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.
Highlights
Almost two-thirds of the human genome is composed of repetitive DNA [1], a proportion of which corresponds to tandem repeats
We examined the human genome (GRCh37/hg19) using the University of California Santa Cruz (UCSC) Genome Browser [26] for the presence of large tandem repeats that displayed high GC content and a signature of repeat units arranged in tandem based on Repeat Masker output
We describe the organization of a novel tDNA tandem repeat on human chromosome 1q23.3 that displays extensive copy number variation (CNV), making it the first tDNA variable number tandem repeats (VNTRs) to be described in the human genome
Summary
Almost two-thirds of the human genome is composed of repetitive DNA [1], a proportion of which corresponds to tandem repeats. Tandem repeats consist of DNA sequences organized into a head-to-tail arrangement, and size of the individual repeating unit varies from just a few base pairs (bp) in the case of microsatellites [2] to several kilobases (kb) for some of the largest tandem repeats in the human genome [3]. A handful of the large tandem repeats, or macrosatellites, are well characterized, with many corresponding to gaps in our genome sequence due to the inherent difficulty with the assembly of repeat DNA [4]. The copy number of individual repeat units within a macrosatellite varies between in-
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