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Method: Aberrant landscapes of maternal meiotic crossovers contribute to aneuploidies in human embryos
- Daniel Ariad,
- Svetlana Madjunkova,
- Mitko Madjunkov,
- Siwei Chen,
- Rina Abramov,
- Clifford Librach,
- and Rajiv C. McCoy
Genome Res. January 2024 34: 70-84; Published in Advance December 1, 2023, doi:10.1101/gr.278168.123
...-specific genetic maps published by deCODE, which were based on whole- sequencing of living parent–offspring trios (Halldorsson et al. 2019), in broad support of the accuracy of our method (Fig. 4). The observed correlation was particularly strong for putative maternal crossovers (r = 0.86) compared with putative...
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Method: Identifying crossovers and shared genetic material in whole genome sequencing data from families
- Kelley Paskov,
- Brianna Chrisman,
- Nathaniel Stockham,
- Peter Yigitcan Washington,
- Kaitlyn Dunlap,
- Jae-Yoon Jung,
- and Dennis P. Wall
Genome Res. October 2023 33: 1747-1756; Published in Advance October 25, 2023, doi:10.1101/gr.277172.122
....5 bp. These crossovers recapitulate existing recombination rate maps, including for the X Chromosome; produce sibling pair IBD that matches expected distributions; and are validated by the haplotype estimation tool SHAPEIT. We provide an efficient, open-source implementation of PhasingFamilies that can...
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Method: Characterization of meiotic recombination intermediates through gene knockouts in founder hybrid mice
- Benjamin Davies,
- Gang Zhang,
- Daniela Moralli,
- Samy Alghadban,
- Daniel Biggs,
- Chris Preece,
- Peter Donnelly,
- and Anjali Gupta Hinch
Genome Res. November 2023 33: 2018-2027; Published in Advance November 17, 2023, doi:10.1101/gr.278024.123
...of DMC1 being downstream from break formation. The signals of RAD51 and RPA in these hotspots have strong correlation with those in Dmc1+/+ mice (Pearson correlation coefficient r = 0.93 and r = 0.96, respectively, for autosomal hotspots). We identified 9023 and 13,348 peaks of RAD51 and RPA in Dmc1...
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Research: Genome-wide variability in recombination activity is associated with meiotic chromatin organization
- Xiaofan Jin,
- Geoff Fudenberg,
- and Katherine S. Pollard
Genome Res. September 2021 31: 1561-1572; Published in Advance July 23, 2021, doi:10.1101/gr.275358.121
..., PC2–PC4 are also negative predictors of crossover likelihood, respectively, indicating that gene bodies, promoters, and extraspatially accessible chromatin are disfavored for crossover formation. We also find a strong positive correlation with chromosomal position as expected from crossover...
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Research: Crossover-active regions of the wheat genome are distinguished by DMC1, the chromosome axis, H3K27me3, and signatures of adaptation
- Andrew J. Tock,
- Daniel M. Holland,
- Wei Jiang,
- Kim Osman,
- Eugenio Sanchez-Moran,
- James D. Higgins,
- Keith J. Edwards,
- Cristobal Uauy,
- F. Chris H. Franklin,
- and Ian R. Henderson
Genome Res. September 2021 31: 1614-1628; Published in Advance August 23, 2021, doi:10.1101/gr.273672.120
...and the chromosome axis protein ASY1 in wheat and investigated their relationships with crossovers, chromatin state, and genetic diversity. DMC1 and ASY1 chromatin immunoprecipitation followed by sequencing (ChIP-seq) revealed strong co-enrichment in the distal, crossover-active regions of the wheat chromosomes...
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Research: Epigenetic activation of meiotic recombination near Arabidopsis thaliana centromeres via loss of H3K9me2 and non-CG DNA methylation
- Charles J. Underwood,
- Kyuha Choi,
- Christophe Lambing,
- Xiaohui Zhao,
- Heïdi Serra,
- Filipe Borges,
- Joe Simorowski,
- Evan Ernst,
- Yannick Jacob,
- Ian R. Henderson,
- and Robert A. Martienssen
Genome Res. April 2018 28: 519-531; Published in Advance March 12, 2018, doi:10.1101/gr.227116.117
...al. 2013). Within this series of mutants, levels of CHG DNA methylation showed a strong negative correlation with CEN3 genetic distance (Pearson's r = −0.93, P = 2.36 × 10−3), whereas CG and CHH methylation were not significantly correlated (Fig. 1D,E; Supplemental Table S2; Stroud et al. 2013...
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ARTICLE: Patterns of Meiotic Recombination on the Long Arm of Human Chromosome 21
- Audrey Lynn,
- Carl Kashuk,
- Michael B. Petersen,
- Jeffrey A. Bailey,
- David R. Cox,
- Stylianos E. Antonarakis,
- and Aravinda Chakravarti
Genome Res. September 1, 2000 10: 1319-1332; doi:10.1101/gr.138100
.... The primary features of recombination on 21q suggest a difference in many aspects of meiosis between males and females. Although recombination is overall more frequent in females than in males, the recombination rate is roughly constant across 21q in female meioses but shows a strong suppression effect...
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Research: Analysis of Arabidopsis genome-wide variations before and after meiosis and meiotic recombination by resequencing Landsberg erecta and all four products of a single meiosis
- Pingli Lu,
- Xinwei Han,
- Ji Qi,
- Jiange Yang,
- Asela J. Wijeratne,
- Tao Li,
- and Hong Ma
Genome Res. March 2012 22: 508-518; Published in Advance November 21, 2011, doi:10.1101/gr.127522.111
...significantly to the understanding of the molecular basis of meiotic recombination, including strong support for the steps in the double-strand break repair model 7These authors contribued equally to this work. 8Present address: Molecular and Cellular Imaging Center (MCIC), Ohio State University/OARDC, Wooster...
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Research: Genetic variation in recalcitrant repetitive regions of the Drosophila melanogaster genome
- Harsh G. Shukla,
- Mahul Chakraborty,
- and J.J. Emerson
Genome Res. September 2025 35: 2023-2040; Published in Advance July 16, 2025, doi:10.1101/gr.280728.125
...on the array (Dover et al. 1993; Elder and Turner 1995; Lower et al. 2018). Untangling patterns of concerted evolution on tandem arrays experiencing different forces requires a comprehensive map of genetic variation spanning such clusters.The cluster of highly conserved histone genes on Chromosome arm 2L...
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Methods: Two-parameter characterization of chromosome-scale recombination rate
- Wentian Li and
- Jan Freudenberg
Genome Res. December 2009 19: 2300-2307; Published in Advance September 14, 2009, doi:10.1101/gr.092676.109
...by introducing a lower bound for the propensity for chiasma formation in a species. Our analysis supports the size of the smaller chromosomes as a strong determinant of -wide RR for the six s studied in this paper (Supplemental Fig. S6). In log–log scale, the correlation coefficient between RR and the shortest...

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