Identification of Specific Genes and Pathways by a Comparative Transcriptomic Study of Hypodermal and Body Muscle Development

Abstract

The development of diverse tissues may be determined by cell fate at the level of cell lineage, especially for hypodermal (Hyp) and body muscle (BM) development in C. elegans. Here, we focused on hypodermal as well as body muscle development in C. elegans and performed a comparative genome study to explore the gene expression patterns and lineage specific regulatory mechanisms by re-mining the existing treasury. The approach of gene set enrichment analysis on related gene expression profiles was also integrated to mine the significantly associated pathways with tissue-specific transcription factors (TFs) regulation. As a result, we have identified different gene expression patterns as well as some of overlapping and specific genes of each lineage between Hyp and BM development. Furthermore, there were some specific regulatory modules identified for 3 TFs, including 5 pathways for HND-1 such as Hedgehog signaling pathway, 11 pathways for ELT-1 such as Calcium signaling pathway, as well as 23 pathways for NHR-25 such as Jak-STAT signaling pathway and some of metabolic pathways. In conclusion, the identification of specific genes and biological pathways by our comparative transcriptomic study may help us better understand the genetic mechanisms between hypodermal and body muscle development in C. elegans.