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Perspective: Understanding the regulatory and transcriptional complexity of the genome through structure
- Tim R. Mercer and
- John S. Mattick
Genome Res. July 2013 23: 1081-1088; doi:10.1101/gr.156612.113
...GL. 2011. Diverse gene reprogramming events occur in the same spatial clusters of distal regulatory elements. Genome Res 21: 697–706. Hakim O, Sung MH, Nakayamada S, Voss TC, Baek S, Hager GL. 2013. Spatial congregation of STAT binding directs selective nuclear architecture during T-cell functional...
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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
...of regulation by DNA methylation, depending on factors such as cell type, developmental stage, and environmental conditions (Gardiner-Garden and Frommer 1987; Jaenisch and Bird 2003; Illingworth and Bird 2009; Loyfer et al. 2023). CG-rich sequences are predominantly found in the 5′-flanking regions of genes...
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Research: Transposon wave remodeled the epigenomic landscape in the rapid evolution of X-Chromosome dosage compensation
- David C.H. Metzger,
- Imogen Porter,
- Brendan Mobley,
- Benjamin A. Sandkam,
- Lydia J.M. Fong,
- Andrew P. Anderson,
- and Judith E. Mank
Genome Res. November 2023 33: 1917-1931; Published in Advance November 21, 2023, doi:10.1101/gr.278127.123
...substantially between the sexes.Genomic regions with sex-biased DNA methylation are enriched for YY1 motifsWe next examined the DNA sequences of the DMRs for the possibility of enriched regulatory elements. Analysis of DMR sequences on the sex chromosome identified 35 putative regulatory elements enriched...
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Research: DNA methylation epitypes highlight underlying developmental and disease pathways in acute myeloid leukemia
- Brian Giacopelli,
- Min Wang,
- Ada Cleary,
- Yue-Zhong Wu,
- Anna Reister Schultz,
- Maximilian Schmutz,
- James S. Blachly,
- Ann-Kathrin Eisfeld,
- Bethany Mundy-Bosse,
- Sebastian Vosberg,
- Philipp A. Greif,
- Rainer Claus,
- Lars Bullinger,
- Ramiro Garzon,
- Kevin R. Coombes,
- Clara D. Bloomfield,
- Brian J. Druker,
- Jeffrey W. Tyner,
- John C. Byrd,
- and Christopher C. Oakes
Genome Res. May 2021 31: 747-761; Published in Advance March 11, 2021, doi:10.1101/gr.269233.120
...uncovered that E13 uses other disease-specific pathways, DNMT3A in the context of E13 may have primarily played a role in premalignant stages or has a non-DNA methylation-dependent role.Because DNA methylation is an important factor controlling gene regulation, in addition to epitype classification, it can...
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Method: Genome-wide determination of RNA stability reveals hundreds of short-lived noncoding transcripts in mammals
- Hidenori Tani,
- Rena Mizutani,
- Kazi Abdus Salam,
- Keiko Tano,
- Kenichi Ijiri,
- Ai Wakamatsu,
- Takao Isogai,
- Yutaka Suzuki,
- and Nobuyoshi Akimitsu
Genome Res. May 2012 22: 947-956; Published in Advance February 27, 2012, doi:10.1101/gr.130559.111
...Genome-wide determination of RNA stability reveals hundreds of short-lived noncoding transcripts in mammals Hidenori Tani 1 , Rena Mizutani 1 , Kazi Abdus Salam 1 , Keiko Tano 1 , Kenichi Ijiri 1 , Ai Wakamatsu 2 , Takao Isogai...
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Research: A nucleosome turnover map reveals that the stability of histone H4 Lys20 methylation depends on histone recycling in transcribed chromatin
- J. Peter Svensson,
- Manu Shukla,
- Victoria Menendez-Benito,
- Ulrika Norman-Axelsson,
- Pauline Audergon,
- Indranil Sinha,
- Jason C. Tanny,
- Robin C. Allshire,
- and Karl Ekwall
Genome Res. June 2015 25: 872-883; Published in Advance March 16, 2015, doi:10.1101/gr.188870.114
...A nucleosome turnover map reveals that the stability of histone H4 Lys20 methylation depends on histone recycling in transcribed chromatin J. Peter Svensson 1 , Manu Shukla 2 , Victoria Menendez-Benito 1 , Ulrika Norman-Axelsson 1 , Pauline...
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Research: CHH islands: de novo DNA methylation in near-gene chromatin regulation in maize
- Jonathan I. Gent,
- Nathanael A. Ellis,
- Lin Guo,
- Alex E. Harkess,
- Yingyin Yao,
- Xiaoyu Zhang,
- and R. Kelly Dawe
Genome Res. April 2013 23: 628-637; Published in Advance December 26, 2012, doi:10.1101/gr.146985.112
...RNA production can induce chromatin modifications. This phenomenon, called RNA-directed DNA methylation (RdDM) establishes cytosine methylation in all sequence contexts. Separate pathways exist to maintain methylation depending on the sequence context (CG, CHG, and CHH; where H is A, C, or T); however, CHH...
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Method: Characterizing the targets of transcription regulators by aggregating ChIP-seq and perturbation expression data sets
- Alexander Morin,
- Eric Ching-Pan Chu,
- Aman Sharma,
- Alex Adrian-Hamazaki,
- and Paul Pavlidis
Genome Res. May 2023 33: 763-778; Published in Advance June 12, 2023, doi:10.1101/gr.277273.122
..., we give an overview of each genomic strategy before describing the aggregation and intersection approaches and their evaluation, leading to a consolidated ranking of candidate regulatory targets.View larger version: In this window In a new window Figure 1. Study overview. (A) Workflow for TR Ch...
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Research: Parent-of-origin-dependent nucleosome organization correlates with genomic imprinting in maize
- Xiaomei Dong,
- Jian Chen,
- Tong Li,
- En Li,
- Xiangbo Zhang,
- Mei Zhang,
- Weibin Song,
- Haiming Zhao,
- and Jinsheng Lai
Genome Res. July 2018 28: 1020-1028; Published in Advance June 14, 2018, doi:10.1101/gr.230201.117
....8% of mat-nucleosomes and 1.5% of allelically analyzed nucleosomes that overlapped with CG_pDMRs (Fig. 3C). The result suggested that the mechanism for the occurrence of the pat-nucleosomes could be different than that of the mat-nucleosomes. For the pat-nucleosomes, it is possible that a DNA methylation–dependent...
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Research: Long genes linked to autism spectrum disorders harbor broad enhancer-like chromatin domains
- Ying-Tao Zhao,
- Deborah Y. Kwon,
- Brian S. Johnson,
- Maria Fasolino,
- Janine M. Lamonica,
- Yoon Jung Kim,
- Boxuan Simen Zhao,
- Chuan He,
- Golnaz Vahedi,
- Tae Hoon Kim,
- and Zhaolan Zhou
Genome Res. July 2018 28: 933-942; Published in Advance May 30, 2018, doi:10.1101/gr.233775.117
...biological processes (Allis and Jenuwein 2016). Numerous modifications on histone tails are known to be associated with various genomic features: Histone 3 lysine 4 monomethylation (H3K4me1) marks poised and active enhancers; histone 3 lysine 27 acetylation (H3K27ac) marks regulatory elements...

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