Spatiotemporal expression profiling of long intervening noncoding RNAs in Caenorhabditis elegans

Weihong Liu,Enchao Yu,Siyu Chen,Yiwen Lu,Xiaopeng Ma,Xiao Liu

doi:10.1038/s41598-017-05427-5

Abstract

To better understand the biological function of long noncoding RNAs, it is critical to determine their spatiotemporal expression patterns. We generated transgenic reporter strains for 149 out of the 170 annotated C. elegans long intervening noncoding RNAs (lincRNAs) and profiled their temporal activity. For the 68 lincRNAs with integrated reporter lines, we profiled their expression at the resolution of single cells in L1 larvae, and revealed that the expression of lincRNAs is more specific, heterogeneous and at lower level than transcription factors (TFs). These expression patterns can be largely attributed to transcriptional regulation because they were observed in assays using reporters of promoter activity. The spatial expression patterns of the 68 lincRNAs were further examined in 18 tissue categories throughout eight developmental stages. We compared the expression dynamics of lincRNAs, miRNAs and TFs during development. lincRNA and miRNA promoters are less active at embryo stage than those of TFs, but become comparable to TFs after embryogenesis. Finally, the lincRNA gene set shows a similar tissue distribution to that of miRNAs and TFs. We also generated a database, CELE, for the storage and retrieval of lincRNA reporter expression patterns and other relevant information. The data and strains described here will provide a valuable guide and resource for future functional exploration of C. elegans lincRNAs.

Highlights

An increasing number of long noncoding RNAs have been identified across species
Transgenic C. elegans strains carrying the PlincRNA::reporter construct were generated by microparticle bombardment as previously described[25]
We found that the average expression level of lincRNAs is much lower than that of the transcription factors (TFs) in every cell type (Fig. 2a), which is consistent with previous RNA-seq results that the mean RPKM of C. elegans lincRNAs is much lower than that of mRNAs16

Summary

Introduction

An increasing number of long noncoding RNAs have been identified across species. most of them are uncharacterized and of unknown function. In C. elegans, Nam and Bartel identified 170 long intervening ncRNAs (lincRNAs) that did not overlap protein-coding transcripts, and 58 antisense long noncoding RNAs that were complementary to protein-coding transcripts They found that long noncoding RNAs tended to express in a tissue- or stage-specific manner[16]. For the 68 integrated lincRNA reporters, we profiled their expression in 363 somatic cells of L1 stage larvae at single-cell resolution. These data revealed that the spatiotemporal distribution of lincRNAs is similar to that of TFs, but lincRNA reporter expression is more tissue specific and heterogeneous. The results and reagent generated in our study will provide a valuable resource to explore the biological function of C. elegans lincRNAs

Methods

Results

Conclusion