Genome-wide analysis of microsatellite repeats in humans: their abundance and density in specific genomic regions
Open accessAbstract
BACKGROUND: Simple sequence repeats (SSRs) are found in most organisms, and occupy about 3% of the human genome. Although it is becoming clear that such repeats are important in genomic organization and function and may be associated with disease conditions, their systematic analysis has not been reported. This is the first report examining the distribution and density of simple sequence repeats (1-6 base-pairs (bp)) in the entire human genome. RESULTS: The densities of SSRs across the human chromosomes were found to be relatively uniform. However, the overall density of SSR was found to be high in chromosome 19. Triplets and hexamers were more predominant in exonic regions compared to intronic and intergenic regions, except for chromosome Y. Comparison of densities of various SSRs revealed that whereas trimers and pentamers showed a similar pattern (500-1,000 bp/Mb) across the chromosomes, di- tetra- and hexa-nucleotide repeats showed patterns of higher (2,000-3,000 bp/Mb) density. Repeats of the same nucleotide were found to be higher than other repeat types. Repeats of A, AT, AC, AAT, AAC, AAG, AGC, AAAC, AAAT, AAAG, AAGG, AGAT predominate, whereas repeats of C, CG, ACT, ACG, AACC, AACG, AACT, AAGC, AAGT, ACCC, ACCG, ACCT, CCCG and CCGG are rare. CONCLUSIONS: The overall SSR density was comparable in all chromosomes. The density of different repeats, however, showed significant variation. Tri- and hexa-nucleotide repeats are more abundant in exons, whereas other repeats are more abundant in non-coding regions.
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Tandem repeat motifs were mostly (>40%) AC- or AG-rich.
“the motifs were predominantly (>40%) AC- (GT- on the opposite strand) or AG- (CT- on the opposite strand) rich”
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- Authors
- Subramanian, S., Mishra, R. K., & Singh, L.
- Affiliations
- Centre for Cellular and Molecular Biology (IN)
- Corresponding author
- Singh, Lalji
- Venue
- Genome Biology
- Published
- 2003-01-23
- Volume
- 4
- Issue
- 2
- Pages
- R13-R13
- ISSN
- 1465-6906 (ISSN-L)
- 1474-760X
- PMC
- PMC151303
- OpenAlex
- W2139353300
- Cited by
- 396
- References
- 23
- Citations by year
- 2026: 14 · 2025: 24 · 2024: 19 · 2023: 11 · 2022: 19 · 2021: 15 · 2020: 22 · 2019: 22 · 2018: 15 · 2017: 20 · 2016: 22 · 2015: 10 · 2014: 15 · 2013: 21 · 2012: 15
- FWCI
- 14.87
- Type
- journal article
- Language
- en
- Open access
- gold
- doi.org
- Licence
- Locations
- Genome biology (publishedVersion)
- Europe PMC (PubMed Central) (publishedVersion, other-oa)
- PubMed Central (publishedVersion, other-oa)
- PubMed (publishedVersion)
- Funders
- Department of Biotechnology, Ministry of Science and Technology, India
- Topics
- Life Sciences › Agricultural and Biological Sciences › Plant Science › Chromosomal and Genetic Variations
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Genomic variations and chromosomal abnormalities
- Health Sciences › Medicine › Pathology and Forensic Medicine › Genetic factors in colorectal cancer
- Keywords
- microsatellite markers, human genome, trinucleotide repeats, hexanucleotide repeats
- MeSH terms
- Humans, Genome, Human, Microsatellite Repeats, Dinucleotide Repeats, Trinucleotide Repeats
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