Abstract
Recent studies show that non-coding RNAs (ncRNAs) can regulate the expression of protein-coding genes and play important roles in mammalian development. Previous studies have revealed that during C. elegans (Caenorhabditis elegans) embryo development, numerous genes in each cell are spatiotemporally regulated, causing the cell to differentiate into distinct cell types and tissues. We ask whether ncRNAs participate in the spatiotemporal regulation of genes in different types of cells and tissues during the embryogenesis of C. elegans. Here, by using marker-free full-length high-depth single-cell RNA sequencing (scRNA-seq) technique, we sequence the whole transcriptomes from 1031 embryonic cells of C. elegans and detect 20,431 protein-coding genes, including 22 cell-type-specific protein-coding markers, and 9843 ncRNAs including 11 cell-type-specific ncRNA markers. We induce a ncRNAs-based clustering strategy as a complementary strategy to the protein-coding gene-based clustering strategy for single-cell classification. We identify 94 ncRNAs that have never been reported to regulate gene expressions, are co-expressed with 1208 protein-coding genes in cell type specific and/or embryo time specific manners. Our findings suggest that these ncRNAs could potentially influence the spatiotemporal expression of the corresponding genes during the embryogenesis of C. elegans.
Highlights
It is known that about 90% of the eukaryotic genome is transcribed only 1–2% of the transcripts, known as messenger RNAs encode proteins, while the majority of transcripts called non-coding RNAs do not encode proteins
To determine the embryonic stages of the cells, we estimated the ‘embryo time’ of each cell by calculating the Pearson correlation between single cell transcriptome profiling and those of whole embryos collected at multiple time points[26], a standard method used by Packer et al.[10]
We have shown that the quantity of expressed protein-coding genes and ncRNAs varied dramatically in different types of cells at the same embryonic stage, and in the same type of cells at different embryonic stages
Summary
It is known that about 90% of the eukaryotic genome is transcribed only 1–2% of the transcripts, known as messenger RNAs (mRNAs) encode proteins, while the majority of transcripts called non-coding RNAs (ncRNAs) do not encode proteins. The genome of C. elegans (WBcel235) harbors 20,447 protein-coding genes and 26,301 annotated ncRNAs, of which only approximately 1300 are far known to play roles in various biological processes[11], including structural components such as tRNAs, rRNAs, small nucleolar RNAs (snoRNAs) and small nuclear RNAs (snRNAs), and regulatory components such as microRNAs (miRNA)[12,13] and long ncRNAs (lncRNAs)[14,15]. Little is known whether ncRNAs may influence the unique and spatiotemporal gene expression during the embryogenesis of C. elegans. To address these questions, we analyzed 1031 whole transcriptomes of cells from mixed stages. We detected a total of 20,436 protein-coding genes and 9843 ncRNAs in these cells, and identified 94 ncRNAs that potentially could impact the spatiotemporal expression of specific genes during the embryogenesis of C. elegans
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