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Research: Distal CpG islands can serve as alternative promoters to transcribe genes with silenced proximal promoters
- Shrutii Sarda,
- Avinash Das,
- Charles Vinson,
- and Sridhar Hannenhalli
Genome Res. April 2017 27: 553-566; Published in Advance February 21, 2017, doi:10.1101/gr.212050.116
...for this article.] In mammalian DNA, cytosines within CpG dinucleotides are heavily methylated throughout the , yet there are several discrete “islands” that contain a high frequency of unmethylated CpG sites. These are called CpG islands (CGI), and their identification has long been considered important...
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Method: Guide Positioning Sequencing identifies aberrant DNA methylation patterns that alter cell identity and tumor-immune surveillance networks
- Jin Li,
- Yan Li,
- Wei Li,
- Huaibing Luo,
- Yanping Xi,
- Shihua Dong,
- Ming Gao,
- Peng Xu,
- Baolong Zhang,
- Ying Liang,
- Qingping Zou,
- Xin Hu,
- Lina Peng,
- Dan Zou,
- Ting Wang,
- Hongbo Yang,
- Cizhong Jiang,
- Shaoliang Peng,
- Feizhen Wu,
- and Wenqiang Yu
Genome Res. February 2019 29: 270-280; Published in Advance January 22, 2019, doi:10.1101/gr.240606.118
...coefficient) with both methods (Supplemental Fig. S1C,D). Further analyses demonstrate that GPS has higher efficiency when detecting DNA methylation in the repetitive elements, CpG islands, and GC-rich region such as promoter regions (Fig. 1D–F; Supplemental Fig. S2). Moreover, the methylation sites detected...
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Research: DNA (de)methylation in embryonic stem cells controls CTCF-dependent chromatin boundaries
- Laura Wiehle,
- Graeme J. Thorn,
- Günter Raddatz,
- Christopher T. Clarkson,
- Karsten Rippe,
- Frank Lyko,
- Achim Breiling,
- and Vladimir B. Teif
Genome Res. May 2019 29: 750-761; Published in Advance April 4, 2019, doi:10.1101/gr.239707.118
...binding, DNA methylation, and gene expression in DKO ESCs and developed biophysical models to predict differential CTCF binding. Methylation-sensitive nucleosome repositioning accounted for a significant portion of CTCF binding loss in DKO ESCs, whereas unmethylated and nucleosome-depleted CpG islands...
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Research: DNA methylation contributes to natural human variation
- Holger Heyn,
- Sebastian Moran,
- Irene Hernando-Herraez,
- Sergi Sayols,
- Antonio Gomez,
- Juan Sandoval,
- Dave Monk,
- Kenichiro Hata,
- Tomas Marques-Bonet,
- Liewei Wang,
- and Manel Esteller
Genome Res. September 2013 23: 1363-1372; Published in Advance August 1, 2013, doi:10.1101/gr.154187.112
..., intragenic methylation has been linked to transcriptional and splicing activities ( Jones 2012), suggesting a sophisticated regulatory potential for this epigenetic modification. DNA methylation levels are closely related to the genomic context, with CpG-rich regions (CpG islands) located in the 59 endof...
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Resource: Dynamic DNA methylation across diverse human cell lines and tissues
- Katherine E. Varley,
- Jason Gertz,
- Kevin M. Bowling,
- Stephanie L. Parker,
- Timothy E. Reddy,
- Florencia Pauli-Behn,
- Marie K. Cross,
- Brian A. Williams,
- John A. Stamatoyannopoulos,
- Gregory E. Crawford,
- Devin M. Absher,
- Barbara J. Wold,
- and Richard M. Myers
Genome Res. March 2013 23: 555-567; Published in Advance January 16, 2013, doi:10.1101/gr.147942.112
...Table S4). These methylation differences associated with cell culture occur predominately as unmethylated CpGs in the bodies of genes involved in regulating cellular proliferation (GO:0042127, P = 5.17 3 10#2;4). Studies of DNA methylation that use cell lines as model systems could use this list...
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Research: Extensive variation and low heritability of DNA methylation identified in a twin study
- Kristina Gervin,
- Martin Hammerø,
- Hanne E. Akselsen,
- Rune Moe,
- Heidi Nygård,
- Ingunn Brandt,
- Håkon K. Gjessing,
- Jennifer R. Harris,
- Dag E. Undlien,
- and Robert Lyle
Genome Res. November 2011 21: 1813-1821; Published in Advance September 26, 2011, doi:10.1101/gr.119685.110
...reveals substantial inter-individual variation in DNA methylation. Classification of the 186 regions into CpG islands, 59 regions, conserved noncoding, and 1814 Genome Research www..org Gervin et al . lic lic Genome Research 1815 www..org Variation and heritability of DNA methylation lit Gervin et al...
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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
...in DNA methylation during erythroid development. Analysis of genomic features revealed that 98% of promoter CpG islands are hypomethylated, while 20%–25% of non-promoter CpG islands are methylated. Proximal promoter sequences of expressed genes are hypomethylated in all cell types, while gene body...
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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
...statistical framework which we call ‘‘M&M’’ (for integration of MeDIP-seq and MRE-seq) that detects DMRs. M&M explicitly models the relationship between DNA methylation level, CpG content, and expected MeDIP and MRE reads in any given genomic context. By analyzing WGBS, MeDIPseq, and MRE-seq data for the same...
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Letter: Lineage-specific DNA methylation in T cells correlates with histone methylation and enhancer activity
- Christian Schmidl,
- Maja Klug,
- Tina J. Boeld,
- Reinhard Andreesen,
- Petra Hoffmann,
- Matthias Edinger,
- and Michael Rehli
Genome Res. July 2009 19: 1165-1174; Published in Advance June 3, 2009, doi:10.1101/gr.091470.109
...neglected in previous studies. Our findings in CD4+ T cells are in line with a recent study in ES cells that also identified promoterdistal regions as the main sites of dynamic changes in DNA methylation upon differentiation (Meissner et al. 2008), andwith a study on tissue-specific CpG island methylation...
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Research: Genome-scale analysis of DNA methylation in lung adenocarcinoma and integration with mRNA expression
- Suhaida A. Selamat,
- Brian S. Chung,
- Luc Girard,
- Wei Zhang,
- Ying Zhang,
- Mihaela Campan,
- Kimberly D. Siegmund,
- Michael N. Koss,
- Jeffrey A. Hagen,
- Wan L. Lam,
- Stephen Lam,
- Adi F. Gazdar,
- and Ite A. Laird-Offringa
Genome Res. July 2012 22: 1197-1211; Published in Advance May 21, 2012, doi:10.1101/gr.132662.111
..., and that hypomethylation largely occurs outside of CpG islands. (B) Volcano plot of the differential DNA methylation analysis. (X-axis) Median b-value difference (median tumor-median NTL); (y-axis) Q-values for each probe (#2;1 3 log10 scale). (Vertical dotted lines) 20% change in b-values; (horizontal dotted line...

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