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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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Research: TET2 binding to enhancers facilitates transcription factor recruitment in hematopoietic cells
- Kasper D. Rasmussen,
- Ivan Berest,
- Sandra Keβler,
- Koutarou Nishimura,
- Lucía Simón-Carrasco,
- George S. Vassiliou,
- Marianne T. Pedersen,
- Jesper Christensen,
- Judith B. Zaugg,
- and Kristian Helin
Genome Res. April 2019 29: 564-575; Published in Advance February 22, 2019, doi:10.1101/gr.239277.118
...for motifs with either methylated or unmethylated CpG sites (Hashimoto et al. 2014; Wang et al. 2017; Yin et al. 2017). As an illustration of this, global loss of DNA methylation in ES cells was shown to unmask previously inaccessible genomic binding sites for the TF NRF1 (Domcke et al. 2015). Moreover, DNA...
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Research: Characterization of DNA methylation reader proteins in Arabidopsis thaliana
- Jonathan Cahn,
- James P.B. Lloyd,
- Ino D. Karemaker,
- Pascal W.T.C. Jansen,
- Jahnvi Pflueger,
- Owen Duncan,
- Jakob Petereit,
- Ozren Bogdanovic,
- A. Harvey Millar,
- Michiel Vermeulen,
- and Ryan Lister
Genome Res. December 2024 34: 2229-2243; Published in Advance December 4, 2024, doi:10.1101/gr.279379.124
...and characterization of the proteins that can bind to DNA methylation (mC readers). Two protein domains were identified to confer the ability to bind to DNA methylation: methyl-binding domain (MBD), first identified in methyl-CpG-binding protein 2 (MeCP2) (Nan et al. 1993), and the SET and RING-associated (SRA) domain...
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Review: The superpowers of imprinting control regions
- Bertille Montibus,
- Franck Court,
- and Philippe Arnaud
Genome Res. January 2026 36: 1-19; Published in Advance December 10, 2025, doi:10.1101/gr.281215.125
...content ≥50% and an observed-to-expected CpG ratio ≥0.6) (Gardiner-Garden and Frommer 1987), not all meet this formal definition. Each imprinting domain is thus controlled by an ICR. One of the key features of these ICRs is that they are methylated only on one of the two parental alleles, and it is widely...
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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
...affect gene expression through epigenetic regulation. At the CpG islands of active gene promoters, R-loop formation helps establish an unmethylated state both by blocking the activity of DNA methyltransferase 1 (Grunseich et al. 2018) and by recruiting the demethylating enzyme TET1 through GADD45A (Arab...
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Research: Changes in H2A.Z occupancy and DNA methylation during B-cell lymphomagenesis
- Melissa L. Conerly,
- Sheila S. Teves,
- Daniel Diolaiti,
- Michelle Ulrich,
- Robert N. Eisenman,
- and Steven Henikoff
Genome Res. October 2010 20: 1383-1390; Published in Advance August 13, 2010, doi:10.1101/gr.106542.110
...and CpG islands by remodelers and transcription factors in the Em-MYC cells. In contrast, the gene body gains in H2A.Z during tumorigenesis were reflected by losses of DNA methylation, which showed a similar expression-dependent pattern in the lymphoma cells as compared with the Em-MYC cells (Fig. 6B...
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Research: Genes for embryo development are packaged in blocks of multivalent chromatin in zebrafish sperm
- Shan-Fu Wu,
- Haiying Zhang,
- and Bradley R. Cairns
Genome Res. April 2011 21: 578-589; Published in Advance March 7, 2011, doi:10.1101/gr.113167.110
...ortholog of mammalian H2A.Z) at developmental loci (Fig. 3A–C; top 250 genes, Supplemental Table 4); intersecting of the respective top 800 genes displays a 40% overlap (correlation P-value < 0.001). GO term analysis showed H2AFV is highly enriched at the promoters of genes involved in transcription...
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Research: Atypical epigenetic and small RNA control of degenerated transposons and their fragments in clonally reproducing Spirodela polyrhiza
- Rodolphe Dombey,
- Daniel Buendía-Ávila,
- Verónica Barragán-Borrero,
- Laura Diezma-Navas,
- Arturo Ponce-Mañe,
- José Mario Vargas-Guerrero,
- Rana Elias,
- and Arturo Marí-Ordóñez
Genome Res. March 2025 35: 522-544; Published in Advance March 4, 2025, doi:10.1101/gr.279532.124
...(RdDM). Best studied in Arabidopsis thaliana, during RdDM, H3K9me2 and DNA methylation recruit the plant-specific RNA polymerases (Pol) IV and V. Pol IV transcripts are processed into 24 nt siRNAs, which, loaded into members of the AGO4/6 clade, target Pol V transcripts to guide the sequence...
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Method: Absolute nucleosome occupancy map for the Saccharomyces cerevisiae genome
- Elisa Oberbeckmann,
- Michael Wolff,
- Nils Krietenstein,
- Mark Heron,
- Jessica L. Ellins,
- Andrea Schmid,
- Stefan Krebs,
- Helmut Blum,
- Ulrich Gerland,
- and Philipp Korber
Genome Res. December 2019 29: 1996-2009; Published in Advance November 6, 2019, doi:10.1101/gr.253419.119
...that methylate either CpG or GpC sites (Jessen et al. 2004; Kilgore et al. 2007; Small et al. 2014).To measure absolute occupancy, it is crucial that the RE- or DNMT-catalyzed reactions reach saturation, which requires that nucleosome dynamics are frozen. This is mostly true for ex vivo–prepared or in vitro...
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Research: Polycomb repressive complex 1 shapes the nucleosome landscape but not accessibility at target genes
- Hamish W. King,
- Nadezda A. Fursova,
- Neil P. Blackledge,
- and Robert J. Klose
Genome Res. October 2018 28: 1494-1507; Published in Advance August 28, 2018, doi:10.1101/gr.237180.118
...at lysine 119 (H2AK119ub1), whereas PRC2 methylates histone H3 on lysine 27 (H3K27me3). In vertebrates, PRC1 and PRC2 are targeted by various mechanisms to gene promoters, particularly those associated with nonmethylated CpG islands (CGIs) (Bracken and Helin 2009; Simon and Kingston 2013; Blackledge et al...
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