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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
...Genomics PLC, Oxford OX1 1JD, United Kingdom ↵4 These authors equally contributed to this work. Corresponding author: anjali.hinch@well.ox.ac.ukAbstractMammalian meiotic recombination proceeds via repair of hundreds of programmed DNA double-strand breaks, which requires choreographed binding of RPA, DMC1...
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Research: Revisiting chromatin packaging in mouse sperm
- Qiangzong Yin,
- Chih-Hsiang Yang,
- Olga S. Strelkova,
- Jingyi Wu,
- Yu Sun,
- Sneha Gopalan,
- Liyan Yang,
- Job Dekker,
- Thomas G. Fazzio,
- Xin Zhiguo Li,
- Johan Gibcus,
- and Oliver J. Rando
Genome Res. December 2023 33: 2079-2093; Published in Advance December 21, 2023, doi:10.1101/gr.277845.123
...Corresponding author: Oliver.Rando@umassmed.eduAbstractMammalian sperm show an unusual and heavily compacted genomic packaging state. In addition to its role in organizing the compact and hydrodynamic sperm head, it has been proposed that sperm chromatin architecture helps to program gene expression...
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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
...in recombination coldspots, potentially indicating that expression of transferases can inhibit formation of chiasmata during meiotic division. Our results provide novel information about recombination rate variation in holocentric organisms and have particular implications for forthcoming research in population...
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Research: Characterization of the distribution and dynamics of chromatin states in the C. elegans germline reveals substantial H3K4me3 remodeling during oogenesis
- Mariateresa Mazzetto,
- Lauren E. Gonzalez,
- Nancy Sanchez,
- and Valerie Reinke
Genome Res. January 2024 34: 57-69; Published in Advance December 26, 2023, doi:10.1101/gr.278247.123
...Mariateresa Mazzetto, Lauren E. Gonzalez, Nancy Sanchez and Valerie Reinke Department of Genetics, Yale University, New Haven, Connecticut 06520, USA Corresponding author: valerie.reinke@yale.eduAbstractChromatin organization in the C. elegans germline is tightly regulated and critical for germ...
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Research: Evolutionarily diverse determinants of meiotic DNA break and recombination landscapes across the genome
- Kyle R. Fowler,
- Mariko Sasaki,
- Neta Milman,
- Scott Keeney,
- and Gerald R. Smith
Genome Res. October 2014 24: 1650-1664; Published in Advance July 14, 2014, doi:10.1101/gr.172122.114
..., the mechanisms and machinery of meiotic recombination are highly diverse among species. Developmentally programmed DNA double-strand breaks (DSBs) initiate meiotic recombination in the organisms studied most thoroughly at the molecular level, the budding yeast Saccharomyces cerevisiae and the fission yeast...
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ARTICLE: A genome-wide distribution of 8-oxoguanine correlates with the preferred regions for recombination and single nucleotide polymorphism in the human genome
- Mizuki Ohno,
- Tomofumi Miura,
- Masato Furuichi,
- Yohei Tominaga,
- Daisuke Tsuchimoto,
- Kunihiko Sakumi,
- and Yusaku Nakabeppu
Genome Res. May 2006 16: 567-575; doi:10.1101/gr.4769606
.... Mutations are sequence variations in the caused by base substitutions, insertions/deletions, duplications, and recombinations, which largely contribute to genomic diversity in living organisms ( Aquadro et al. 2001 ; Nevo 2001 ). Mutagenesis is known to be a biological outcome of processing damaged DNA...
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Research: Nascent chromatin occupancy profiling reveals locus- and factor-specific chromatin maturation dynamics behind the DNA replication fork
- Mónica P. Gutiérrez,
- Heather K. MacAlpine,
- and David M. MacAlpine
Genome Res. July 2019 29: 1123-1133; Published in Advance June 19, 2019, doi:10.1101/gr.243386.118
...with mature or bulk chromatin (Fig. 3A).View larger version: In this window In a new window Figure 3. Genome-wide nucleosome positioning and occupancy in nascent and mature chromatin. (A) Genome-wide distribution of nascent, mature, and bulk nucleosome positioning. Approximately 70,000 high...
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Research: Environmentally induced plasticity of programmed DNA elimination boosts somatic variability in Paramecium tetraurelia
- Valerio Vitali,
- Rebecca Hagen,
- and Francesco Catania
Genome Res. October 2019 29: 1693-1704; Published in Advance September 23, 2019, doi:10.1101/gr.245332.118
...nuclear differentiation might have a direct impact on the biochemical efficiency of the excision machinery. They might also alter DNA repair pathways coupled with IES elimination. Consistent with this latter hypothesis, intracellular processes coupled with DNA repair, such as meiotic recombination...
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Research: Numerical and spatial patterning of yeast meiotic DNA breaks by Tel1
- Neeman Mohibullah and
- Scott Keeney
Genome Res. February 2017 27: 278-288; Published in Advance December 6, 2016, doi:10.1101/gr.213587.116
...recombination are dangerous lesions that can disrupt integrity, so meiotic cells regulate their number, timing, and distribution. Mechanisms of this regulation remain poorly understood. Here, we use Spo11-oligonucleotide complexes, a byproduct of DSB formation, to reveal aspects of the contribution...
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ARTICLE: Genome-wide regulatory complexity in yeast promoters: Separation of functionally conserved and neutral sequence
- Chen-Shan Chin,
- Jeffrey H. Chuang,
- and Hao Li
Genome Res. February 2005 15: 205-213; Published in Advance January 14, 2005, doi:10.1101/gr.3243305
...Genome-wide regulatory complexity in yeast promoters: Separation of functionally conserved and neutral sequence Chen-Shan Chin 1 , Jeffrey H. Chuang 1 , and Hao Li 2 Department of Biochemistry and Biophysics, University of California, San...

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