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Resource: Epigenomic analysis reveals prevalent contribution of transposable elements to cis-regulatory elements, tissue-specific expression, and alternative promoters in zebrafish
- Hyung Joo Lee,
- Yiran Hou,
- Ju Heon Maeng,
- Nakul M. Shah,
- Yujie Chen,
- Heather A. Lawson,
- Hongbo Yang,
- Feng Yue,
- and Ting Wang
Genome Res. July 2022 32: 1424-1436; Published in Advance June 1, 2022, doi:10.1101/gr.276052.121
...for specific transcription factor binding motifs. We found that active TE elements from subfamilies DNA-AT-2_DR, DNA-2-2_DR, hAT-N39_DR, and DNA9TA1 show enrichment for Gfi1b, Nkx2.1, HOXD13, and NF-kB motifs, respectively (Fig. 3H; Supplemental Fig. S5A). Among the zebrafish transcription factors...
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Research: Genome-wide DNA methylation patterns in LSH mutant reveals de-repression of repeat elements and redundant epigenetic silencing pathways
- Weishi Yu,
- Carl McIntosh,
- Ryan Lister,
- Iris Zhu,
- Yixing Han,
- Jianke Ren,
- David Landsman,
- Eunice Lee,
- Victorino Briones,
- Minoru Terashima,
- Robert Leighty,
- Joseph R. Ecker,
- and Kathrin Muegge
Genome Res. October 2014 24: 1613-1623; Published in Advance August 28, 2014, doi:10.1101/gr.172015.114
...KOMEFs comprises promoter regions of proteincoding and noncoding RNA genes. The extent of methylation loss is greatest at intergenic regions and promoter regions that are CG poor, and maximum methylation decrease is observed at silent genes. This implies that HELLS is primarily required for DNA methylation...
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Research: NF-Y coassociates with FOS at promoters, enhancers, repetitive elements, and inactive chromatin regions, and is stereo-positioned with growth-controlling transcription factors
- Joseph D. Fleming,
- Giulio Pavesi,
- Paolo Benatti,
- Carol Imbriano,
- Roberto Mantovani,
- and Kevin Struhl
Genome Res. August 2013 23: 1195-1209; Published in Advance April 17, 2013, doi:10.1101/gr.148080.112
...immunoprecipitation (ChIP), formaldehyde-assisted isolation of regulatory elements (FAIRE), and DNase I hypersensitivity techniques coupled to massively parallel DNA sequencing, such classification of functional genomic regions has been done in several cell lines in the context of ENCODE (The ENCODE Project...
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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
...enrichment just upstream of TSSs could stem from additional transcription in these regions (Supplemental Fig. 2). H3K4me3 and CpG methylation target mutually exclusive regions In vertebrates, DNA methylation at CpG dinucleotides is found throughout large parts of the , but is excluded from sites of H3K4...
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Research: Genome-wide DNA methylation profiles in hematopoietic stem and progenitor cells reveal overrepresentation of ETS transcription factor binding sites
- Amber Hogart,
- Jens Lichtenberg,
- Subramanian S. Ajay,
- Stacie Anderson,
- NIH Intramural Sequencing Center,
- Elliott H. Margulies,
- and David M. Bodine
Genome Res. August 2012 22: 1407-1418; Published in Advance June 8, 2012, doi:10.1101/gr.132878.111
.....org overrepresentation of multiple ETS sites within the intergenic partition. These complementary patterns of transcription factor motifs suggest that DNA methylation may modulate ETS transcription factor occupancy during hematopoietic development. Other transcription factor motifs such as the NFAT (nuclear factor...
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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
...of de novo methylation of DNA between embryonic day (E) 4.5 and E8.5 (Fig. 2A). To study the role of EHMT2 in DNA methylation, we used an Ehmt2 knockout line in which a LacZ cassette inserted after exon 11 results in truncated transcripts lacking the Ankyrin (ANK) repeats and the catalytic SET 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
...allele-specific gene expression across large imprinted domains. In this review, we highlight the features that define ICRs as a distinct class of cis-regulatory regions, from their ability to maintain germline-inherited DNA methylation to their multifunctional roles in transcriptional control. For each...
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Resource: Genome-wide high resolution parental-specific DNA and histone methylation maps uncover patterns of imprinting regulation in maize
- Mei Zhang,
- Shaojun Xie,
- Xiaomei Dong,
- Xin Zhao,
- Biao Zeng,
- Jian Chen,
- Hui Li,
- Weilong Yang,
- Hainan Zhao,
- Gaokui Wang,
- Zongliang Chen,
- Silong Sun,
- Andrew Hauck,
- Weiwei Jin,
- and Jinsheng Lai
Genome Res. January 2014 24: 167-176; Published in Advance October 16, 2013, doi:10.1101/gr.155879.113
...that DNA demethylation is required but not sufficient for targeting of PRC2 complex (Mathieu et al. 2005; Stroud et al. 2013). Since several noncoding RNAs (particularly MNCs) were shown to be associated with PEGs, we speculate that maternal DNA demethylation around PEGs may potentially lead...
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Research: Cell type–specific DNA methylation at intragenic CpG islands in the immune system
- Aimée M. Deaton,
- Shaun Webb,
- Alastair R.W. Kerr,
- Robert S. Illingworth,
- Jacky Guy,
- Robert Andrews,
- and Adrian Bird
Genome Res. July 2011 21: 1074-1086; Published in Advance May 31, 2011, doi:10.1101/gr.118703.110
...-TSS-associated CGIs, specifically those located within transcription units (Fig. 2C,D). Altogether, 2% of intragenic CGIs were involved in DNA methylation transitions, compared to 0.28% of annotated promoter CGIs (Fig. 2D). Thus, intragenic CGIs are distinct from TSS-associated and intergenic CGIs with regard to cell...
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Method: Functional DNA methylation differences between tissues, cell types, and across individuals discovered using the M&M algorithm
- Bo Zhang,
- Yan Zhou,
- Nan Lin,
- Rebecca F. Lowdon,
- Chibo Hong,
- Raman P. Nagarajan,
- Jeffrey B. Cheng,
- Daofeng Li,
- Michael Stevens,
- Hyung Joo Lee,
- Xiaoyun Xing,
- Jia Zhou,
- Vasavi Sundaram,
- GiNell Elliott,
- Junchen Gu,
- Taoping Shi,
- Philippe Gascard,
- Mahvash Sigaroudinia,
- Thea D. Tlsty,
- Theresa Kadlecek,
- Arthur Weiss,
- Henriette O’Geen,
- Peggy J. Farnham,
- Cécile L. Maire,
- Keith L. Ligon,
- Pamela A.F. Madden,
- Angela Tam,
- Richard Moore,
- Martin Hirst,
- Marco A. Marra,
- Baoxue Zhang,
- Joseph F. Costello,
- and Ting Wang
Genome Res. September 2013 23: 1522-1540; Published in Advance June 26, 2013, doi:10.1101/gr.156539.113
...among different tissue types, cell types, and individuals, potentially underscoring divergent epigenetic regulation at different scales of phenotypic diversity. We find that differential DNA methylation at enhancer elements, with concurrent changes in histone modifications and transcription factor...
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