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Method: Fast inference of genetic recombination rates in biobank scale data
- Ardalan Naseri,
- William Yue,
- Shaojie Zhang,
- and Degui Zhi
Genome Res. July 2023 33: 1015-1022; Published in Advance June 22, 2023, doi:10.1101/gr.277676.123
...from 0% to 0.2%. In summary, FastRecomb unleashes the power of biobank-scale haplotype panels for estimating population-specific genetic maps. Given the fact that some human populations may have unique recombination hot spots and their genetic map may differ, it is essential to estimate their unique...
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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
...during meiosis. Errors in this process lead to negative health outcomes, whereas variability in recombination rate affects evolution. In mammals, most crossovers occur in hotspots defined by PRDM9 motifs, although PRDM9 binding peaks are not all equally hot. We hypothesize that dynamic patterns...
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Method: Identifying chromosomal subpopulations based on their recombination histories advances the study of the genetic basis of phenotypic traits
- Carlos Ruiz-Arenas,
- Alejandro Cáceres,
- Marcos López,
- Dolors Pelegrí-Sisó,
- Josefa González,
- and Juan R. González
Genome Res. December 2020 30: 1802-1814; Published in Advance November 17, 2020, doi:10.1101/gr.258301.119
...is a main source of genetic variability. However, the potential role of the variation generated by recombination in phenotypic traits, including diseases, remains unexplored because there is currently no method to infer chromosomal subpopulations based on recombination pattern differences. We developed...
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Resource: Exploration of fine-scale recombination rate variation in the domestic horse
- Samantha K. Beeson,
- James R. Mickelson,
- and Molly E. McCue
Genome Res. October 2019 29: 1744-1752; Published in Advance August 21, 2019, doi:10.1101/gr.243311.118
.... Mammalian recombination hot spots: properties, control and evolution. Nat Rev Genet 11: 221–233. doi:10.1038/nrg2712 ↵Pedregosa F, Varoquaux G, Gramfort A, Michel V, Thirion B, Grisel O, Blondel M, Prettenhofer P, Weiss R, Dubourg V, et al. 2011. Scikit-learn: machine learning in Python. J Mach Learn Res 12...
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LETTER: Mutation hot spots in mammalian mitochondrial DNA
- Nicolas Galtier,
- David Enard,
- Yoan Radondy,
- Eric Bazin,
- and Khalid Belkhir
Genome Res. February 2006 16: 215-222; Published in Advance December 14, 2005, doi:10.1101/gr.4305906
...is obviously of primary interest given the many diseases associated with mitochondrial mutations in humans. Now back to the mutation hot spots versus recombination debate. This study aimed at testing whether mutation hot spots actually occurred in the coding region of the mitochondrial . The answer...
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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
...segregation. During meiosis, centromeres are suppressed for inter-homolog crossover, as recombination in these regions can cause chromosome missegregation and aneuploidy. Plant centromeres are surrounded by transposon-dense pericentromeric heterochromatin that is epigenetically silenced by histone 3 lysine 9...
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Resource: Indels, structural variation, and recombination drive genomic diversity in Plasmodium falciparum
- Alistair Miles,
- Zamin Iqbal,
- Paul Vauterin,
- Richard Pearson,
- Susana Campino,
- Michel Theron,
- Kelda Gould,
- Daniel Mead,
- Eleanor Drury,
- John O'Brien,
- Valentin Ruano Rubio,
- Bronwyn MacInnis,
- Jonathan Mwangi,
- Upeka Samarakoon,
- Lisa Ranford-Cartwright,
- Michael Ferdig,
- Karen Hayton,
- Xin-zhuan Su,
- Thomas Wellems,
- Julian Rayner,
- Gil McVean,
- and Dominic Kwiatkowski
Genome Res. September 2016 26: 1288-1299; Published in Advance August 16, 2016, doi:10.1101/gr.203711.115
...) yielding a total of 1194 COs, 230 NCOs, and 331 conversion tracts for further analysis (Supplemental Figs. S10, S11). Gene coding regions are warm-spots and centromeres are cold-spots of CO recombination Combining CO events from all three crosses, the total map length of the core was 15.7 Morgans (95...
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Method: De novo mutation rates at the single-mutation resolution in a human HBB gene region associated with adaptation and genetic disease
- Daniel Melamed,
- Yuval Nov,
- Assaf Malik,
- Michael B. Yakass,
- Evgeni Bolotin,
- Revital Shemer,
- Edem K. Hiadzi,
- Karl L. Skorecki,
- and Adi Livnat
Genome Res. March 2022 32: 488-498; Published in Advance January 14, 2022, doi:10.1101/gr.276103.121
...(Inoue et al. 2001; Crow et al. 2009; Dumas et al. 2012; Losos 2017; Kratochwil et al. 2019; Kratochwil and Meyer 2019; Lind 2019; Xie et al. 2019), to its contribution to recurrent genetic disease and cancer (Lupski 1998; McClellan and King 2010; Veltman and Brunner 2012; Shendure and Akey 2015).The...
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Method: Sensitive mapping of recombination hotspots using sequencing-based detection of ssDNA
- Pavel P. Khil,
- Fatima Smagulova,
- Kevin M. Brick,
- R. Daniel Camerini-Otero,
- and Galina V. Petukhova
Genome Res. May 2012 22: 957-965; Published in Advance February 24, 2012, doi:10.1101/gr.130583.111
...recombination hot spots. Annu Rev Genet 41: 369–399. ↵ Bellve AR, Cavicchia JC, Millette CF, O'Brien DA, Bhatnagar YM, Dym M Bellve AR, Cavicchia JC, Millette CF, O'Brien DA, Bhatnagar YM, Dym M. 1977. Spermatogenic cells of the prepuberal mouse. Isolation and morphological characterization. J Cell Biol 74: 68...
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Method: An extended set of yeast-based functional assays accurately identifies human disease mutations
- Song Sun,
- Fan Yang,
- Guihong Tan,
- Michael Costanzo,
- Rose Oughtred,
- Jodi Hirschman,
- Chandra L. Theesfeld,
- Pritpal Bansal,
- Nidhi Sahni,
- Song Yi,
- Analyn Yu,
- Tanya Tyagi,
- Cathy Tie,
- David E. Hill,
- Marc Vidal,
- Brenda J. Andrews,
- Charles Boone,
- Kara Dolinski,
- and Frederick P. Roth
Genome Res. May 2016 26: 670-680; Published in Advance March 14, 2016, doi:10.1101/gr.192526.115
...HYC-LEU2. These modifications were achieved by separate PCR amplification of the pHiDest-DB backbone and natMX4 cassette followed by homologous recombination in yeast. Sequences of primers used are listed in Supplemental Table S5. The wild-type or mutated disease-associated ORFs and the GFP gene were...
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