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Research: Disclosing the crosstalk among DNA methylation, transcription factors, and histone marks in human pluripotent cells through discovery of DNA methylation motifs
- Phuc-Loi Luu,
- Hans R. Schöler,
- and Marcos J. Araúzo-Bravo
Genome Res. December 2013 23: 2013-2029; Published in Advance October 22, 2013, doi:10.1101/gr.155960.113
...by the CpGMMs at the CpG level are biologically relevant since they could work as recognition sites for the agents that perform DNA methylation and demethylation. Actually, it has already been found (Mohn and Schu¨beler 2009; Lienert et al. 2011) that the methylation changes due to single CpG mutations have...
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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
...at single CpG resolution. In this pairwise comparison,we usedM&MorMEDIPS to define anyDMR inwhich fetal NSCs had a higher methylation level than H1 ESC as a hypermethylated DMR, and any DMR in which fetal NSCs had a lower methylation level thanH1ESCas a hypomethylatedDMR.Based on ranked P-values, we used...
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Method: Single-cell methylome landscapes of mouse embryonic stem cells and early embryos analyzed using reduced representation bisulfite sequencing
- Hongshan Guo,
- Ping Zhu,
- Xinglong Wu,
- Xianlong Li,
- Lu Wen,
- and Fuchou Tang
Genome Res. December 2013 23: 2126-2135; Published in Advance October 31, 2013, doi:10.1101/gr.161679.113
...as the complement of the intragenic regions. Calculation of CpG site methylation levels Themethylation level of each single CpG site was estimated as the number of reported Cs (methylated) divided by the total number of reported Cs (methylated) or Ts (unmethylated) at the same position of the reference...
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Methods: Comprehensive high-throughput arrays for relative methylation (CHARM)
- Rafael A. Irizarry,
- Christine Ladd-Acosta,
- Benilton Carvalho,
- Hao Wu,
- Sheri A. Brandenburg,
- Jeffrey A. Jeddeloh,
- Bo Wen,
- and Andrew P. Feinberg
Genome Res. May 2008 18: 780-790; Published in Advance March 3, 2008, doi:10.1101/gr.7301508
...specific single-CpG dinucleotides or amplicons. These include MethyLight ( Eads et al. 2000 ), COBRA ( Xiong and Laird 1997 ), bisulfite pyrosequencing ( Dupont et al. 2004 ), and the Illumina GoldenGate methylation assay ( Bibikova et al. 2006 ). While sensitive, specific, and relatively inexpensive, none...
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Methods: MEDME: An experimental and analytical methodology for the estimation of DNA methylation levels based on microarray derived MeDIP-enrichment
- Mattia Pelizzola,
- Yasuo Koga,
- Alexander Eckehart Urban,
- Michael Krauthammer,
- Sherman Weissman,
- Ruth Halaban,
- and Annette M. Molinaro
Genome Res. October 2008 18: 1652-1659; Published in Advance September 2, 2008, doi:10.1101/gr.080721.108
...human melanocytes compared to a melanoma cell strain. Despite the low resolution typical of methods based on immunoprecipitation, we show that model-derived estimates of DNA methylation provide relatively high correlation with measured absolute and relative levels, as validated by bisulfite genomic DNA...
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Method: Simultaneous assessment of human genome and methylome data in a single experiment using limited deamination of methylated cytosine
- Bo Yan,
- Duan Wang,
- and Laurence Ettwiller
Genome Res. June 2024 34: 904-913; Published in Advance June 10, 2024, doi:10.1101/gr.278294.123
...represent about or less than the average size of a single CpG island (CGI), a resolution that is compatible with most epigenetic applications. Indeed, functional genomic regions ranging between a few hundred and a few thousand bases tend to be regionally methylated or unmethylated in concert (Chen et al...
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Research: Widespread contribution of transposable elements to the innovation of gene regulatory networks
- Vasavi Sundaram,
- Yong Cheng,
- Zhihai Ma,
- Daofeng Li,
- Xiaoyun Xing,
- Peter Edge,
- Michael P. Snyder,
- and Ting Wang
Genome Res. December 2014 24: 1963-1976; Published in Advance October 15, 2014, doi:10.1101/gr.168872.113
...in two pairs of human and mouse cell lines (representing two cell lineages), along with epigenomic profiles, including DNA methylation and six histone modifications. Overall, we found that 20% of binding sites were embedded within TEs. This number varied across different TFs, ranging from 2% to 40%. We...

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