CTCF binding site classes exhibit distinct evolutionary, genomic, epigenomic and transcriptomic features.

Genome Biology
Kobby EssienSridhar Hannenhalli

Abstract

CTCF (CCCTC-binding factor) is an evolutionarily conserved zinc finger protein involved in diverse functions ranging from negative regulation of MYC, to chromatin insulation of the beta-globin gene cluster, to imprinting of the Igf2 locus. The 11 zinc fingers of CTCF are known to differentially contribute to the CTCF-DNA interaction at different binding sites. It is possible that the differences in CTCF-DNA conformation at different binding sites underlie CTCF's functional diversity. If so, the CTCF binding sites may belong to distinct classes, each compatible with a specific functional role. We have classified approximately 26,000 CTCF binding sites in CD4+ T cells into three classes based on their similarity to the well-characterized CTCF DNA-binding motif. We have comprehensively characterized these three classes of CTCF sites with respect to several evolutionary, genomic, epigenomic, transcriptomic and functional features. We find that the low-occupancy sites tend to be cell type specific. Furthermore, while the high-occupancy sites associate with repressive histone marks and greater gene co-expression within a CTCF-flanked block, the low-occupancy sites associate with active histone marks and higher gene expression. We fou...Continue Reading

References

May 17, 2000·Bioinformatics·G D Stormo
Aug 30, 2001·Trends in Genetics : TIG·R OhlssonV Lobanenkov
Mar 21, 2002·Proceedings of the National Academy of Sciences of the United States of America·Andrew I SuJohn B Hogenesch
Oct 9, 2002·Mammalian Genome : Official Journal of the International Mammalian Genome Society·Samuel Levy, Sridhar Hannenhalli
Apr 18, 2003·Human Molecular Genetics·Terrence S Furey, David Haussler
Jul 23, 2003·Human Molecular Genetics·Minjie DuPaul D Sadowski
Jul 29, 2003·Proceedings of the National Academy of Sciences of the United States of America·John D Storey, Robert Tibshirani
Dec 3, 2003·Molecular and Cellular Biology·Wendy M GombertAnton Krumm
Jan 13, 2004·Science·Andrew M FedoriwMarisa S Bartolomei
Apr 13, 2004·Proceedings of the National Academy of Sciences of the United States of America·Andrew I SuJohn B Hogenesch
Jun 18, 2005·Bioinformatics·Sridhar Hannenhalli, Li-San Wang
Sep 20, 2005·Genome Research·Belinda GiardineAnton Nekrutenko
Dec 31, 2005·Nucleic Acids Research·V MatysE Wingender
May 2, 2006·Proceedings of the National Academy of Sciences of the United States of America·Sébastien VigneauPhilippe Clerc
Sep 6, 2006·Circulation·Sridhar HannenhalliThomas P Cappola
Oct 31, 2006·PLoS Genetics·Robert W RapkinsJennifer A Marshall Graves
Jan 11, 2007·Molecular and Cellular Biology·Igor ChernukhinElena Klenova
Jan 16, 2007·Molecular Cell·Mary E DonohoeJeannie T Lee
Apr 20, 2007·Proceedings of the National Academy of Sciences of the United States of America·Xiaohui XieEric S Lander
Aug 9, 2007·Trends in Genetics : TIG·Timothy A HoreJennifer A Marshall Graves
Jun 6, 2008·PLoS Biology·Carol A EdwardsAnne C Ferguson-Smith
Jul 16, 2008·BioEssays : News and Reviews in Molecular, Cellular and Developmental Biology·Maria GauseDale Dorsett
Aug 8, 2008·Nucleic Acids Research·Raja JothiKeji Zhao
Aug 30, 2008·Annual Review of Genetics·Bernhard Payer, Jeannie T Lee
Oct 17, 2008·The EMBO Journal·Helen HeathNiels Galjart
Apr 24, 2009·Journal of Cell Science·Jordanka Zlatanova, Paola Caiafa
Jul 1, 2009·Cell·Jennifer E Phillips, Victor G Corces

❮ Previous
Next ❯

Citations

Nov 30, 2012·Nucleic Acids Research·Jesse D ZiebarthYan Cui
Aug 16, 2013·Proceedings. Biological Sciences·Alexander J Stewart, Joshua B Plotkin
May 8, 2013·Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences·Sjoerd Johannes Bastiaan Holwerda, Wouter de Laat
Feb 16, 2011·Molecular and Cellular Biology·Purnima SinghPiroska E Szabó
Jun 2, 2011·Molecular and Cellular Biology·Shu LinMarisa S Bartolomei
Nov 26, 2010·Biochemistry and Cell Biology = Biochimie Et Biologie Cellulaire·Michèle Amouyal
Sep 8, 2011·Biochemistry and Cell Biology = Biochimie Et Biologie Cellulaire·Oliver Weth, Rainer Renkawitz
Jan 25, 2012·International Journal of Molecular Sciences·Shahram GolbabapourMaryam Hajrezaei
Aug 19, 2015·Biochemistry and Cell Biology = Biochimie Et Biologie Cellulaire·Thomas Dixon-McDougall, Carolyn Brown
Dec 23, 2015·Neurogastroenterology and Motility : the Official Journal of the European Gastrointestinal Motility Society·J W WileyB D Athey
Apr 6, 2011·Journal of Cellular Physiology·Francesco Paolo Fiorentino, Antonio Giordano
Sep 1, 2015·BMC Genomics·Rongxin FangZhihua Zhang
Apr 17, 2014·Epigenetics : Official Journal of the DNA Methylation Society·Ekaterina S GushchanskayaSergey V Razin
Jan 10, 2013·Current Opinion in Genetics & Development·Kevin Van Bortle, Victor G Corces
Mar 25, 2014·Current Opinion in Genetics & Development·Amy D MarshallJohn E J Rasko
Jun 26, 2013·Cell·Sha SunJeannie T Lee
Jul 7, 2011·Cell·Yesu Jeon, Jeannie T Lee
May 24, 2013·Nucleic Acids Research·Justin MalinSridhar Hannenhalli
Oct 26, 2012·The Behavioral and Brain Sciences·Evan Charney
Nov 5, 2014·Molecular and Cellular Biology·Jose Paolo MagbanuaRobert White
Apr 20, 2018·Nature Communications·Yu Amanda GuoAnders Jacobsen Skanderup
Nov 26, 2010·Proceedings of the National Academy of Sciences of the United States of America·Mirco FanelliSaverio Minucci

❮ Previous
Next ❯

Methods Mentioned

BETA
ChIP-seq
immunoprecipitation
ChIP

Software Mentioned

R package
UCSC browser
_ SCAN
Galaxy
RepeatMasker
DAVID
PWM

Related Concepts

Related Feeds

CREs: Gene & Cell Therapy

Gene and cell therapy advances have shown promising outcomes for several diseases. The role of cis-regulatory elements (CREs) is crucial in the design of gene therapy vectors. Here is the latest research on CREs in gene and cell therapy.