title: Human tRNA genes function as chromatin insulators.
abstract: Insulators help separate active chromatin domains from silenced ones. In yeast, gene promoters act as insulators to block the spread of Sir and HP1 mediated silencing while in metazoans most insulators are multipartite autonomous entities. tDNAs are repetitive sequences dispersed throughout the human genome and we now show that some of these tDNAs can function as insulators in human cells. Using computational methods, we identified putative human tDNA insulators. Using silencer blocking, transgene protection and repressor blocking assays we show that some of these tDNA-containing fragments can function as barrier insulators in human cells. We find that these elements also have the ability to block enhancers from activating RNA pol II transcribed promoters. Characterization of a putative tDNA insulator in human cells reveals that the site possesses chromatin signatures similar to those observed at other better-characterized eukaryotic insulators. Enhanced 4C analysis demonstrates that the tDNA insulator makes long-range chromatin contacts with other tDNAs and ETC sites but not with intervening or flanking RNA pol II transcribed genes.
authors.affiliation: Department of MCD Biology, University of California, Santa Cruz, CA, USA.
authors.forename: Jesse R
authors.initials: JR
authors.lastname: Raab
authors.forename: Jonathan
authors.initials: J
authors.lastname: Chiu
authors.forename: Jingchun
authors.initials: J
authors.lastname: Zhu
authors.forename: Sol
authors.initials: S
authors.lastname: Katzman
authors.forename: Sreenivasulu
authors.initials: S
authors.lastname: Kurukuti
authors.forename: Paul A
authors.initials: PA
authors.lastname: Wade
authors.forename: David
authors.initials: D
authors.lastname: Haussler
authors.forename: Rohinton T
authors.initials: RT
authors.lastname: Kamakaka
mesh_terms: D000818:Animals; D002460:Cell Line; D002843:Chromatin / Q000235:genetics; D002886:Chromosomes, Human, Pair 17 / Q000235:genetics; D019295:Computational Biology / Q000379:methods; D004271:DNA, Fungal / Q000235:genetics / Q000378:metabolism; D004742:Enhancer Elements, Genetic / Q000235:genetics; D020868:Gene Silencing; D006801:Humans; D038101:Insulator Elements / Q000235:genetics*; D056484:Jumonji Domain-Containing Histone Demethylases / Q000235:genetics; D008322:Mammals / Q000235:genetics; D011485:Protein Binding; D012320:RNA Polymerase III / Q000378:metabolism; D012343:RNA, Transfer / Q000235:genetics*; D012568:Schizosaccharomyces / Q000235:genetics; D016415:Sequence Alignment; D026801:Synteny; D019474:Transcription Factors, TFIII / Q000378:metabolism; D014158:Transcription, Genetic / Q000235:genetics; D019076:Transgenes; D000098832:Transcription Factor TFIIIC
chemical_list: D002843:Chromatin; D004271:DNA, Fungal; D019474:Transcription Factors, TFIII; D000098832:Transcription Factor TFIIIC; D012343:RNA, Transfer; D056484:Jumonji Domain-Containing Histone Demethylases; D012320:RNA Polymerase III
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