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Research: Nucleosomes and DNA methylation shape meiotic DSB frequency in Arabidopsis thaliana transposons and gene regulatory regions
- Kyuha Choi,
- Xiaohui Zhao,
- Andrew J. Tock,
- Christophe Lambing,
- Charles J. Underwood,
- Thomas J. Hardcastle,
- Heïdi Serra,
- Juhyun Kim,
- Hyun Seob Cho,
- Jaeil Kim,
- Piotr A. Ziolkowski,
- Nataliya E. Yelina,
- Ildoo Hwang,
- Robert A. Martienssen,
- and Ian R. Henderson
Genome Res. April 2018 28: 532-546; Published in Advance March 12, 2018, doi:10.1101/gr.225599.117
...in a plant . To further explore the relationship between meiotic recombination and epigenetic information, in plant genes versus repeats, we mapped SPO11-1-oligonucleotides, crossovers, and chromatin throughout the ∼135 Mb Arabidopsis thaliana , which contains diverse DNA and RNA transposons...
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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
...in which the minisatellite shows meiotic instability depends on the coincidence of a tandem repeat with a DSB hotspot. Conversely, minisatellites can be made unstable in mitosis in yeast strains deficient for some aspects of DNA replication ( Kokoska et al. 1998 ), so the yeast model has already provided...
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RESOURCE: Sequence-based estimation of minisatellite and microsatellite repeat variability
- Matthieu Legendre,
- Nathalie Pochet,
- Theodore Pak,
- and Kevin J. Verstrepen
Genome Res. December 2007 17: 1787-1796; Published in Advance October 31, 2007, doi:10.1101/gr.6554007
...be an additional source of variability ( Viguera et al. 2001 ). Repeats appear to be evenly distributed across the , and repeats located near meiotic hot spots are not noticeably more polymorphic than those located in recombination cold spots ( Richard and Dujon 2006 ). This suggests that the mutation frequency...
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Research: Characterizing nucleotide variation and expansion dynamics in human-specific variable number tandem repeats
- Meredith M. Course,
- Arvis Sulovari,
- Kathryn Gudsnuk,
- Evan E. Eichler,
- and Paul N. Valdmanis
Genome Res. August 2021 31: 1313-1324; Published in Advance July 9, 2021, doi:10.1101/gr.275560.121
...evolution pointed toward both mitotic/meiotic recombination and replication slippage as influencing VNTR expansion and variability (Jeffreys et al. 1985). Repeat directionality (or polarity) has been observed in STRs, where the directionality played a role in instability of the repeat (Eichler et al. 1995...
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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
...minisatellite. CEB310—which exhibited meiotic mutation events, but which we do not here classify as hypermutable—is unusual in that its sequence is 80% AT. It is reminiscent of the tandem repeats studied in Giraudeau et al. (1999) , that is, minisatellites made up of degenerated microsatellite-like repeated...
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Research: Selection and thermostability suggest G-quadruplexes are novel functional elements of the human genome
- Wilfried M. Guiblet,
- Michael DeGiorgio,
- Xiaoheng Cheng,
- Francesca Chiaromonte,
- Kristin A. Eckert,
- Yi-Fei Huang,
- and Kateryna D. Makova
Genome Res. July 2021 31: 1136-1149; Published in Advance June 29, 2021, doi:10.1101/gr.269589.120
...in their thermostability, and this may affect their function. Yet, G4s may also hinder replication, transcription, and translation and may increase instability and mutation rates. Therefore, depending on their genomic location, thermostability, and functionality, G4 loci might evolve under different selective pressures...
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Research: PRDM9 binding organizes hotspot nucleosomes and limits Holliday junction migration
- Christopher L. Baker,
- Michael Walker,
- Shimpei Kajita,
- Petko M. Petkov,
- and Kenneth Paigen
Genome Res. May 2014 24: 724-732; Published in Advance March 6, 2014, doi:10.1101/gr.170167.113
...regions >1 kb nearly devoid of nucleosomes in an arrangement that is similar for meiotic and somatic cells; however, this is difficult to accept given the much repeated observation that hotspots sequences are enriched for H3K4me3 nucleosomes. Shenkar et al. (1991) reported one hotspot that contained...
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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
...( Jeffreys et al. 1998 ). It is therefore possible that the insulin minisatellite may also be associated with a weak hotspot perhaps 3′ to the minisatellite. Consistent with this, sperm mutation studies have revealed a low frequency recombination-based mode of repeat DNA instability in the germline...
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LETTER: Closing the Gaps on Human Chromosome 19 Revealed Genes With a High Density of Repetitive Tandemly Arrayed Elements
- Sun-Hee Leem,
- Natalay Kouprina,
- Jane Grimwood,
- Jung-Hyun Kim,
- Michael Mullokandov,
- Young-Ho Yoon,
- Ji-Youn Chae,
- Jenna Morgan,
- Susan Lucas,
- Paul Richardson,
- Chris Detter,
- Tijana Glavina,
- Eddy Rubin,
- J. Carl Barrett,
- and Vladimir Larionov
Genome Res. February 2004 14: 239-246; Published in Advance January 12, 2004, doi:10.1101/gr.1929904
...in instability of the sequences in microbe hosts, including large blocks of micro- and minisatellites and a high density of Alu repeats. Sequencing of the gap regions, in both BAC and YAC forms, allowed us to generate a complete sequence of four genes, including the neuronal cell signaling gene SCK1/SLI...
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Research: Rare allelic forms of PRDM9 associated with childhood leukemogenesis
- Julie Hussin,
- Daniel Sinnett,
- Ferran Casals,
- Youssef Idaghdour,
- Vanessa Bruat,
- Virginie Saillour,
- Jasmine Healy,
- Jean-Christophe Grenier,
- Thibault de Malliard,
- Stephan Busche,
- Jean-François Spinella,
- Mathieu Larivière,
- Greg Gibson,
- Anna Andersson,
- Linda Holmfeldt,
- Jing Ma,
- Lei Wei,
- Jinghui Zhang,
- Gregor Andelfinger,
- James R. Downing,
- Charles G. Mullighan,
- and Philip Awadalla
Genome Res. March 2013 23: 419-430; Published in Advance December 5, 2012, doi:10.1101/gr.144188.112
...and histone modifications, are associated with genomic instabilities and cancers (Fernandez-Capetillo et al. 2004; Helleday 2010), and congenital genomic rearrangements and aneuploidies have been associated with errors in meiotic recombination (Hassold and Hunt 2001; Sasaki et al. 2010). Such gross genomic...
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