Single-Cell Atlas of the Drosophila Leg Disc Identifies a Long Non-Coding RNA in Late Development

Abstract

The Drosophila imaginal disc has been an excellent model for the study of developmental gene regulation. In particular, long non-coding RNAs (lncRNAs) have gained widespread attention in recent years due to their important role in gene regulation. Their specific spatiotemporal expressions further support their role in developmental processes and diseases. In this study, we explored the role of a novel lncRNA in Drosophila leg development by dissecting and dissociating w1118 third-instar larval third leg (L3) discs into single cells and single nuclei, and performing single-cell RNA-sequencing (scRNA-seq) and single-cell assays for transposase-accessible chromatin (scATAC-seq). Single-cell transcriptomics analysis of the L3 discs across three developmental timepoints revealed different cell types and identified lncRNA:CR33938 as a distal specific gene with high expression in late development. This was further validated by fluorescence in-situ hybridization (FISH). The scATAC-seq results reproduced the single-cell transcriptomics landscape and elucidated the distal cell functions at different timepoints. Furthermore, overexpression of lncRNA:CR33938 in the S2 cell line increased the expression of leg development genes, further elucidating its potential role in development.

Noncoding RNA Regulation of Hormonal and Metabolic Systems in the Fruit Fly Drosophila

“…Among all, 21% and 42% lncRNAs were significantly up-regulated at late-embryonic and late-larval stages, respectively, suggesting a drastic change in transcriptome throughout different life stages [ 141 ]. For example, leg development in Drosophila is dependent on lncRNA:CR33938 and a mutant of this lncRNA results in alteration of expression level in leg development genes [ 129 ]. Relevant to the metamorphosis process that is regulated by the ecdysone signalling pathways, a study on the hormone response network for ecdysone reveals four ecdysone-induced lncRNAs: CR43432 , CR43626 , CR45391 , and CR45424 , without any further analysis [ 142 ].…”