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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
...in Arabidopsis thaliana inbred lines. Nature 465: 627–631. ↵Benson G. 1999. Tandem repeats finder: a program to analyze DNA sequences. Nucleic Acids Res 27: 573–580. ↵Bilgin Sonay T, Carvalho T, Robinson M, Greminger M, Krutzen M, Comas D, Highnam G, Mittelman DA, Sharp AJ, Marques-Bonet T, et al. 2015. Tandem...
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Research: A novel quantitative trait locus implicates Msh3 in the propensity for genome-wide short tandem repeat expansions in mice
- Mikhail O. Maksimov,
- Cynthia Wu,
- David G. Ashbrook,
- Flavia Villani,
- Vincenza Colonna,
- Nima Mousavi,
- Nichole Ma,
- Lu Lu,
- Jonathan K. Pritchard,
- Alon Goren,
- Robert W. Williams,
- Abraham A. Palmer,
- and Melissa Gymrek
Genome Res. May 2023 33: 689-702; Published in Advance May 1, 2023, doi:10.1101/gr.277576.122
...microsatellite alterations at selected tetranucleotide repeats (EMAST) and to lower levels of MSI at dinucleotide repeats (Haugen et al. 2008; Campregher et al. 2012).Naturally occurring sequence variants in Msh3 have been shown to act as modifiers of the stability of CAG repeats in both mice and humans. Tomé et...
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Research: Genome-wide evidence for selection acting on single amino acid repeats
- Wilfried Haerty and
- G. Brian Golding
Genome Res. June 2010 20: 755-760; Published in Advance January 7, 2010, doi:10.1101/gr.101246.109
.... Highly constrained proteins contain an unexpectedly large number of amino acid tandem repeats. Genomics 89: 316–325. Ramensky VE, Nurtdinov RN, Neverov AD, Mironov AA, GelfandMS. 2008. Positive selection in alternatively spliced exons of human genes. Am J Hum Genet 83: 94–98. Rolfsmeier ML, Lahue RS...
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Research: Germline mutation rates and the long-term phenotypic effects of mutation accumulation in wild-type laboratory mice and mutator mice
- Arikuni Uchimura,
- Mayumi Higuchi,
- Yohei Minakuchi,
- Mizuki Ohno,
- Atsushi Toyoda,
- Asao Fujiyama,
- Ikuo Miura,
- Shigeharu Wakana,
- Jo Nishino,
- and Takeshi Yagi
Genome Res. August 2015 25: 1125-1134; Published in Advance June 30, 2015, doi:10.1101/gr.186148.114
.... All capable females were bred in a one-to-one natural mating with a male sibling over a 1-wk period, and mating was repeated as necessary to obtain the required number of mice. Sibling males were selected arbitrarily. Mice with prostration (possibly due to thymic lymphoma or hydrocephaly) were...
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Research: Intron evolution in Neurospora: the role of mutational bias and selection
- Yu Sun,
- Carrie A. Whittle,
- Pádraic Corcoran,
- and Hanna Johannesson
Genome Res. January 2015 25: 100-110; Published in Advance October 23, 2014, doi:10.1101/gr.175653.114
...al. 2003). Mechanisms for intron gain Intron gain via NHEJ is expected to leave short direct repeats (;5–12 bp) spanning both sides of intron-exon borders, a pattern that may be gradually erased by accumulated nucleotide substitutions over time (Li et al. 2009; Farlow et al. 2011). We scanned...
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Research: Extensive chromosomal reshuffling drives evolution of virulence in an asexual pathogen
- Ronnie de Jonge,
- Melvin D. Bolton,
- Anja Kombrink,
- Grardy C.M. van den Berg,
- Koste A. Yadeta,
- and Bart P.H.J. Thomma
Genome Res. August 2013 23: 1271-1282; Published in Advance May 16, 2013, doi:10.1101/gr.152660.112
...1), collectively amounting to 236,785 nonredundant polymorphic sites. Of these, 78,342 (32.9%) occurred in protein-coding regions, of which 55% were synonymous, not affecting the protein sequence, and 45% were nonsynonymous (Table 1). To determine selection strength, the ratio of nonsynonymous (d...
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Method: Proteome-wide discovery of mislocated proteins in cancer
- KiYoung Lee,
- Kyunghee Byun,
- Wonpyo Hong,
- Han-Yu Chuang,
- Chan-Gi Pack,
- Enkhjargal Bayarsaikhan,
- Sun Ha Paek,
- Hyosil Kim,
- Hye Young Shin,
- Trey Ideker,
- and Bonghee Lee
Genome Res. August 2013 23: 1283-1294; Published in Advance May 14, 2013, doi:10.1101/gr.155499.113
...a conditional location predictor (CoLP). Using CoLP, we mapped the locations of over 10,000 proteins in normal human brain and in glioma. The prediction showed 0.9 accuracy using 100 location tests of 20 randomly selected proteins. Of the 10,000 proteins, over 150 have a strong likelihood of mislocation under...
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Research: Genome-wide patterns of natural variation reveal strong selective sweeps and ongoing genomic conflict in Drosophila mauritiana
- Viola Nolte,
- Ram Vinay Pandey,
- Robert Kofler,
- and Christian Schlötterer
Genome Res. January 2013 23: 99-110; Published in Advance October 10, 2012, doi:10.1101/gr.139873.112
...Genome-wide patterns of natural variation reveal strong selective sweeps and ongoing genomic conflict in Drosophila mauritiana Viola Nolte , Ram Vinay Pandey , Robert Kofler and Christian Schlötterer 1 Institut für Populationsgenetik...
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LETTER: Highly efficient concerted evolution in the ribosomal DNA repeats: Total rDNA repeat variation revealed by whole-genome shotgun sequence data
- Austen R.D. Ganley and
- Takehiko Kobayashi
Genome Res. February 2007 17: 184-191; Published in Advance January 2, 2007, doi:10.1101/gr.5457707
...explain this pattern, although in this case selection is the critical force maintaining the repeats. The level of intragenomic variation is the key difference between these two forms of evolution. The prohibitive size and repetitive nature of large repeat arrays have made determination of the absolute...
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Review: The structure, function, and evolution of plant centromeres
- Matthew Naish and
- Ian R. Henderson
Genome Res. February 2024 34: 161-178; Published in Advance March 14, 2024, doi:10.1101/gr.278409.123
...to spindle microtubules during cell division. Notably, although centromeres maintain a conserved function in chromosome segregation, the underlying DNA sequences are diverse both within and between species and are predominantly repetitive in nature. The repeat content of centromeres includes high-copy tandem...
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