.5 embryos (this study). To generate the heatmaps, we counted the density of reads from theChIP-seqWIG files in 200-bpwindows and divided by the density of reads in the same windows...
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Research: Evolutionary conservation of the eumetazoan gene regulatory landscape
- Michaela Schwaiger,
- Anna Schönauer,
- André F. Rendeiro,
- Carina Pribitzer,
- Alexandra Schauer,
- Anna F. Gilles,
- Johannes B. Schinko,
- Eduard Renfer,
- David Fredman,
- and Ulrich Technau
Genome Res. April 2014 24: 639-650; Published in Advance March 18, 2014, doi:10.1101/gr.162529.113
...the distributions of H3K4me3, H3K4me2, and H3K27ac are very similar (Fig. 1B; Supplemental Fig. S1), H3K36me3 is enriched within gene bodies of the same genes, starting immediately after the TSS. CpG methylation localizes to gene bodies (Zemach et al. 2010) and its levels correlate with H3K36me3 (Fig. 1B...
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Research: Characterization of the neural stem cell gene regulatory network identifies OLIG2 as a multifunctional regulator of self-renewal
- Juan L. Mateo,
- Debbie L.C. van den Berg,
- Maximilian Haeussler,
- Daniela Drechsel,
- Zachary B. Gaber,
- Diogo S. Castro,
- Paul Robson,
- Q. Richard Lu,
- Gregory E. Crawford,
- Paul Flicek,
- Laurence Ettwiller,
- Joachim Wittbrodt,
- François Guillemot,
- and Ben Martynoga
Genome Res. January 2015 25: 41-56; Published in Advance October 7, 2014, doi:10.1101/gr.173435.114
...signal for H3K4me2 and H3K4me3 than distal cluster 2 (Fig. 1C,E; Supplemental Fig. S2B,C). Distal cluster 5 regions were the only distal DHSs marked with H3K27me3. The remaining clusters (distal clusters 3 and 4) possessed a H3K4me1+, H3K27ac-low profile that has previously been designated as a poised...
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Research: Comprehensive functional annotation of ESR1-driven enhancers in breast cancer reveals hierarchical activity independent of genomic and epigenomic contexts
- Yanis Zekri,
- Sebastian Gregoricchio,
- Elif Yapıcı,
- Chia-Chi Flora Huang,
- Tunç Morova,
- Umut Berkay Altıntaş,
- Gozde Korkmaz,
- Nathan A. Lack,
- and Wilbert Zwart
Genome Res. July 2025 35: 1530-1543; Published in Advance June 10, 2025, doi:10.1101/gr.280320.124
...data sets used is given in Supplemental Table 3. (E) Heat map of overlap between ERBS subgroups and 73 histone mark data sets (Supplemental Table 4). Active (red) and repressive (blue) histone marks are indicated. (F) Average density profiles for H3K4me1, H3K4me2, H3K4me3, and H3K27ac at ERBS in MCF-7...
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Research: Coassembly of REST and its cofactors at sites of gene repression in embryonic stem cells
- Hong-Bing Yu,
- Rory Johnson,
- Galih Kunarso,
- and Lawrence W. Stanton
Genome Res. August 2011 21: 1284-1293; Published in Advance June 1, 2011, doi:10.1101/gr.114488.110
...at RE1 sites may be an important factor in productive gene repression. To test this, we performed similar clustering analysis using available wide epigenetic maps derived from ESC (Fig. 3B). We included maps of histone modifications associated with active enhancers (H3K4me1, H3K4me2), active promoters...
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Research: Systematic identification and characterization of exon–intron circRNAs
- Yinchun Zhong,
- Yan Yang,
- Xiaolin Wang,
- Bingbing Ren,
- Xueren Wang,
- Ge Shan,
- and Liang Chen
Genome Res. March 2024 34: 376-393; Published in Advance April 12, 2024, doi:10.1101/gr.278590.123
...and RNAPII Ser2P ChIP-seq signals around the transcription start site (TSS) regions of the indicated groups of genes in the K562, GM12878, and HeLa-S3 cell lines. (E) DNase-seq and ChIP-seq signals of H3K9ac, H3K27ac, H3K4me1, H3K4me2, H3K4me3, and H3K79me2 around the TSS regions of the indicated group...
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Research: Genome-wide profiles of H3K9me3, H3K27me3 modifications, and DNA methylation during diapause of Asian corn borer (Ostrinia furnacalis)
- Pengfei Lv,
- Xingzhuo Yang,
- Xianguo Zhao,
- Zhangwu Zhao,
- and Juan Du
Genome Res. May 2024 34: 725-739; Published in Advance June 12, 2024, doi:10.1101/gr.278661.123
...and H3K27me3 were significantly down-regulated in the head of diapause larvae (Fig. 1A,B). However, H3K4me2, H3K14ac, and H3K27ac remained unaffected (Fig. 1C–E). Additionally, H3K9me3 and H3K27me3 were also found to be down-regulated in the body of diapause larvae (Supplemental Fig. S1A,B). Note...

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