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Research: Lambdoid phages with abundant Chi recombination hotspots reflect diverse viral strategies for recombination-dependent growth
- Clarence Zheng,
- Sherwood R. Casjens,
- Alan R. Davidson,
- Susan K. Amundsen,
- and Gerald R. Smith
Genome Res. August 2025 35: 1767-1780; Published in Advance July 10, 2025, doi:10.1101/gr.280248.124
...Fagagna et al. 2003; Bhattacharyya et al. 2018; Wilkinson et al. 2022). P22 Abc2 binds to the RecC subunit and blocks activation at Chi recombination hotspots (Murphy and Lewis 1993; Wilkinson et al. 2022). λ Gam and ø80 GamL have very different amino acid sequences (i.e., are different sequence types...
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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
..., Uniformed Services University of the Health Sciences, Bethesda, Maryland 20814, USA ↵3 These authors contributed equally to this work. AbstractMeiotic DNA double-stranded breaks (DSBs) initiate genetic recombination in discrete areas of the called recombination hotspots. DSBs can be directly mapped using...
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Research: Unexpectedly low recombination rates and presence of hotspots in termite genomes
- Turid Everitt,
- Tilman Rönneburg,
- Daniel Elsner,
- Anna Olsson,
- Yuanzhen Liu,
- Tuuli Larva,
- Judith Korb,
- and Matthew T. Webster
Genome Res. May 2025 35: 1124-1137; Published in Advance March 20, 2025, doi:10.1101/gr.279180.124
...Unexpectedly low recombination rates and presence of hotspots in termite s Turid Everitt1,5, Tilman Rönneburg1,5, Daniel Elsner2, Anna Olsson1, Yuanzhen Liu1, Tuuli Larva1, Judith Korb2,3 and Matthew T. Webster1,4 1Medical Biochemistry and Microbiology, Uppsala University, 751 23 Uppsala, Sweden; 2...
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Research: Multiple paralogs and recombination mechanisms contribute to the high incidence of 22q11.2 deletion syndrome
- Lisanne Vervoort,
- Nicolas Dierckxsens,
- Marta Sousa Santos,
- Senne Meynants,
- Erika Souche,
- Ruben Cools,
- Tracy Heung,
- Koen Devriendt,
- Hilde Peeters,
- Donna M. McDonald-McGinn,
- Ann Swillen,
- Jeroen Breckpot,
- Beverly S. Emanuel,
- Hilde Van Esch,
- Anne S. Bassett,
- and Joris R. Vermeesch
Genome Res. April 2025 35: 786-797; Published in Advance November 13, 2024, doi:10.1101/gr.279331.124
...-read sequencing cannot resolve the complex segmental duplications (SDs) to provide direct confirmation of the hypothesis that the rearrangements are caused by nonallelic homologous recombination between the low copy repeats on Chromosome 22 (LCR22s). To enable haplotype-specific assembly and rearrangement mapping...
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Method: Localizing unmapped sequences with families to validate the Telomere-to-Telomere assembly and identify new hotspots for genetic diversity
- Brianna Chrisman,
- Chloe He,
- Jae-Yoon Jung,
- Nate Stockham,
- Kelley Paskov,
- Peter Washington,
- Juli Petereit,
- and Dennis P. Wall
Genome Res. October 2023 33: 1734-1746; Published in Advance October 25, 2023, doi:10.1101/gr.277175.122
..., as well as a median region length of 1.3 Mb. ASLAN again showed a slight preference toward localizing to Chromosome 6, which has a disproportionate number of recombination points. There are some specific hotspots for incorrect localizations, as shown by the spikes in Chromosomes 6 and 8 in Supplemental...
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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
.... For 500-kb resolution, all the methods achieve a high correlation coefficient close to one. We also analyzed the five highest recombination rate locations in deCODE (Chr 20) to examine how the hotspots are replicated. We compared the top five recombination rates inferred by different tools to deCODE using...
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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
...for RAD51 and 8.1a, 9.1a, and 9.1b for RPA). We observed that RAD51 and RPA ChIP-seq reads cluster into small regions that match known recombination hotspots identified by mapping of these proteins in Dmc1+/+ mice with the same genetic background (Hinch et al. 2019), which is consistent with the role...
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Resource: The fine-scale recombination rate variation and associations with genomic features in a butterfly
- Aleix Palahí i Torres,
- Lars Höök,
- Karin Näsvall,
- Daria Shipilina,
- Christer Wiklund,
- Roger Vila,
- Peter Pruisscher,
- and Niclas Backström
Genome Res. May 2023 33: 810-823; Published in Advance June 12, 2023, doi:10.1101/gr.277414.122
.... This protein recognizes specific sequence motifs where histone H3 trimethylation is induced, which explains that most recombination events occur in a limited portion of the , that is, recombination hotspots (e.g., Myers et al. 2005; Grey et al. 2011). The gene PRDM9 is found in several vertebrate...
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Research: Variation in mutation, recombination, and transposition rates in Drosophila melanogaster and Drosophila simulans
- Yiguan Wang,
- Paul McNeil,
- Rashidatu Abdulazeez,
- Marta Pascual,
- Susan E. Johnston,
- Peter D. Keightley,
- and Darren J. Obbard
Genome Res. April 2023 33: 587-598; Published in Advance April 10, 2023, doi:10.1101/gr.277383.122
...Departament de Genètica, Microbiologia i Estadística and IRBio, Universitat de Barcelona, 08028 Barcelona, Spain Corresponding author: yiguan.wang@ed.ac.ukAbstractThe rates of mutation, recombination, and transposition are core parameters in models of evolution. They impact genetic diversity, responses...
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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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