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Research: Cohesin organizes 3D DNA contacts surrounding active enhancers in C. elegans
- Jun Kim,
- Haoyu Wang,
- and Sevinç Ercan
Genome Res. May 2025 35: 1108-1123; Published in Advance April 10, 2025, doi:10.1101/gr.279365.124
...other species, enhancers are distinguished from promoters based on enrichment of distinct and conserved histone modifications, including H3K27 acetylation and H3K4 methylation (Evans et al. 2016; Daugherty et al. 2017). Mapping enhancer chromatin features and analyses of individual genes suggest...
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Resource: Binding profiles for 961 Drosophila and C. elegans transcription factors reveal tissue-specific regulatory relationships
- Michelle Kudron,
- Louis Gevirtzman,
- Alec Victorsen,
- Bridget C. Lear,
- Jiahao Gao,
- Jinrui Xu,
- Swapna Samanta,
- Emily Frink,
- Adri Tran-Pearson,
- Chau Huynh,
- Dionne Vafeados,
- Ann Hammonds,
- William Fisher,
- Martha Wall,
- Greg Wesseling,
- Vanessa Hernandez,
- Zhichun Lin,
- Mary Kasparian,
- Kevin White,
- Ravi Allada,
- Mark Gerstein,
- LaDeana Hillier,
- Susan E. Celniker,
- Valerie Reinke,
- and Robert H. Waterston
Genome Res. December 2024 34: 2319-2334; Published in Advance October 22, 2024, doi:10.1101/gr.279037.124
...are a rich resource for the community that should fuel and guide future investigations into TF function. To facilitate data accessibility and utility, all strains expressing green fluorescent protein (GFP)-tagged TFs are available at the stock centers for each organism. The chromatin immunoprecipitation...
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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
...assays in IGN, such as transcriptome profiling (RNA-seq), histone modification profiling via chromatin immunoprecipitation (ChIP-seq), and chromatin accessibility profiling via assay for transposon-accessible chromatin (ATAC-seq) (Sanchez et al. 2023).In this study, we characterized C. elegans chromatin...
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Resource: Comprehensive characterization of tissue-specific chromatin accessibility in L2 Caenorhabditis elegans nematodes
- Timothy J. Durham,
- Riza M. Daza,
- Louis Gevirtzman,
- Darren A. Cusanovich,
- Olubusayo Bolonduro,
- William Stafford Noble,
- Jay Shendure,
- and Robert H. Waterston
Genome Res. October 2021 31: 1952-1969; Published in Advance April 22, 2021, doi:10.1101/gr.271791.120
...in other single-cell genomics technologies can now also characterize the regulatory context of the that gives rise to these gene expression levels at a single-cell resolution. To explore the regulatory DNA of individual cell types in C. elegans, we collected single-cell chromatin accessibility data using...
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Mini-Review: The chromatin tapestry as a framework for neurodevelopment
- Ben Nolan,
- Timothy E. Reznicek,
- Christopher T. Cummings,
- and M. Jordan Rowley
Genome Res. October 2024 34: 1477-1486; doi:10.1101/gr.278408.123
...neurodevelopment (de la Torre-Ubieta et al. 2018). Mannens et al. (2024) describe paired chromatin accessibility and transcription changes across the entire human brain throughout the first trimester, revealing the interconnectedness between chromatin accessibility and transcriptional activity for facilitating...
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Resource: Dynamic transcriptional and chromatin accessibility landscape of medaka embryogenesis
- Yingshu Li,
- Yongjie Liu,
- Hang Yang,
- Ting Zhang,
- Kiyoshi Naruse,
- and Qiang Tu
Genome Res. June 2020 30: 924-937; Published in Advance June 26, 2020, doi:10.1101/gr.258871.119
...RNAs (lncRNAs) encoded in the ; we obtained the temporal expression profiles of all these genes during embryogenesis and identified those that use different isoforms across developmental stages. Furthermore, we acquired chromatin accessibility dynamics and investigated cis- and trans-regulatory logic...
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Research: Chromatin loop dynamics during cellular differentiation are associated with changes to both anchor and internal regulatory features
- Marielle L. Bond,
- Eric S. Davis,
- Ivana Y. Quiroga,
- Anubha Dey,
- Manjari Kiran,
- Michael I. Love,
- Hyejung Won,
- and Douglas H. Phanstiel
Genome Res. August 2023 33: 1258-1268; Published in Advance September 12, 2023, doi:10.1101/gr.277397.122
...establishment and were consistent with chromatin looping playing a role in transcriptional activation and/or enhancement; however, these results also revealed strong correlations between differential looping and other regulatory features including chromatin accessibility, histone H3K27 acetylation, and AP-1...
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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
...developmental stages of C. elegans embryogenesisAlthough transcripts on average increased in stability over time (Fig. 4D), we identified a subset of transcripts with faster decay at later stages of embryogenesis (Fig. 5A). These genes were enriched for terms such as structural constituent of chromatin...
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Research: AP-1 subunits converge promiscuously at enhancers to potentiate transcription
- Jungkyun Seo,
- D. Dewran Koçak,
- Luke C. Bartelt,
- Courtney A. Williams,
- Alejandro Barrera,
- Charles A. Gersbach,
- and Timothy E. Reddy
Genome Res. April 2021 31: 538-550; Published in Advance March 5, 2021, doi:10.1101/gr.267898.120
...) Hi-C chromatin interaction maps coupled with chromatin accessibility (DNase-seq) and active enhancer markers (H3K27ac) (D'Ippolito et al. 2018; McDowell et al. 2018; Fulco et al. 2019); and (3) linear proximity in the .Changes in AP-1 hotspots were linked to more potent changes in gene expression...
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Research: Natural variation in C. elegans short tandem repeats
- Gaotian Zhang,
- Ye Wang,
- and Erik C. Andersen
Genome Res. October 2022 32: 1852-1861; Published in Advance October 4, 2022, doi:10.1101/gr.277067.122
...diversity across the species (Andersen et al. 2012). The selective sweeps were thought to have purged diversity from the centers of Chromosomes I, IV, and V, and the left arm of the X Chromosome from the C. elegans global population. However, recent sampling efforts of wild C. elegans revealed higher...
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