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Method: Genome-wide nucleosome map and cytosine methylation levels of an ancient human genome
- Jakob Skou Pedersen,
- Eivind Valen,
- Amhed M. Vargas Velazquez,
- Brian J. Parker,
- Morten Rasmussen,
- Stinus Lindgreen,
- Berit Lilje,
- Desmond J. Tobin,
- Theresa K. Kelly,
- Søren Vang,
- Robin Andersson,
- Peter A. Jones,
- Cindi A. Hoover,
- Alexei Tikhonov,
- Egor Prokhortchouk,
- Edward M. Rubin,
- Albin Sandelin,
- M. Thomas P. Gilbert,
- Anders Krogh,
- Eske Willerslev,
- and Ludovic Orlando
Genome Res. March 2014 24: 454-466; Published in Advance December 3, 2013, doi:10.1101/gr.163592.113
...nucleosome map and methylation levels were confirmed by the recovery of the expected signals at promoter regions, exon/intron boundaries, and CTCF sites. The top-scoring nucleosome calls revealed distinct DNA positioning biases, attesting to nucleotide-level accuracy. The ancient methylation levels exhibited...
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Research: Genome-wide and parental allele-specific analysis of CTCF and cohesin DNA binding in mouse brain reveals a tissue-specific binding pattern and an association with imprinted differentially methylated regions
- Adam R. Prickett,
- Nikolaos Barkas,
- Ruth B. McCole,
- Siobhan Hughes,
- Samuele M. Amante,
- Reiner Schulz,
- and Rebecca J. Oakey
Genome Res. October 2013 23: 1624-1635; Published in Advance June 26, 2013, doi:10.1101/gr.150136.112
...contributed equally to this work. Abstract DNA binding factors are essential for regulating gene expression. CTCF and cohesin are DNA binding factors with central roles in chromatin organization and gene expression. We determined the sites of CTCF and cohesin binding to DNA in mouse brain, genome...
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Research: Widespread plasticity in CTCF occupancy linked to DNA methylation
- Hao Wang,
- Matthew T. Maurano,
- Hongzhu Qu,
- Katherine E. Varley,
- Jason Gertz,
- Florencia Pauli,
- Kristen Lee,
- Theresa Canfield,
- Molly Weaver,
- Richard Sandstrom,
- Robert E. Thurman,
- Rajinder Kaul,
- Richard M. Myers,
- and John A. Stamatoyannopoulos
Genome Res. September 2012 22: 1680-1688; doi:10.1101/gr.136101.111
.... The binding sites for the chromatin insulator protein CTCF map to DNA methylation-free domains -wide. Genome Res 14: 1594–1602. Neph S, Kuehn MS, Reynolds AP, Haugen E, Thurman RE, Johnson AK, Rynes E, Maurano MT, Vierstra J, Thomas S, et al. 2012a. BEDOPS: High performance genomic feature operations...
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LETTER: Global analysis of the insulator binding protein CTCF in chromatin barrier regions reveals demarcation of active and repressive domains
- Suresh Cuddapah,
- Raja Jothi,
- Dustin E. Schones,
- Tae-Young Roh,
- Kairong Cui,
- and Keji Zhao
Genome Res. January 2009 19: 24-32; Published in Advance December 3, 2008, doi:10.1101/gr.082800.108
...it plays a role in chromatin domain barriers between active and repressive domains. Here, we used ChIP-seq to map the genome-wide binding sites of CTCF in three cell types and identified significant binding of CTCF to the boundaries of repressive chromatin domains marked by H3K27me3. Although we find...
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Research: Dioxin receptor and SLUG transcription factors regulate the insulator activity of B1 SINE retrotransposons via an RNA polymerase switch
- Angel Carlos Román,
- Francisco J. González-Rico,
- Eduardo Moltó,
- Henar Hernando,
- Ana Neto,
- Cristina Vicente-Garcia,
- Esteban Ballestar,
- José L. Gómez-Skarmeta,
- Jana Vavrova-Anderson,
- Robert J. White,
- Lluís Montoliu,
- and Pedro M. Fernández-Salguero
Genome Res. March 2011 21: 422-432; Published in Advance February 3, 2011, doi:10.1101/gr.111203.110
..., perhaps through recruitment of parylated CTCF. It has been suggested that insulators and SINEs have a role in chromatin compartmentalization. Based on the accumulation of heterochromatic marks downstream of B1-X35S, we performed a comparative epigenomic analysis (from NCBI GEO repository GSE12241...
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RESOURCE: An integrated resource for genome-wide identification and analysis of human tissue-specific differentially methylated regions (tDMRs)
- Vardhman K. Rakyan,
- Thomas A. Down,
- Natalie P. Thorne,
- Paul Flicek,
- Eugene Kulesha,
- Stefan Gräf,
- Eleni M. Tomazou,
- Liselotte Bäckdahl,
- Nathan Johnson,
- Marlis Herberth,
- Kevin L. Howe,
- David K. Jackson,
- Marcos M. Miretti,
- Heike Fiegler,
- John C. Marioni,
- Ewan Birney,
- Tim J.P. Hubbard,
- Nigel P. Carter,
- Simon Tavaré,
- and Stephan Beck
Genome Res. September 2008 18: 1518-1529; Published in Advance June 24, 2008, doi:10.1101/gr.077479.108
...to current efforts in understanding the epigenetic code, and its role in tissue-specific function in mammals. Results Genome-wide mapping of human tissue-specific DNA methylation profiles We based our DNA methylation profiling strategy on a recently developed technique—methylated DNA immunoprecipitation (Me...
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Letter: Endonuclease-sensitive regions of human spermatozoal chromatin are highly enriched in promoter and CTCF binding sequences
- Ali Arpanahi,
- Martin Brinkworth,
- David Iles,
- Stephen A. Krawetz,
- Agnieszka Paradowska,
- Adrian E. Platts,
- Myriam Saida,
- Klaus Steger,
- Philip Tedder,
- and David Miller
Genome Res. August 2009 19: 1338-1349; Published in Advance July 7, 2009, doi:10.1101/gr.094953.109
...was used to precipitate H4ac-associated DNA from total sperm chromatin for hybridization to the NimbleGen human HG18 promoter arrays (http://www. nimblegen.com). Genome-wide colocalization of H4K12ac binding and endonuclease accessibility was significantly correlated (rs = 0.42, P < 0.0001), indicating...

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