Molecular mechanisms for maintenance of G-rich short tandem repeats capable of adopting G4 DNA structures

2006 ◽  
Vol 598 (1-2) ◽  
pp. 120-131 ◽  
Author(s):  
Hitoshi Nakagama ◽  
Kumiko Higuchi ◽  
Etsuko Tanaka ◽  
Naoto Tsuchiya ◽  
Katsuhiko Nakashima ◽  
...  
Keyword(s):  
Short Tandem Repeats ◽  
Molecular Mechanisms ◽  
Tandem Repeats ◽  
Dna Structures ◽  
G4 Dna ◽  
Short Tandem

scholarly journals APOBEC mutagenesis is low in most types of non-B DNA structures, unlike other types of cancer mutagenesis

2021 ◽  
Author(s):  
Gennady V Ponomarev ◽  
Bulat Fatykhov ◽  
Vladimir A Nazarov ◽  
Ruslan Abasov ◽  
Evgeny Shvarov ◽  
...  
Keyword(s):  
Short Tandem Repeats ◽  
Tandem Repeats ◽  
Somatic Mutations ◽  
Direct Repeats ◽  
Uv Mutagenesis ◽  
Dna Structures ◽  
G Quadruplex ◽  
The Impact ◽  
Very High ◽  
Short Tandem

While somatic mutations are known to be enriched in genome regions with non-canonical DNA secondary structure, the impact of particular mutagens still needs to be elucidated. Here, we demonstrate that in human cancers, the APOBEC mutagenesis is not enriched in direct repeats, mirror repeats, short tandem repeats, and G-quadruplexes, and even decreased below its level in B-DNA for cancer samples with very high APOBEC activity. In contrast, we observe that the APOBEC-induced mutational density is positively associated with APOBEC activity in inverted repeats (cruciform structures), where the impact of cytosine at the 3'-end of the hairpin loop is substantial. Surprisingly, the APOBEC-signature mutation density per TC motif in the single-stranded DNA of a G-quadruplex (G4) is lower than in the four-stranded part of G4 and in B-DNA. The APOBEC mutagenesis, as well as the UV-mutagenesis in melanoma samples are absent in Z-DNA regions, due to depletion of their mutational signature motifs.

scholarly journals DNA polymerase stalling at structured DNA constrains the expansion of Short Tandem Repeats

2020 ◽  
Author(s):  
Pierre Murat ◽  
Guillaume Guilbaud ◽  
Julian E. Sale
Keyword(s):  
Dna Synthesis ◽  
Dna Polymerase ◽  
Dna Sequences ◽  
Short Tandem Repeats ◽  
Tandem Repeats ◽  
Dna Structures ◽  
The Impact ◽  
Eukaryotic Genomes ◽  
Polymerase Slippage ◽  
Short Tandem

AbstractBackgroundShort 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 so, 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.

Population Genetics of Y-Chromosome Short Tandem Repeats in Humans

1997 ◽  
Vol 45 (3) ◽  
pp. 265-270 ◽  
Author(s):  
Anna Pérez-Lezaun ◽  
Francesc Calafell ◽  
Mark Seielstad ◽  
Eva Mateu ◽  
David Comas ◽  
...  
Keyword(s):  
Population Genetics ◽  
Y Chromosome ◽  
Short Tandem Repeats ◽  
Tandem Repeats ◽  
Short Tandem

Conditional Genotypic Probabilities for Microsatellite Loci

Genetics ◽  
2000 ◽  
Vol 155 (4) ◽  
pp. 1973-1980
Author(s):  
Jinko Graham ◽  
James Curran ◽  
B S Weir
Keyword(s):  
Short Tandem Repeats ◽  
Tandem Repeats ◽  
Dirichlet Distribution ◽  
Forensic Dna ◽  
Match Probability ◽  
Microsatellite Genotype ◽  
Allelic State ◽  
Forensic Assessments ◽  
Dna Profiles ◽  
Short Tandem

Abstract Modern forensic DNA profiles are constructed using microsatellites, short tandem repeats of 2–5 bases. In the absence of genetic data on a crime-specific subpopulation, one tool for evaluating profile evidence is the match probability. The match probability is the conditional probability that a random person would have the profile of interest given that the suspect has it and that these people are different members of the same subpopulation. One issue in evaluating the match probability is population differentiation, which can induce coancestry among subpopulation members. Forensic assessments that ignore coancestry typically overstate the strength of evidence against the suspect. Theory has been developed to account for coancestry; assumptions include a steady-state population and a mutation model in which the allelic state after a mutation event is independent of the prior state. Under these assumptions, the joint allelic probabilities within a subpopulation may be approximated by the moments of a Dirichlet distribution. We investigate the adequacy of this approximation for profiled loci that mutate according to a generalized stepwise model. Simulations suggest that the Dirichlet theory can still overstate the evidence against a suspect with a common microsatellite genotype. However, Dirichlet-based estimators were less biased than the product-rule estimator, which ignores coancestry.

scholarly journals Short Tandem Repeats Define a Gestational Origin for Metastatic Choriocarcinoma

2019 ◽  
Vol 108 (2) ◽  
pp. e115-e117
Author(s):  
Kelly Brown ◽  
Robert Homer ◽  
Marina Baine ◽  
Justin D. Blasberg
Keyword(s):  
Short Tandem Repeats ◽  
Tandem Repeats ◽  
Short Tandem

scholarly journals Sex-Specific Migration Patterns in Central Asian Populations, Revealed by Analysis of Y-Chromosome Short Tandem Repeats and mtDNA

1999 ◽  
Vol 65 (1) ◽  
pp. 208-219 ◽  
Author(s):  
Anna Pérez-Lezaun ◽  
Francesc Calafell ◽  
David Comas ◽  
Eva Mateu ◽  
Elena Bosch ◽  
...  
Keyword(s):  
Y Chromosome ◽  
Short Tandem Repeats ◽  
Tandem Repeats ◽  
Migration Patterns ◽  
Asian Populations ◽  
Central Asian ◽  
Short Tandem
Sign in / Sign up

Export Citation Format

Share Document