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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
...the presence of full-length PRDM9 genes in the s of both species, which suggests recombination hotspots in termites might be determined by PRDM9, as they are in mammals. We also find that recombination rates in genes are correlated with inferred levels of germline DNA methylation. The finding of low...
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Research: KRAB zinc-finger proteins regulate endogenous retroviruses to sculpt germline transcriptomes and genome evolution
- Kai Otsuka,
- Akihiko Sakashita,
- So Maezawa,
- Richard M. Schultz,
- and Satoshi H. Namekawa
Genome Res. March 2025 35: 417-431; Published in Advance March 12, 2025, doi:10.1101/gr.279924.124
...functions other than transcriptional repression, may still be evolving toward TE regulation, or may have lost some of their targets owing to the arms race. For example, PRDM9, a well-conserved, and the most ancient, type of KZFP, functions as the determinant of meiotic DNA double-strand break sites during...
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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
...Spring Harbor Laboratory, Cold Spring Harbor, New York 11724, USA Corresponding author: irh25@cam.ac.ukAbstractMeiotic recombination initiates from DNA double-strand breaks (DSBs) generated by SPO11 topoisomerase-like complexes. Meiotic DSB frequency varies extensively along eukaryotic chromosomes...
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Research: The organization of genome duplication is a critical determinant of the landscape of genome maintenance
- Blanca Gómez-Escoda and
- Pei-Yun Jenny Wu
Genome Res. August 2018 28: 1179-1192; Published in Advance June 22, 2018, doi:10.1101/gr.224527.117
...role in shaping the landscape of maintenance.Genome duplication is highly regulated to promote the faithful transmission of the genetic material during cell proliferation. In eukaryotes, DNA synthesis requires the coordinated assembly of conserved factors at the sites of replication initiation...
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Research: Death of PRDM9 coincides with stabilization of the recombination landscape in the dog genome
- Erik Axelsson,
- Matthew T. Webster,
- Abhirami Ratnakumar,
- The LUPA Consortium,
- Chris P. Ponting,
- and Kerstin Lindblad-Toh
Genome Res. January 2012 22: 51-63; Published in Advance October 17, 2011, doi:10.1101/gr.124123.111
..., USA Analysis of diverse eukaryotes has revealed that recombination events cluster in discrete genomic locations known as hotspots. In humans, a zinc-finger protein, PRDM9, is believed to initiate recombination in >40% of hotspots by binding to a specific DNA sequence motif. However, the PRDM9 coding...
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Research: Candida albicans isolates contain frequent heterozygous structural variants and transposable elements within genes and centromeres
- Ursula Oggenfuss,
- Robert T. Todd,
- Natthapon Soisangwan,
- Bailey Kemp,
- Alison Guyer,
- Annette Beach,
- and Anna Selmecki
Genome Res. April 2025 35: 824-838; Published in Advance October 22, 2024, doi:10.1101/gr.279301.124
...mechanisms, including TE mobilization or homologous repair following DNA-double-stranded breaks (Todd et al. 2019, Berdan et al. 2021).The human fungal pathogen Candida albicans is an asexual diploid organism that displays significant genomic plasticity (Vande Zande et al. 2023). SVs are important drivers...
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PERSPECTIVE: The opossum genome: Insights and opportunities from an alternative mammal
- Paul B. Samollow
Genome Res. August 2008 18: 1199-1215; doi:10.1101/gr.065326.107
...be found in Samollow et al. (2007) . In a broader context, M. domestica provides a unique model system with which to explore the roles of large-scale structure, local DNA sequence characteristics, variation in chromatin configuration, and sex in determining rates and patterns of meiotic recombination (for...
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Research: De novo transcriptome assembly of mouse male germ cells reveals novel genes, stage-specific bidirectional promoter activity, and noncoding RNA expression
- Mark E. Gill,
- Alexia Rohmer,
- Serap Erkek-Ozhan,
- Ching-Yeu Liang,
- Sunwoo Chun,
- Evgeniy A. Ozonov,
- and Antoine H.F.M. Peters
Genome Res. December 2023 33: 2060-2078; Published in Advance December 21, 2023, doi:10.1101/gr.278060.123
..., a wide variety of processes occur requiring distinctive transcriptional programs and regulation (Fig. 1A). In early meiotic prophase, DNA double-strand breaks (DSBs) are formed as a necessary intermediate for meiotic recombination and the subsequent reductional chromosome division during meiosis I...
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Resource: RefSeq Functional Elements as experimentally assayed nongenic reference standards and functional interactions in human and mouse
- Catherine M. Farrell,
- Tamara Goldfarb,
- Sanjida H. Rangwala,
- Alexander Astashyn,
- Olga D. Ermolaeva,
- Vichet Hem,
- Kenneth S. Katz,
- Vamsi K. Kodali,
- Frank Ludwig,
- Craig L. Wallin,
- Kim D. Pruitt,
- and Terence D. Murphy
Genome Res. January 2022 32: 175-188; Published in Advance December 7, 2021, doi:10.1101/gr.275819.121
...contain many types of functional elements, including conventional protein-coding and noncoding genes; gene regulatory elements; architectural elements; and elements associated with DNA replication, recombination, and repair. Among those, conventional genes have received the most attention...
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Research: Diversification and collapse of a telomere elongation mechanism
- Bastien Saint-Leandre,
- Son C. Nguyen,
- and Mia T. Levine
Genome Res. June 2019 29: 920-931; Published in Advance May 28, 2019, doi:10.1101/gr.245001.118
...were robust to multiple percentage similarity thresholds to the consensus, minimizing the likelihood that we inadvertently underestimated copy number owing to highly diverged variants (Supplemental Table S4). qPCR on genomic DNA in cases of extreme copy number differences across species validated...

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