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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
...changes during this developmental transition. The active histone modification H3K4me3 shows particularly dynamic remodeling as germ cells differentiate into oocytes, which suggests a mechanism for establishing early transcription of essential genes during zygotic activation. This analysis highlights...
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Research: Widespread association of the Argonaute protein AGO2 with meiotic chromatin suggests a distinct nuclear function in mammalian male reproduction
- Kimberly N. Griffin,
- Benjamin William Walters,
- Haixin Li,
- Huafeng Wang,
- Giulia Biancon,
- Toma Tebaldi,
- Carolyn B. Kaya,
- Jean Kanyo,
- TuKiet T. Lam,
- Andy L. Cox,
- Stephanie Halene,
- Jean-Ju Chung,
- and Bluma J. Lesch
Genome Res. September 2022 32: 1655-1668; Published in Advance September 15, 2022, doi:10.1101/gr.276578.122
...transcripts in a developmentally dynamic manner. (A) Genome browser tracks (mm10) showing representative AGO2 ChIP peaks in two replicates from each cell type and from Ago2 cKO mixed meiotic and postmeiotic cells. (B) Enrichment of AGO2 on chromatin in premeiotic, meiotic, and postmeiotic male germ cells...
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Research: Nucleosomal signatures impose nucleosome positioning in coding and noncoding sequences in the genome
- Sara González,
- Alicia García,
- Enrique Vázquez,
- Rebeca Serrano,
- Mar Sánchez,
- Luis Quintales,
- and Francisco Antequera
Genome Res. November 2016 26: 1532-1543; Published in Advance September 23, 2016, doi:10.1101/gr.207241.116
...et al. 2013a), which is widely used in the analysis of nucleosome dynamics (Chen et al. 2013b; Beh et al. 2015; Sebé-Pedrós et al. 2016). This tool allows comparing the position of the nucleosome dyad and the degree of positioning and occupancy of individual nucleosomes between different MNase...
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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
...dimethylation (H3K9me2), and DNA methylation in CG and non-CG sequence contexts. However, the role of these chromatin modifications in control of meiotic recombination in the pericentromeres is not fully understood. Here, we show that disruption of Arabidopsis thaliana H3K9me2 and non-CG DNA methylation...
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Research: DNA-guided establishment of nucleosome patterns within coding regions of a eukaryotic genome
- Leslie Y. Beh,
- Manuel M. Müller,
- Tom W. Muir,
- Noam Kaplan,
- and Laura F. Landweber
Genome Res. November 2015 25: 1727-1738; Published in Advance September 1, 2015, doi:10.1101/gr.188516.114
...remained constant in both log-phase and starved nutritional conditions, consistent with previous studies showing that this property remains largely invariant between diverse developmental and nutritional states (Zhang et al. 2011a). Other reports have suggested that nucleosome spacingmay vary between...
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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
.... Abstract Fission yeast Rec12 (Spo11 homolog) initiates meiotic recombination by forming developmentally programmed DNA double-strand breaks (DSBs). DSB distributions influence patterns of heredity and genome evolution, but the basis of the highly nonrandom choice of Rec12 cleavage sites is poorly...
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Research: Adaptation of centromeres to breakage through local genomic and epigenomic remodeling in wheat
- Jingwei Zhou,
- Yuhong Huang,
- Huan Ma,
- Yiqian Chen,
- Chuanye Chen,
- Fangpu Han,
- and Handong Su
Genome Res. November 2025 35: 2461-2471; Published in Advance September 30, 2025, doi:10.1101/gr.280913.125
...Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China; 3State Key Laboratory of Seed Innovation, Institute of Genetics and Developmental Biology, Chinese Academy...
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Resource: Epigenomics of embryogenesis in turbot
- Oscar Aramburu,
- Belen G Pardo,
- Ada Jimenez-Gonzalez,
- Andrés Blanco-Hortas,
- Daniel Macqueen,
- Carmen Bouza,
- and Paulino Martinez
Genome Res. November 4, 2025 gr.280355.124; Published in Advance November 4, 2025, doi:10.1101/gr.280355.124
...developmental stage transitions, highlighting the dynamic regulation 525 associated with the specification and differentiation of diverse cell types 526 comprising the turbot body plan. Chromatin state analyses provided further 527 insights into changes in chromatin state and CRE activity after ZGA is 528...
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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
...-Toneu and Peters 2023). A number of studies have mapped the locations of retained nucleosomes, with the majority of reports in humans and mice finding nucleosomes enriched at CpG island regulatory elements associated with key developmental genes (Arpanahi et al. 2009; Hammoud et al. 2009; Brykczynska et al. 2010...
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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
...synapsis, undergo global transcriptional silencing, a process known as meiotic sex chromosome inactivation (MSCI) (Turner 2007). MSCI is dependent on several proteins involved in DNA damage response (Turner 2007), and the chromatin state established during this process has been found to persist even after...
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