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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
...are available for predicting the presence of CpG islands in DNA sequences. Examples include the CpGplot tool from the European Molecular Biology Open Software Suite (EMBOSS) (Rice et al. 2000), the CpG Island Searcher (Takai and Jones 2003), CpGProD (Ponger and Mouchiroud 2002), and CpGPAP (Chuang et al. 2012...
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Mini-Review: The paradox of R-loops: guardians of the genome or drivers of disease?
- Shachinthaka D. Dissanayaka Mudiyanselage,
- Phillip Wulfridge,
- and Kavitha Sarma
Genome Res. September 2025 35: 1919-1928; Published in Advance August 6, 2025, doi:10.1101/gr.278992.124
...RNA-polymerase-II-transcribed genes. Cell 151: 835–846. doi:10.1016/j.cell.2012.09.041 ↵Arab K, Karaulanov E, Musheev M, Trnka P, Schäfer A, Grummt I, Niehrs C. 2019. GADD45A binds R-loops and recruits TET1 to CpG island promoters. Nat Genet 51: 217–223. doi:10.1038/s41588-018-0306-6 ↵Ariel F, Lucero...
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Research: Decoding the function of bivalent chromatin in development and cancer
- Dhirendra Kumar,
- Senthilkumar Cinghu,
- Andrew J. Oldfield,
- Pengyi Yang,
- and Raja Jothi
Genome Res. December 2021 31: 2170-2184; Published in Advance October 19, 2021, doi:10.1101/gr.275736.121
...plots showing the distribution of CpG dinucleotide frequency at promoters (±500 bp of TSS) of genes within each the four classes defined in Figure 2B. (E) Statistics summarizing the performance of the multinomial logistic regression-based machine learning method for predicting chromatin state of mouse...
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Research: A genome-wide analysis of common fragile sites: What features determine chromosomal instability in the human genome?
- Arkarachai Fungtammasan,
- Erin Walsh,
- Francesca Chiaromonte,
- Kristin A. Eckert,
- and Kateryna D. Makova
Genome Res. June 2012 22: 993-1005; Published in Advance March 28, 2012, doi:10.1101/gr.134395.111
...of biological interpretability and high R-squared value), aCFSs are predominantly located in G-negative chromosomal bands and away from centromeres, are enriched in Alu repeats, and have high DNA flexibility. In alternative models, CpG island density, H3K4me1 coverage, and mononucleotide microsatellite...
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Research: Cohesin-based chromatin interactions enable regulated gene expression within preexisting architectural compartments
- Vlad C. Seitan,
- Andre J. Faure,
- Ye Zhan,
- Rachel Patton McCord,
- Bryan R. Lajoie,
- Elizabeth Ing-Simmons,
- Boris Lenhard,
- Luca Giorgetti,
- Edith Heard,
- Amanda G. Fisher,
- Paul Flicek,
- Job Dekker,
- and Matthias Merkenschlager
Genome Res. December 2013 23: 2066-2077; Published in Advance September 3, 2013, doi:10.1101/gr.161620.113
...of the H3K4me3 histone modification; the binding of RAD21, CTCF, NIPBL, andMediator, RNA Pol II, paused RNA Pol II at the promoter (Hendrix et al. 2008); the presence of promoter CpG islands (CGI); and gene length. We determined the relative importance of each variable in the multivariate model and ranked...
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Research: Kinetics of Xist-induced gene silencing can be predicted from combinations of epigenetic and genomic features
- Lisa Barros de Andrade e Sousa,
- Iris Jonkers,
- Laurène Syx,
- Ilona Dunkel,
- Julie Chaumeil,
- Christel Picard,
- Benjamin Foret,
- Chong-Jian Chen,
- John T. Lis,
- Edith Heard,
- Edda G. Schulz,
- and Annalisa Marsico
Genome Res. July 2019 29: 1087-1099; Published in Advance June 7, 2019, doi:10.1101/gr.245027.118
...features, we defined 18 genomic features, including distance of each gene's TSS to the Xist locus, the next TAD border, or the next full-length LINE element; gene overlap with LADs, LINEs, and CpG islands; and strength and number of 3D chromatin interactions of gene promoters with other genomic elements...
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Method: Effect of minichromosome maintenance protein 2 deficiency on the locations of DNA replication origins
- Dimiter Kunnev,
- Amy Freeland,
- Maochun Qin,
- Robert W. Leach,
- Jianmin Wang,
- Rajani M. Shenoy,
- and Steven C. Pruitt
Genome Res. April 2015 25: 558-569; Published in Advance March 11, 2015, doi:10.1101/gr.176099.114
...defined regions of the . A recurrent observation from studies based on SNS prepared using lambda exonuclease is that sequences from CpG islands, and GC-rich regions of the chromosome generally, are enriched. Corresponding author: steven.pruitt@roswellpark.org Article published online before print. Article...
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Research: Epigenetic modification and inheritance in sexual reversal of fish
- Changwei Shao,
- Qiye Li,
- Songlin Chen,
- Pei Zhang,
- Jinmin Lian,
- Qiaomu Hu,
- Bing Sun,
- Lijun Jin,
- Shanshan Liu,
- Zongji Wang,
- Hongmei Zhao,
- Zonghui Jin,
- Zhuo Liang,
- Yangzhen Li,
- Qiumei Zheng,
- Yong Zhang,
- Jun Wang,
- and Guojie Zhang
Genome Res. April 2014 24: 604-615; Published in Advance February 2, 2014, doi:10.1101/gr.162172.113
...showed that the majority of CpGs in exons, introns, and repeats were hypermethylated (methylation level >0.75), whereas hypomethylated CpGs (methylated level <0.25) were relatively enriched in gene promoters and CpG islands (CGIs) (Fig. 1E; Supplemental Fig. S3B). Furthermore, ovary harboredmore...

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