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Research: The role of DNA methylation in directing the functional organization of the cancer epigenome
- Fides D. Lay,
- Yaping Liu,
- Theresa K. Kelly,
- Heather Witt,
- Peggy J. Farnham,
- Peter A. Jones,
- and Benjamin P. Berman
Genome Res. April 2015 25: 467-477; Published in Advance March 6, 2015, doi:10.1101/gr.183368.114
...-deficient derivative. The NOMe-seq accessibility assay unexpectedly revealed symmetrical and transcription-independent nucleosomal phasing across active, poised, and inactive genomic elements. DNA methylation abolished this phasing primarily at enhancers and CpG island (CGI) promoters, with little effect on insulators...
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Research: Genome-scale analysis of metazoan replication origins reveals their organization in specific but flexible sites defined by conserved features
- Christelle Cayrou,
- Philippe Coulombe,
- Alice Vigneron,
- Slavica Stanojcic,
- Olivier Ganier,
- Isabelle Peiffer,
- Eric Rivals,
- Aurore Puy,
- Sabine Laurent-Chabalier,
- Romain Desprat,
- and Marcel Méchali
Genome Res. September 2011 21: 1438-1449; Published in Advance July 12, 2011, doi:10.1101/gr.121830.111
...DNA is generally believed to constitute late replicating domains. However, accumulating evidences indicate that a subset of heterochromatin DNA replicates early in S phase (Hayashi et al. 2009) and this is the case for Drosophila chromosome 4 (Schwaiger et al. 2009). We detected a positive...
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Research: Global DNA hypomethylation coupled to repressive chromatin domain formation and gene silencing in breast cancer
- Gary C. Hon,
- R. David Hawkins,
- Otavia L. Caballero,
- Christine Lo,
- Ryan Lister,
- Mattia Pelizzola,
- Armand Valsesia,
- Zhen Ye,
- Samantha Kuan,
- Lee E. Edsall,
- Anamaria Aranha Camargo,
- Brian J. Stevenson,
- Joseph R. Ecker,
- Vineet Bafna,
- Robert L. Strausberg,
- Andrew J. Simpson,
- and Bing Ren
Genome Res. February 2012 22: 246-258; Published in Advance December 7, 2011, doi:10.1101/gr.125872.111
...large 10-kb bins. To gain insight into which genomic features are more likely to undergo hypomethylation, we examined the methylation level at single cytosine residues spanning exons, intragenic regions, or intergenic regions. The distribution of cytosine methylation frequency at exons in HCC1954...
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Research: Impact of replication timing on non-CpG and CpG substitution rates in mammalian genomes
- Chun-Long Chen,
- Aurélien Rappailles,
- Lauranne Duquenne,
- Maxime Huvet,
- Guillaume Guilbaud,
- Laurent Farinelli,
- Benjamin Audit,
- Yves d'Aubenton-Carafa,
- Alain Arneodo,
- Olivier Hyrien,
- and Claude Thermes
Genome Res. April 2010 20: 447-457; Published in Advance January 26, 2010, doi:10.1101/gr.098947.109
...values of the methylation level (ML) in early- and late-replicating regions (see Methods, Determination of the Transition Rate at Methylated CpG Sites): it is almost constant, slightly decreasing Chen et al. 450 Genome Research www..org G G lic ili lic ili ili lik lly lly Mutation rates and replication...
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Research: A CRISPR knockout screen identifies SETDB1-target retroelement silencing factors in embryonic stem cells
- Kei Fukuda,
- Akihiko Okuda,
- Kosuke Yusa,
- and Yoichi Shinkai
Genome Res. June 2018 28: 846-858; Published in Advance May 4, 2018, doi:10.1101/gr.227280.117
...and de Lange 2008; Xin et al. 2008), but very little is known about the role of the shelterin complex in retroelement silencing. It was recently reported that shelterin components promote facultative heterochromatin assembly at internal chromosomal sites containing late replication origins in fission...
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Resource: Integrating and mining the chromatin landscape of cell-type specificity using self-organizing maps
- Ali Mortazavi,
- Shirley Pepke,
- Camden Jansen,
- Georgi K. Marinov,
- Jason Ernst,
- Manolis Kellis,
- Ross C. Hardison,
- Richard M. Myers,
- and Barbara J. Wold
Genome Res. December 2013 23: 2136-2148; Published in Advance October 29, 2013, doi:10.1101/gr.158261.113
...; 8 Center for Comparative Genomics and Bioinformatics, The Pennsylvania State University, University Park, Pennsylvania 16802, USA; 9 Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, Pennsylvania 16802, USA; 10 Hudson...
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