Comprehensive characterization of tissue-specific chromatin accessibility in L2 Caenorhabditis elegans nematodes
- Timothy J. Durham1,7,
- Riza M. Daza1,
- Louis Gevirtzman1,
- Darren A. Cusanovich2,
- Olubusayo Bolonduro1,8,
- William Stafford Noble1,3,
- Jay Shendure1,4,5,6 and
- Robert H. Waterston1
- 1Department of Genome Sciences, University of Washington, Seattle, Washington 98195, USA;
- 2Department of Cellular and Molecular Medicine, University of Arizona, Tucson, Arizona 85721, USA;
- 3Paul G. Allen School of Computer Science and Engineering, University of Washington, Seattle, Washington 98195, USA;
- 4Howard Hughes Medical Institute, Chevy Chase, Maryland 20815, USA;
- 5Brotman Baty Institute for Precision Medicine, Seattle, Washington 98195, USA;
- 6Allen Discovery Center for Cell Lineage Tracing, University of Washington, Seattle, Washington 98195, USA
Abstract
Recently developed single-cell technologies allow researchers to characterize cell states at ever greater resolution and scale. Caenorhabditis elegans is a particularly tractable system for studying development, and recent single-cell RNA-seq studies characterized the gene expression patterns for nearly every cell type in the embryo and at the second larval stage (L2). Gene expression patterns give insight about gene function and into the biochemical state of different cell types; recent advances in other single-cell genomics technologies can now also characterize the regulatory context of the genome 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 the sci-ATAC-seq assay in L2 larvae to match the available single-cell RNA-seq data set. By using a novel implementation of the latent Dirichlet allocation algorithm, we identify 37 clusters of cells that correspond to different cell types in the worm, providing new maps of putative cell type–specific gene regulatory sites, with promise for better understanding of cellular differentiation and gene regulation.
Footnotes
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[Supplemental material is available for this article.]
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Article published online before print. Article, supplemental material, and publication date are at https://www.genome.org/cgi/doi/10.1101/gr.271791.120.
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Freely available online through the Genome Research Open Access option.
- Received September 15, 2020.
- Accepted April 13, 2021.
This article, published in Genome Research, is available under a Creative Commons License (Attribution 4.0 International), as described at http://creativecommons.org/licenses/by/4.0/.
