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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
.... 2016), we initially speculated that H3K4me3 remodeling occurred upon transcriptional reactivation of the zygotic in the early embryo, which is initiated at the four-cell stage and gradually increases over the next several cell divisions before reaching steady-state levels (Robertson and Lin 2015...
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Research: Genome-wide profiles of H3K9me3, H3K27me3 modifications, and DNA methylation during diapause of Asian corn borer (Ostrinia furnacalis)
- Pengfei Lv,
- Xingzhuo Yang,
- Xianguo Zhao,
- Zhangwu Zhao,
- and Juan Du
Genome Res. May 2024 34: 725-739; Published in Advance June 12, 2024, doi:10.1101/gr.278661.123
...armigera, Polycomb group (PcG) proteins regulate PTTH production and prevent diapause entry through the control of H3K27me3 (Lu et al. 2013). By ovary-specific knockdown of histone mark writers and erasers, DiVito Evans et al. (2023) showed that H3K4me3 and H3K36me1 depletion promotes reproductive diapause...
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Research: Loss of multilevel 3D genome organization during breast cancer progression
- Roberto Rossini,
- Saleh Oshaghi,
- Maxim Nekrasov,
- Aurélie Bellanger,
- Renae Domaschenz,
- Yasmin Dijkwel,
- Mohamed Abdelhalim,
- Rahul Agrawal,
- Marit Ledsaak,
- Philippe Collas,
- Ragnhild Eskeland,
- David Tremethick,
- and Jonas Paulsen
Genome Res. January 2026 36: 20-37; Published in Advance October 9, 2025, doi:10.1101/gr.280791.125
..., B2 and B3 show features of heterochromatin, with enrichment of repressive histone marks (H3K27me3) and lamin B1. Compared with the other subcompartments, A0 and B0 are the least enriched in active and repressive histone marks, respectively, raising the interesting possibility that they could be more...
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Research: A genome-wide survey reveals a diverse array of enhancers coordinates the Drosophila innate immune response
- Lianne B Cohen,
- Tamara Hadzic,
- Caitlin Sauer,
- Julia R Gibbs,
- and Zeba Wunderlich
Genome Res. April 15, 2026 gr.281432.125; Published in Advance April 15, 2026, doi:10.1101/gr.281432.125
...A -wide survey reveals a diverse array of enhancers coordinates the Drosophila 1 innate immune response 2 3 Lianne B. Cohen1, 2, Tamara Hadzic2, 3, Caitlin Sauer1, 2, Julia R. Gibbs1, 2, Zeba Wunderlich1, 2, 3, 4 4* 5 1. Department of Biology, Boston University, Boston, MA 02215, USA 6 2...
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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
...-mediated repression allows activation of ERV enhancers upon entry into meiosis. This regulatory feature is observed for independently evolved KZFPs and ERVs in mice and humans, suggesting evolutionary conservation in mammals. Further, we show that KZFP-targeted ERVs are underrepresented on the sex chromosomes...
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Research: Dynamics of broad H3K4me3 domains uncover an epigenetic switch between cell identity and cancer-related genes
- Mohamed Belhocine,
- Mathieu Simonin,
- José David Abad Flores,
- Agata Cieslak,
- Iris Manosalva,
- Lydie Pradel,
- Charlotte Smith,
- Eve-Lyne Mathieu,
- Guillaume Charbonnier,
- Joost H.A. Martens,
- Hendrik G. Stunnenberg,
- Muhammad Ahmad Maqbool,
- Aneta Mikulasova,
- Lisa J. Russell,
- Daniel Rico,
- Denis Puthier,
- Pierre Ferrier,
- Vahid Asnafi,
- and Salvatore Spicuglia
Genome Res. July 2022 32: 1328-1342; Published in Advance June 23, 2021, doi:10.1101/gr.266924.120
...be contained in the spread of epigenetic modifications over a genomic locus. Large megabase-sized chromatin domains have been described for the repressive chromatin mark H3K9me3 in senescence cells spanning large chromosomal regions (Soufi et al. 2012) or activating H3K4me3 in mammalian oocytes (Dahl et al...
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Research: A DNA methylation haplotype block landscape in human tissues and preimplantation embryos reveals regulatory elements defined by comethylation patterns
- Yan Feng,
- Zhiqiang Zhang,
- Yuyang Hong,
- Yi Ding,
- Leiqin Liu,
- Siqi Gao,
- Hai Fang,
- and Jiantao Shi
Genome Res. December 2023 33: 2041-2052; Published in Advance November 8, 2023, doi:10.1101/gr.278146.123
...was calculated as the percentage of CpG sites covered by H3K4me3 ChIP-seq peaks. (C) Enrichment of B cell ChIA-PET (Pol II) tags in tissue MHBs. The enrichment was tested using the R package LOLA, with the union of MHBs from all tissues as the background. (D) An example genomic track showing that chromatin...
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Resource: CGC1, a new reference genome for Caenorhabditis elegans
- Kazuki Ichikawa,
- Massa J. Shoura,
- Karen L. Artiles,
- Dae-Eun Jeong,
- Chie Owa,
- Haruka Kobayashi,
- Yoshihiko Suzuki,
- Manami Kanamori,
- Yu Toyoshima,
- Yuichi Iino,
- Ann E. Rougvie,
- Lamia Wahba,
- Andrew Z. Fire,
- Erich M. Schwarz,
- and Shinichi Morishita
Genome Res. August 2025 35: 1902-1918; Published in Advance July 15, 2025, doi:10.1101/gr.280274.124
...protein-coding gene sets. To define CGC1 genomic coordinates for sequences that either are shared with N2 (Supplemental Data File 10) or are unique to CGC1 (Supplemental Data File 11) to which genes or transcripts could be assigned, we aligned the two assemblies and identified uniquely aligned blocks...
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Research: Centromeric instability and chromoanasynthesis observed in nine supernumerary marker chromosomes resolved with long-read genome sequencing
- Kristine Bilgrav Saether,
- Angelo Salazar Mantero,
- Marlene Ek,
- Maria Pettersson,
- Elisabeth Syk Lundberg,
- Christopher M. Grochowski,
- Claudia M.B. Carvalho,
- Jesper Eisfeldt,
- and Anna Lindstrand
Genome Res. April 2026 36: 661-670; Published in Advance March 25, 2026, doi:10.1101/gr.281175.125
...the exact coordinates of involved genomic segments and genes (Supplemental Table S2) whether the duplication or triplication of specific genes contribute to the phenotype remains unclear, as transcriptional activity and downstream effects were not assessed.We and others have previously shown that lr...
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Research: Single-cell multi-omics of human preimplantation embryos shows susceptibility to glucocorticoids
- Cheng Zhao,
- Savana Biondic,
- Katherine Vandal,
- Åsa K. Björklund,
- Michael Hagemann-Jensen,
- Theresa Maria Sommer,
- Jesica Canizo,
- Stephen Clark,
- Pascal Raymond,
- Daniel R. Zenklusen,
- Nicolas Rivron,
- Wolf Reik,
- and Sophie Petropoulos
Genome Res. September 2022 32: 1627-1641; Published in Advance August 10, 2022, doi:10.1101/gr.276665.122
...,324,000–27,329,000) revealed overlapping CpG islands with H3K27me3 histone modification, which suggests that multiple genomic-feature elements and epigenetic regulators synergistically regulate PTK2B gene expression.Given that the mural and polar sublineages displayed a differential response to glucocorticoid exposure, we...
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