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Comprehensive characterization of tissue-specific chromatin accessibility in L2 Caenorhabditis elegans nematodes

ABSTRACT: Recently developed single cell technologies allow researchers to characterize cell states at ever greater resolution and scale. C. 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 are useful for learning about gene function and give insight into the biochemical state of different cell types; however, in order to understand these cell types, we must also determine how these gene expression levels are regulated. We present the first single cell ATAC-seq study in C. elegans. We collected data in L2 larvae to match the available single cell RNA-seq data set, and identify tissue-specific chromatin accessibility patterns that align well with existing data, including the L2 single cell RNA-seq results. Using a novel implementation of the Latent Dirichlet Allocation algorithm, our chromatin accessibility data provide new insights into which genomic loci may be participating in cell type-specific gene regulation, with promise for better understanding of cellular differentiation and gene regulation in the worm.

ORGANISM(S): Caenorhabditis elegans

PROVIDER: GSE157017 | GEO | 2021/04/12

REPOSITORIES: GEO

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