ArticleGenome biology2020
DNA polymerase stalling at structured DNA constrains the expansion of short tandem repeats.
Article in Genome biology, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 43 papers.
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Who cites it
43 citing papers in PubMed, 71 citations in OpenAlex.
- Magnesium Concentration Modulates Replication Slippage of Mesophilic and Thermophilic DNA Polymerases In Vitro.International journal of molecular sciences · 2026Article
- Genomic distribution characteristics and interspecific differences of microsatellite landscapes in Felidae.BMC genomics · 2026Article
- The role of the nuclear pore complex in the stability of disease-related short tandem DNA repeats.Nucleic acids research · 2026Article
- Non-B DNA structures and their contributions to genetic diversity, aging, and disease.Nucleic acids research · 2026Review
- Emergence and Tandem Repeat-Mediated Elongation of a Translated De Novo Open Reading Frame in Human Oncogenic RNA Gene VPS9D1-AS1 (MYU).Genome biology and evolution · 2026Article
- A Statistical Framework to Infer the Mutation Model of Tandem Repeat Variants.bioRxiv : the preprint server for biology · 2026Article
- Pentanucleotide guanine-rich WGGGW repeats, including CANVAS AGGGA repeats, form a variety of noncanonical structures.Nucleic acids research · 2026Article
- The repertoire of short tandem repeats across the tree of life.Genome biology · 2025Article
- Inherent instability of simple DNA repeats shapes an evolutionarily stable distribution of repeat lengths.Nature communications · 2025Article
- How DNA secondary structures drive replication fork instability.DNA repair · 2025Review
- Comparative analysis of single-stranded and non-canonical DNA formation in human and other ape cells with telomere-to-telomere genomes.bioRxiv : the preprint server for biology · 2025Article
- Diverse short tandem repeat sequences influence gene regulation in human populations.Genome biology · 2025Article
- Comprehensive identification of pathogenic tandem repeat expansions in sporadic amyotrophic lateral sclerosis: advantages of long-read vs. short-read sequencing.Experimental biology and medicine (Maywood, N.J.) · 2025Article
- DNA replication initiation drives focal mutagenesis and rearrangements in human cancers.Nature communications · 2024Article
- DRED: A Comprehensive Database of Genes Related to Repeat Expansion Diseases.Genomics, proteomics & bioinformatics · 2024Article
- Large-scale analysis of small molecule-RNA interactions using multiplexed RNA structure libraries.Communications chemistry · 2024Article
- G-quadruplex landscape and its regulation revealed by a new antibody capture method.Oncotarget · 2024Article
- Ancient and Modern Genomes Reveal Microsatellites Maintain a Dynamic Equilibrium Through Deep Time.Genome biology and evolution · 2024Article
- Article
- Polymorphic short tandem repeats make widespread contributions to blood and serum traits.Cell genomics · 2023Article
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Authors and funding
3 authors at 1 institution in 1 country.
Funding
Abstract
backgroundShort tandem repeats (STRs) contribute significantly to de novo mutagenesis, driving phenotypic diversity and genetic disease. Although highly diverse, their repetitive sequences induce DNA polymerase slippage and stalling, leading to length and sequence variation. However, current studies of DNA synthesis through STRs are restricted to a handful of selected sequences, limiting our broader understanding of their evolutionary behaviour and hampering the characterisation of the determinants of their abundance and stability in eukaryotic genomes.
resultsWe perform a comprehensive analysis of DNA synthesis at all STR permutations and interrogate the impact of STR sequence and secondary structure on their genomic representation and mutability. To do this, we developed a high-throughput primer extension assay that allows monitoring of the kinetics and fidelity of DNA synthesis through 20,000 sequences comprising all STR permutations in different lengths. By combining these measurements with population-scale genomic data, we show that the response of a model replicative DNA polymerase to variously structured DNA is sufficient to predict the complex genomic behaviour of STRs, including abundance and mutational constraints. We demonstrate that DNA polymerase stalling at DNA structures induces error-prone DNA synthesis, which constrains STR expansion.
conclusionsOur data support a model in which STR length in eukaryotic genomes results from a balance between expansion due to polymerase slippage at repeated DNA sequences and point mutations caused by error-prone DNA synthesis at DNA structures.
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.