title: A novel tRNA variable number tandem repeat at human chromosome 1q23.3 is implicated as a boundary element based on conservation of a CTCF motif in mouse.
abstract: The human genome contains numerous large tandem repeats, many of which remain poorly characterized. Here we report a novel transfer RNA (tRNA) tandem repeat on human chromosome 1q23.3 that shows extensive copy number variation with 9-43 repeat units per allele and displays evidence of meiotic and mitotic instability. Each repeat unit consists of a 7.3 kb GC-rich sequence that binds the insulator protein CTCF and bears the chromatin hallmarks of a bivalent domain in human embryonic stem cells. A tRNA containing tandem repeat composed of at least three 7.6-kb GC-rich repeat units reside within a syntenic region of mouse chromosome 1. However, DNA sequence analysis reveals that, with the exception of the tRNA genes that account for less than 6% of a repeat unit, the remaining 7.2 kb is not conserved with the notable exception of a 24 base pair sequence corresponding to the CTCF binding site, suggesting an important role for this protein at the locus.
authors.affiliation: Department of Biological Science, Florida State University, Tallahassee, FL 32306-4295, USA.
authors.forename: Emily M
authors.initials: EM
authors.lastname: Darrow
authors.affiliation: Department of Biological Science, Florida State University, Tallahassee, FL 32306-4295, USA chadwick@bio.fsu.edu.
authors.forename: Brian P
authors.initials: BP
authors.lastname: Chadwick
mesh_terms: D000483:Alleles; D000818:Animals; D001483:Base Sequence; D001665:Binding Sites; D000076246:CCCTC-Binding Factor; D002460:Cell Line; D002478:Cells, Cultured; D002843:Chromatin / Q000378:metabolism; D002878:Chromosomes, Human, Pair 1; D017124:Conserved Sequence; D004247:DNA / Q000737:chemistry / Q000378:metabolism; D056915:DNA Copy Number Variations; D020077:Endogenous Retroviruses; D020862:GC Rich Sequence; D006801:Humans; D038101:Insulator Elements; D008540:Meiosis / Q000235:genetics; D051379:Mice; D018598:Minisatellite Repeats; D008938:Mitosis / Q000235:genetics; D059372:Nucleotide Motifs; D011323:Primates; D012343:RNA, Transfer / Q000235:genetics*; D012097:Repressor Proteins / Q000378:metabolism*; D020079:Terminal Repeat Sequences
chemical_list: D000076246:CCCTC-Binding Factor; C000619697:CTCF protein, human; D002843:Chromatin; C000619698:Ctcf protein, mouse; D012097:Repressor Proteins; D004247:DNA; D012343:RNA, Transfer
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