ArticleMobile DNA2020
Finding and extending ancient simple sequence repeat-derived regions in the human genome.
Article in Mobile DNA, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 20 papers.
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Who cites it
20 citing papers in PubMed.
- The role of the nuclear pore complex in the stability of disease-related short tandem DNA repeats.Nucleic acids research · 2026Article
- Birth-Death Dynamics of Microsatellites: Mechanistic Insights from Orthologous Loci in Felidae.Genes · 2025Article
- Diverse short tandem repeat sequences influence gene regulation in human populations.Genome biology · 2025Article
- Emerging drivers of DNA repeat expansions.Biochemical Society transactions · 2025Review
- Comparative genomics of endophytic fungi Apiospora malaysiana with related ascomycetes indicates adaptation attuned to lifestyle choices with potential sustainable cellulolytic activity.DNA research : an international journal for rapid publication of reports on genes and genomes · 2025Article
- Recurrent DNA nicks drive massive expansions of (GAA)Proceedings of the National Academy of Sciences of the United States of America · 2024Article
- Sequence composition changes in short tandem repeats: heterogeneity, detection, mechanisms and clinical implications.Nature reviews. Genetics · 2024Review
- Short tandem repeat expansions in cortical layer-specific genes implicate in phenotypic severity and adaptability of autism spectrum disorder.Psychiatry and clinical neurosciences · 2024Article
- Functional implications of paralog genes in polyglutamine spinocerebellar ataxias.Human genetics · 2023Review
- Article
- Pattern and variation in simple sequence repeat (SSR) at different genomic regions and its implications to maize evolution and breeding.BMC genomics · 2023Article
- A postmortem MRI study of cerebrovascular disease and iron content at end-stage of fragile X-associated tremor/ataxia syndrome.Research square · 2023Article
- Methodologies for theGenes · 2022Review
- Comprehensive genetic diagnosis of tandem repeat expansion disorders with programmable targeted nanopore sequencing.Science advances · 2022Article
- Advancing genomic technologies and clinical awareness accelerates discovery of disease-associated tandem repeat sequences.Genome research · 2022Review
- Finding and Characterizing Repeats in Plant Genomes.Methods in molecular biology (Clifton, N.J.) · 2022Article
- Molecular mechanisms underlying nucleotide repeat expansion disorders.Nature reviews. Molecular cell biology · 2021Review
- The Simple Biology of Flipons and Condensates Enhances the Evolution of Complexity.Molecules (Basel, Switzerland) · 2021Review
- An update on the neurological short tandem repeat expansion disorders and the emergence of long-read sequencing diagnostics.Acta neuropathologica communications · 2021Review
- Review
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Authors and funding
5 authors.
Funding
Abstract
backgroundPreviously, 3% of the human genome has been annotated as simple sequence repeats (SSRs), similar to the proportion annotated as protein coding. The origin of much of the genome is not well annotated, however, and some of the unidentified regions are likely to be ancient SSR-derived regions not identified by current methods. The identification of these regions is complicated because SSRs appear to evolve through complex cycles of expansion and contraction, often interrupted by mutations that alter both the repeated motif and mutation rate. We applied an empirical, kmer-based, approach to identify genome regions that are likely derived from SSRs.
resultsThe sequences flanking annotated SSRs are enriched for similar sequences and for SSRs with similar motifs, suggesting that the evolutionary remains of SSR activity abound in regions near obvious SSRs. Using our previously described P-clouds approach, we identified 'SSR-clouds', groups of similar kmers (or 'oligos') that are enriched near a training set of unbroken SSR loci, and then used the SSR-clouds to detect likely SSR-derived regions throughout the genome.
conclusionsOur analysis indicates that the amount of likely SSR-derived sequence in the human genome is 6.77%, over twice as much as previous estimates, including millions of newly identified ancient SSR-derived loci. SSR-clouds identified poly-A sequences adjacent to transposable element termini in over 74% of the oldest class of
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