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Research: Intragenic repeat expansion in the cell wall protein gene HPF1 controls yeast chronological aging
- Benjamin P. Barré,
- Johan Hallin,
- Jia-Xing Yue,
- Karl Persson,
- Ekaterina Mikhalev,
- Agurtzane Irizar,
- Sylvester Holt,
- Dawn Thompson,
- Mikael Molin,
- Jonas Warringer,
- and Gianni Liti
Genome Res. May 2020 30: 697-710; Published in Advance April 10, 2020, doi:10.1101/gr.253351.119
...of intragenic tandem repeats within the N-terminal domain of HPF1 was sufficient to cause pronounced life span shortening. Life span impairment by HPF1 was buffered by rapamycin but not by calorie restriction. The HPF1 repeat expansion shifted yeast cells from a sedentary to a buoyant state, thereby increasing...
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LETTER: Predicting Human Minisatellite Polymorphism
- France Denoeud,
- Gilles Vergnaud,
- and Gary Benson
Genome Res. May 1, 2003 13: 856-867; Published in Advance April 14, 2003, doi:10.1101/gr.574403
...below, would preclude finding both highly polymorphic and hypermutable repeats. The purpose of this report is to define inexpensive strategies to accelerate the search for highly polymorphic minisatellites. The goal has been the development of sequence-based predictive criteria for polymorphism. Results...
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Research: Tandem repeat variation in human and great ape populations and its impact on gene expression divergence
- Tugce Bilgin Sonay,
- Tiago Carvalho,
- Mark D. Robinson,
- Maja P. Greminger,
- Michael Krützen,
- David Comas,
- Gareth Highnam,
- David Mittelman,
- Andrew Sharp,
- Tomàs Marques-Bonet,
- and Andreas Wagner
Genome Res. November 2015 25: 1591-1599; Published in Advance August 19, 2015, doi:10.1101/gr.190868.115
...andmicrosatellite repeat variability.Genome Res17: 1787–1796. Lehner B. 2008. Selection to minimise noise in living systems and its implications for the evolution of gene expression. Mol Syst Biol 4: 170. Li Y-C, Korol AB, Fahima T, Beiles A, Nevo E. 2002. Microsatellites: genomic distribution, putative functions...
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Method: Multisample motif discovery and visualization for tandem repeats
- Yaran Zhang,
- Marc Hulsman,
- Alex Salazar,
- Niccolò Tesi,
- Lydian Knoop,
- Sven van der Lee,
- Sanduni Wijesekera,
- Jana Krizova,
- Erik-Jan Kamsteeg,
- and Henne Holstege
Genome Res. April 2025 35: 850-862; Published in Advance November 13, 2024, doi:10.1101/gr.279278.124
..., we addressed this issue by aligning sequences based on their motif composition, performing alignment on so-called “motif sequences,” which lead to a more biologically relevant alignment. This approach also enhances the visual representation and comparability of repeat loci, particularly for analyzing...
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LETTER: Global Haplotype Diversity in the Human Insulin Gene Region
- John D.H. Stead,
- Matthew E. Hurles,
- and Alec J. Jeffreys
Genome Res. September 2003 13: 2101-2111; doi:10.1101/gr.948003
...will be biased upwards, as individuals were selected for sequencing based on maximal diversity at the minisatellite, similar estimates were derived from haplotype data (described below) on unselected chromosomes, which will be biased downwards because only known variants were typed on most chromosomes (data...
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REVIEW: Minisatellites: Mutability and Genome Architecture
- Gilles Vergnaud and
- France Denoeud
Genome Res. July 1, 2000 10: 899-907; doi:10.1101/gr.10.7.899
...provided the first highly polymorphic, multiallelic markers for linkage studies ( Nakamura et al. 1987 ). The usefulness of polymorphic minisatellites (also called VNTRs for variable number of tandem repeats) in the early stages of human mapping is reflected in the Centre d'Etude du Polymorphisme Humain...
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Research: Massive variation of short tandem repeats with functional consequences across strains of Arabidopsis thaliana
- Maximilian O. Press,
- Rajiv C. McCoy,
- Ashley N. Hall,
- Joshua M. Akey,
- and Christine Queitsch
Genome Res. August 2018 28: 1169-1178; Published in Advance July 3, 2018, doi:10.1101/gr.231753.117
...author: queitsch@uw.eduAbstractShort tandem repeat (STR) mutations may comprise more than half of the mutations in eukaryotic coding DNA, yet STR variation is rarely examined as a contributor to complex traits. We assessed this contribution across a collection of 96 strains of Arabidopsis thaliana...
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LETTER: Abundance and length of simple repeats in vertebrate genomes are determined by their structural properties
- Albino Bacolla,
- Jacquelynn E. Larson,
- Jack R. Collins,
- Jian Li,
- Aleksandar Milosavljevic,
- Peter D. Stenson,
- David N. Cooper,
- and Robert D. Wells
Genome Res. October 2008 18: 1545-1553; Published in Advance August 7, 2008, doi:10.1101/gr.078303.108
...) Initial sequencing and analysis of the human . Nature 409 : 860 – 921 . ↵ Legendre, M. , Pochet, N. , Pak, T. , Verstrepen, K.J. ( 2007 ) Sequence-based estimation of minisatellite and microsatellite repeat variability . Genome Res. 17 : 1787 – 1796 . ↵ Lin, Y. , Dion, V. , Wilson, J.H. ( 2006...
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Research: Natural variation in C. elegans short tandem repeats
- Gaotian Zhang,
- Ye Wang,
- and Erik C. Andersen
Genome Res. October 2022 32: 1852-1861; Published in Advance October 4, 2022, doi:10.1101/gr.277067.122
...types of mutations, such as single nucleotide variants (SNVs) and short insertions or deletions (indels) (Lynch 2010; Sun et al. 2012; Willems et al. 2016; Gymrek et al. 2017). The precise mutation rates of STRs are highly variable across different loci and are affected by motif sequences and repeat...
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Method: MIPSTR: a method for multiplex genotyping of germline and somatic STR variation across many individuals
- Keisha D. Carlson,
- Peter H. Sudmant,
- Maximilian O. Press,
- Evan E. Eichler,
- Jay Shendure,
- and Christine Queitsch
Genome Res. May 2015 25: 750-761; Published in Advance February 6, 2015, doi:10.1101/gr.182212.114
...tandem repeats (STRs), which are also known as microsatellites, significantly contributes to phenotypic variation, evolutionary adaptation, and human disease (Gemayel et al. 2012). STRs consist of short (2–10 bp) DNA sequences (units) that are repeated head to tail. The presence of multiple identical...

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