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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
...of differences in gene regulation across germ layers in Drosophila embryogenesis (Cusanovich et al. 2018b), the generation of an atlas of 85 different clusters of cells from 13 different mouse tissues (Cusanovich et al. 2018a), and the identification of cell types in hippocampal tissue from mice (Sinnamon et al...
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Research: Integrating genetic variation with deep learning provides context for variants impacting transcription factor binding during embryogenesis
- Olga M. Sigalova,
- Mattia Forneris,
- Frosina Stojanovska,
- Bingqing Zhao,
- Rebecca R. Viales,
- Adam Rabinowitz,
- Fayrouz Hammal,
- Benoît Ballester,
- Judith B. Zaugg,
- and Eileen E.M. Furlong
Genome Res. May 2025 35: 1138-1153; Published in Advance April 15, 2025, doi:10.1101/gr.279652.124
...al. 2005; Potthoff and Olson 2007; Zdobnov et al. 2020), with highly conserved DNA-binding domains (Carlsson and Mahlapuu 2002; Chang et al. 2015).View larger version: In this window In a new window Figure 1. Profiling transcription factor (TF) binding in F1 embryos of Drosophila melanogaster. (A...
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Research: The role of transposon activity in shaping cis-regulatory element evolution after whole-genome duplication
- Øystein Monsen,
- Lars Grønvold,
- Alex Datsomor,
- Thomas Harvey,
- James Kijas,
- Alexander Suh,
- Torgeir R. Hvidsten,
- and Simen Rød Sandve
Genome Res. March 2025 35: 475-488; Published in Advance February 12, 2025, doi:10.1101/gr.278931.124
...with the tissue-specific TE-CREs (Fig. 2E). We also found that tissue-specific TE-CREs were associated with tissue bias in gene expression (Fig. 2F), supporting a regulatory effect of TE-CREs.One reason for TE-CREs tending to be specific to the liver rather than the brain (Fig. 2D) could be owing to differences...
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Resource: Murine single-cell RNA-seq reveals cell-identity- and tissue-specific trajectories of aging
- Jacob C. Kimmel,
- Lolita Penland,
- Nimrod D. Rubinstein,
- David G. Hendrickson,
- David R. Kelley,
- and Adam Z. Rosenthal
Genome Res. December 2019 29: 2088-2103; Published in Advance November 21, 2019, doi:10.1101/gr.253880.119
...a classical question in aging biology: Do different tissues age in the same way? Transcriptomic analysis at the bulk tissue level revealed tissue-specific features of aging in several studies (Schumacher et al. 2008; Jonker et al. 2013; Ori et al. 2015; Benayoun et al. 2019). Proteomic analysis of brain...
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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
...to the regulation of mRNA decay may result from other binding sites for regulatory RNAs and proteins that act in specific contexts.High transcript accumulation is associated with increased mRNA stabilityThroughout C. elegans embryogenesis, many genes accumulate to high transcript levels. Although this requires high...
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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
...the dynamism of the chromatin landscape across developmental transitions and provides a resource for future investigation into epigenetic regulatory mechanisms in germ cells.Epigenetic mechanisms are essential to correctly establish tissue-specific gene expression programs during development. At the genomic...
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Research: Distinctive regulatory architectures of germline-active and somatic genes in C. elegans
- Jacques Serizay,
- Yan Dong,
- Jürgen Jänes,
- Michael Chesney,
- Chiara Cerrato,
- and Julie Ahringer
Genome Res. December 2020 30: 1752-1765; Published in Advance October 22, 2020, doi:10.1101/gr.265934.120
...expression (CV) as a metric, we considered genes in the bottom 20% of CV values to have broad ubiquitous expression and those in the top 20% to have highly regulated expression (e.g., tissue specificity). As found in C. elegans, we observed that promoters of broadly expressed genes in Drosophila...
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Resource: Chromatin accessibility dynamics reveal novel functional enhancers in C. elegans
- Aaron C. Daugherty,
- Robin W. Yeo,
- Jason D. Buenrostro,
- William J. Greenleaf,
- Anshul Kundaje,
- and Anne Brunet
Genome Res. December 2017 27: 2096-2107; Published in Advance November 15, 2017, doi:10.1101/gr.226233.117
...as a transcriptional activator, in part due to its ability to increase chromatin accessibility (Adkins et al. 2006). Like Drosophila GAF, C. elegans EOR-1 is a transcriptional activator in the Ras/ERK signaling pathway that has been suggested to also repress gene expression (Liu et al. 2011a). GAF and EOR-1 are also...
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Research: Cohesin regulates tissue-specific expression by stabilizing highly occupied cis-regulatory modules
- Andre J. Faure,
- Dominic Schmidt,
- Stephen Watt,
- Petra C. Schwalie,
- Michael D. Wilson,
- Huiling Xu,
- Robert G. Ramsay,
- Duncan T. Odom,
- and Paul Flicek
Genome Res. November 2012 22: 2163-2175; Published in Advance July 10, 2012, doi:10.1101/gr.136507.111
..., Scc2 in budding yeast), which is required for loading of cohesin onto chromatin (Rollins et al. 2004). Although essential for sister chromatid cohesion, Nipped-B was first identified in Drosophila melanogaster as a result of its function in gene regulation, where it was suggested to facilitate...
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Research: Cis-acting variation is common across regulatory layers but is often buffered during embryonic development
- Swann Floc'hlay,
- Emily S. Wong,
- Bingqing Zhao,
- Rebecca R. Viales,
- Morgane Thomas-Chollier,
- Denis Thieffry,
- David A. Garfield,
- and Eileen E.M. Furlong
Genome Res. February 2021 31: 211-224; Published in Advance December 11, 2020, doi:10.1101/gr.266338.120
...accessibility, histone modifications, and gene expression in F1 embryos generated from eight Drosophila crosses at three embryonic stages, yielding a comprehensive data set of 240 samples spanning multiple regulatory layers. Genetic variation (allelic imbalance) impacts gene expression more frequently than...
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