An updated C. elegans nuclear body muscle transcriptome for studies in muscle formation and function

Abstract

The body muscle is an important tissue used in organisms for proper viability and locomotion. Although this tissue is generally well studied and characterized, and many pathways have been elucidated throughout the years, we still lack a comprehensive understanding of its transcriptome and how it controls muscle development and function. Here, we have updated a nuclear FACS sorting-based methodology to isolate and sequence a high-quality muscle transcriptome from Caenorhabditis elegans mixed-stage animals. We have identified 2848 muscle-specific protein-coding genes, including 78 transcription factors and 206 protein-coding genes containing an RNA binding domain. We studied their interaction network, performed a detailed promoter analysis, and identified novel muscle-specific cis-acting elements. We have also identified 16 high-quality muscle-specific miRNAs, studied their function in vivo using fluorochrome-based analyses, and developed a high-quality C. elegans miRNA interactome incorporating other muscle-specific datasets produced by our lab and others.Our study expands our understanding of how muscle tissue functions in C. elegans andin turn provides results that can in the future be applied to humans to study muscular-related diseases.

A Comprehensive Analysis of 3-UTRs in Caenorhabditis elegans

“…Throughout the years, our lab has refined the 3’UTR collection in C. elegans in the whole animal and in several somatic tissues in various stages of development 10,13,14,24,26,27 ( Main Figure 1B ).…”

A lineage-resolved cartography of microRNA promoter activity in C. elegans empowers multidimensional developmental analysis

“…These studies, primarily conducted at the organismal or tissue levels, have revealed that miRNA expression is spatiotemporally specific, providing guidance for dissecting miRNA function during development. For instance, studies have employed methods like tissue-specific isolation or labeling of miRNAs followed by sequencing to characterize miRNAs enriched in specific tissues of interest in model organisms 13 , 17 , 20 , 22 – 24 . Although recent advances in single-cell genomics enable sequencing of protein-coding genes in developing cells at a single-cell resolution 25 , a similar analysis for miRNAs faces technical challenges in high-throughput sequencing of miRNAs in single cells and accurately determining cell identities.…”

A comprehensive analysis of 3′UTRs in Caenorhabditis elegans

“…Throughout the years, our lab has refined the 3′UTR collection in C. elegans in the whole animal and in several somatic tissues in various stages of development ( 10 , 13 , 14 , 24 , 26 , 27 ) (main Figure 1B ). Our previous C. elegans 3′UTRome (v2), which is currently available in WormBase, contains 3′UTR boundaries for 14788 genes corresponding to 23084 3′UTR isoforms (73% of all protein-coding genes included in the WS250 release) (main Figure 1B ).…”