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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
...transcription, the accompanying changes to chromatin structure and how those changes contribute to correct activation in the early embryo are not well characterized (Robert et al. 2015).Functional and genomic studies have revealed some epigenetic regulatory mechanisms that influence germline chromatin...
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Resource: Multitissue single-nucleus RNA-seq reveals cell type–specific regulatory patterns of alternative polyadenylation in pigs
- Qiuhan Wen,
- Zhen Wang,
- Qi Bao,
- Tianli Ding,
- Haihan Zhang,
- Jianbo Li,
- Zhuang Liu,
- Jieping Huang,
- and Guoqiang Yi
Genome Res. September 2025 35: 2116-2129; Published in Advance June 16, 2025, doi:10.1101/gr.280095.124
...Global 3′ UTR shortening, exhibiting cell type–specific patterns, has been reported in some model organisms, such as mice and Drosophila (Shulman and Elkon 2019; Lee et al. 2022). However, in pigs, the dynamics of these patterns, particularly at single-cell resolution, remain largely unexplored. Given...
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Research: Developmental timing of programmed DNA elimination in Paramecium tetraurelia recapitulates germline transposon evolutionary dynamics
- Coralie Zangarelli,
- Olivier Arnaiz,
- Mickaël Bourge,
- Kevin Gorrichon,
- Yan Jaszczyszyn,
- Nathalie Mathy,
- Loïc Escoriza,
- Mireille Bétermier,
- and Vinciane Régnier
Genome Res. November/December 2022 32: 2028-2042; Published in Advance November 23, 2022, doi:10.1101/gr.277027.122
...) that coexist with a polyploid somatic macronucleus (MAC) responsible for gene expression. During sexual processes (conjugation of compatible reactive partners or a self-fertilization process called autogamy), the MICs undergo meiosis and transmit the germline to the diploid zygotic nucleus through...
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Resource: A spatiotemporally resolved atlas of mRNA decay in the C. elegans embryo reveals differential regulation of mRNA stability across stages and cell types
- Felicia Peng,
- C. Erik Nordgren,
- and John Isaac Murray
Genome Res. August 2024 34: 1235-1252; Published in Advance August 14, 2024, doi:10.1101/gr.278980.124
...by type and stage (Fig. 4B). From a central group of progenitor cells, trajectories formed that generally reflected progression through embryogenesis and that branched out into major cell types. Projecting data from individual biological replicates using the UMAP algorithm revealed similar cell clustering...
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Research: Tempo and mode of regulatory evolution in Drosophila
- Joseph D. Coolon,
- C. Joel McManus,
- Kraig R. Stevenson,
- Brenton R. Graveley,
- and Patricia J. Wittkopp
Genome Res. May 2014 24: 797-808; Published in Advance February 24, 2014, doi:10.1101/gr.163014.113
...accumulate with divergence time. Here, we address these issues by comparing gene expression among strains and species of Drosophila with a range of divergence times and use F1 hybrids to examine inheritance patterns and disentangle cis- and trans-regulatory changes. We find that the fixation of compensatory...
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Research: Evolution of splicing regulatory networks in Drosophila
- C. Joel McManus,
- Joseph D. Coolon,
- Jodi Eipper-Mains,
- Patricia J. Wittkopp,
- and Brenton R. Graveley
Genome Res. May 2014 24: 786-796; Published in Advance February 10, 2014, doi:10.1101/gr.161521.113
...(Irimia et al. 2009). More recently, the splicing patterns of 13 human exons were examined in a transgenic mouse, revealing that cisregulatory changes contributed significantly to interspecies differences in exon skipping (Barbosa-Morais et al. 2012). A similar survey from Drosophila F1 hybrid head tissue...
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Research: High-throughput sequencing reveals extraordinary fluidity of miRNA, piRNA, and siRNA pathways in nematodes
- Zhen Shi,
- Taiowa A. Montgomery,
- Yan Qi,
- and Gary Ruvkun
Genome Res. March 2013 23: 497-508; Published in Advance January 30, 2013, doi:10.1101/gr.149112.112
...be advantageous in an arms race against invading nucleic acids. We found that gonochoristic species that mate at every generation possess much larger numbers of piRNAs than androdioecious species that primarily self-fertilize. In Drosophila, maternally deposited piRNAs can silence paternal transposons (Brennecke...
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Resource: Zebrafish transposable elements show extensive diversification in age, genomic distribution, and developmental expression
- Ni-Chen Chang,
- Quirze Rovira,
- Jonathan Wells,
- Cédric Feschotte,
- and Juan M. Vaquerizas
Genome Res. July 2022 32: 1408-1423; Published in Advance January 5, 2022, doi:10.1101/gr.275655.121
...such somatic expression facilitate transposition in the germline? One possibility is that somatic expression provides an indirect route for TEs to enter the germline; this has been observed during oogenesis in Drosophila melanogaster, where TEs expressed in support cells surrounding the oocytes either infect...
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Research: Transposable elements drive the evolution of metazoan zinc finger genes
- Jonathan N. Wells,
- Ni-Chen Chang,
- John McCormick,
- Caitlyn Coleman,
- Nathalie Ramos,
- Bozhou Jin,
- and Cédric Feschotte
Genome Res. August 2023 33: 1325-1339; Published in Advance September 15, 2023, doi:10.1101/gr.277966.123
...). This finding is consistent with previous functional studies of Drosophila ZAD-ZNFs (Kasinathan et al. 2020) and our observation that the copy number of dipteran ZNFs does not correlate with the number of TE copies (Supplemental Data 1). Notably, we also found that in all species both retroelements and DNA...
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Resource: Small RNA expression and miRNA modification dynamics in human oocytes and early embryos
- Pauliina Paloviita,
- Christel Hydén-Granskog,
- Dawit A. Yohannes,
- Priit Paluoja,
- Juha Kere,
- Juha S. Tapanainen,
- Kaarel Krjutškov,
- Timo Tuuri,
- Urmo Võsa,
- and Sanna Vuoristo
Genome Res. August 2021 31: 1474-1485; doi:10.1101/gr.268193.120
....106054.110 ↵Bushati N, Stark A, Brennecke J, Cohen SM. 2008. Temporal reciprocity of miRNAs and their targets during the maternal-to-zygotic transition in Drosophila. Curr Biol 18: 501–506. doi:10.1016/j.cub.2008.02.081 ↵Christou-Kent M, Dhellemmes M...

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