ArticleGenome research2004
Inverted repeat structure of the human genome: the X-chromosome contains a preponderance of large, highly homologous inverted repeats that contain testes genes.
Article in Genome research, 2004. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 166 papers, 1 of them a synthesis that pooled it.
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Who cites it
166 citing papers in PubMed, 1 synthesis or guideline pooled it, 289 citations in OpenAlex.
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- A survey of human cancer-germline genes: Linking X chromosome localization, DNA methylation and sex-biased expression in early embryos.PLoS genetics · 2025Article
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- Large tandem repeats of grass frog (Rana temporaria) in silico and in situ.BMC genomics · 2025Article
- Where Did the Y Chromosome in the Spiny Rat Go, and How Did It Get There?Molecular biology and evolution · 2025Article
- invertiaDB: a database of inverted repeats across organismal genomes.Nucleic acids research · 2025Article
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- Complete chloroplast genomes of three Polygala species and indel marker development for identification of authentic polygalae radix (Polygala tenuifolia).Genes & genomics · 2025Article
106 more citing papers are in PubMed but not listed here.
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Authors and funding
5 authors at 2 institutions in 2 countries.
Funding
Abstract
We have performed the first genome-wide analysis of the Inverted Repeat (IR) structure in the human genome, using a novel and efficient software package called Inverted Repeats Finder (IRF). After masking of known repetitive elements, IRF detected 22,624 human IRs characterized by arm size from 25 bp to >100 kb with at least 75% identity, and spacer length up to 100 kb. This analysis required 6 h on a desktop PC. In all, 166 IRs had arm lengths >8 kb. From this set, IRs were excluded if they were in unfinished/unassembled regions of the genome, or clustered with other closely related IRs, yielding a set of 96 large IRs. Of these, 24 (25%) occurred on the X-chromosome, although it represents only approximately 5% of the genome. Of the X-chromosome IRs, 83.3% were >/=99% identical, compared with 28.8% of autosomal IRs. Eleven IRs from Chromosome X, one from Chromosome 11, and seven already described from Chromosome Y contain genes predominantly expressed in testis. PCR analysis of eight of these IRs correctly amplified the corresponding region in the human genome, and six were also confirmed in gorilla or chimpanzee genomes. Similarity dot-plots revealed that 22 IRs contained further secondary homologous structures partially categorized into three distinct patterns. The prevalence of large highly homologous IRs containing testes genes on the X- and Y-chromosomes suggests a possible role in male germ-line gene expression and/or maintaining sequence integrity by gene conversion.
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