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Research: H3K36 dimethylation shapes the epigenetic interaction landscape by directing repressive chromatin modifications in embryonic stem cells
- Haifen Chen,
- Bo Hu,
- Cynthia Horth,
- Eric Bareke,
- Phillip Rosenbaum,
- Sin Young Kwon,
- Jacinthe Sirois,
- Daniel N. Weinberg,
- Faith M. Robison,
- Benjamin A. Garcia,
- Chao Lu,
- William A. Pastor,
- and Jacek Majewski
Genome Res. May 2022 32: 825-837; Published in Advance April 8, 2022, doi:10.1101/gr.276383.121
.... 2020; Ren et al. 2020). The reverse mechanisms—how DNA methylation affects histone modifications—are not yet fully understood. There clearly exists an inverse relationship between H3K27me3 and DNA methylation. In undifferentiated cells, PRC2 nucleates at unmethylated CpG islands (Jermann et al. 2014...
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Research: Expanded methylome and quantitative trait loci detection by long-read profiling of personal DNA
- Cristian Groza,
- Bing Ge,
- Warren A. Cheung,
- Tomi Pastinen,
- and Guillaume Bourque
Genome Res. April 2025 35: 644-652; Published in Advance March 20, 2025, doi:10.1101/gr.279240.124
.... Nat Commun 15: 657. doi:10.1038/s41467-024-44980-2 ↵Hattori N, Abe T, Hattori N, Suzuki M, Matsuyama T, Yoshida S, Li E, Shiota K. 2004. Preference of DNA methyltransferases for CpG islands in mouse embryonic stem cells. Genome Res 14: 1733–1740. doi:10.1101/gr.2431504 Hickey G, Monlong J, Ebler J...
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Research: Locus-resolution analysis of L1 regulation and retrotransposition potential in mouse embryonic development
- Patricia Gerdes,
- Dorothy Chan,
- Mischa Lundberg,
- Francisco J. Sanchez-Luque,
- Gabriela O. Bodea,
- Adam D. Ewing,
- Geoffrey J. Faulkner,
- and Sandra R. Richardson
Genome Res. September 2023 33: 1465-1481; Published in Advance October 5, 2023, doi:10.1101/gr.278003.123
...represent monomer units. Dark gray box represents unique (nonmonomeric) region within 5′ UTR. Orange strokes represent CpG dinucleotides. Red boxes represent YY1 binding sites. (B) Experimental design of mouse L1 locus-specific bisulfite sequencing. Genomic DNA was extracted from tissues of C57BL6/J mice...
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Research: The dynamics of DNA methylation fidelity during mouse embryonic stem cell self-renewal and differentiation
- Lei Zhao,
- Ming-an Sun,
- Zejuan Li,
- Xue Bai,
- Miao Yu,
- Min Wang,
- Liji Liang,
- Xiaojian Shao,
- Stephen Arnovitz,
- Qianfei Wang,
- Chuan He,
- Xuemei Lu,
- Jianjun Chen,
- and Hehuang Xie
Genome Res. August 2014 24: 1296-1307; Published in Advance May 16, 2014, doi:10.1101/gr.163147.113
...Logo: a sequence logo generator. Genome Res 14: 1188–1190. Doi A, Park IH,Wen B,Murakami P, AryeeMJ, Irizarry R, Herb B, Ladd-Acosta C, Rho J, Loewer S, et al. 2009. Differential methylation of tissue- and cancer-specific CpG island shores distinguishes human induced pluripotent stem cells, embryonic stem cells...
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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
...Cell type–specific DNA methylation at intragenic CpG islands in the immune system Aimée M. Deaton 1 , Shaun Webb 1 , Alastair R.W. Kerr 1 , Robert S. Illingworth 1 , Jacky Guy 1 , Robert Andrews 2 and Adrian Bird 1 , 3...
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Research: ZFX acts as a transcriptional activator in multiple types of human tumors by binding downstream from transcription start sites at the majority of CpG island promoters
- Suhn Kyong Rhie,
- Lijun Yao,
- Zhifei Luo,
- Heather Witt,
- Shannon Schreiner,
- Yu Guo,
- Andrew A. Perez,
- and Peggy J. Farnham
Genome Res. March 2018 28: 310-320; Published in Advance February 2, 2018, doi:10.1101/gr.228809.117
..., Orlov YL, Zhang W, Jiang J, et al. 2008. Integration of external signaling pathways with the core transcriptional network in embryonic stem cells. Cell 133: 1106–1117. ↵Deaton AM, Bird A. 2011. CpG islands and the regulation of transcription. Genes Dev 25: 1010–1022. ↵Desjarlais JR, Berg JM. 1992...
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Research: Combinatorial DNA methylation codes at repetitive elements
- Christophe Papin,
- Abdulkhaleg Ibrahim,
- Stéphanie Le Gras,
- Amandine Velt,
- Isabelle Stoll,
- Bernard Jost,
- Hervé Menoni,
- Christian Bronner,
- Stefan Dimitrov,
- and Ali Hamiche
Genome Res. June 2017 27: 934-946; Published in Advance March 27, 2017, doi:10.1101/gr.213983.116
...a major role in cell differentiation. [Supplemental material is available for this article.] DNA methylation is an epigenetic modification essential for mammalian development (Okano et al. 1999). In mammals, the cytosine bases at position 5 in CpG dinucleotides are modified -wide by dedicatedmethyl...
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Research: Inherited DNA methylation primes the establishment of accessible chromatin during genome activation
- Guifen Liu,
- Wen Wang,
- Shengen Hu,
- Xiangxiu Wang,
- and Yong Zhang
Genome Res. July 2018 28: 998-1007; Published in Advance May 29, 2018, doi:10.1101/gr.228833.117
...), whereas the prediction power was 24.6% weaker for the local lowest DNA methylation level (Fig. 3D; Supplemental Fig. S6B; see Supplemental Methods). Our results show that accessible promoters that emerge during ZGA are clearly associated with DNA methylation patterns, especially the unmethylated CpG...
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Method: Genome-wide DNA methylation profiling using the methylation-dependent restriction enzyme LpnPI
- Ruben Boers,
- Joachim Boers,
- Bas de Hoon,
- Christel Kockx,
- Zeliha Ozgur,
- Anco Molijn,
- Wilfred van IJcken,
- Joop Laven,
- and Joost Gribnau
Genome Res. January 2018 28: 88-99; Published in Advance December 8, 2017, doi:10.1101/gr.222885.117
...and Meissner 2013). Normal methylation is essential for embryonic development, aging, and phenotype; aberrant methylation is closely associated with disease. Mammalian DNA methylation is mainly restricted to cytosines in the context of a CpG dinucleotide (Ramsahoye et al. 2000). Many gene regulatory regions...
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Research: The chromatin environment shapes DNA replication origin organization and defines origin classes
- Christelle Cayrou,
- Benoit Ballester,
- Isabelle Peiffer,
- Romain Fenouil,
- Philippe Coulombe,
- Jean-Christophe Andrau,
- Jacques van Helden,
- and Marcel Méchali
Genome Res. December 2015 25: 1873-1885; Published in Advance November 11, 2015, doi:10.1101/gr.192799.115
...1992). Conversely, recent analyses revealed the presence of GC-rich elements in eukaryotic origins, such as CpG islands (CGI) (Delgado et al. 1998; Prioleau 2009; Cayrou et al. 2011; Costas et al. 2011) and an Origin G-rich Repeated Element (OGRE) that can form G4 (Cayrou et al. 2011, 2012a). G4were...

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