The differential expression of long non-coding RNAs and their associated regulation networks in Drosophila melanogaster subject to starvation stress
Author of the article:GAO Li-Bin;LI Mei-Zhen;HE Kang;LI Fei
Author's Workplace:Institute of Insect Sciences, Zhejiang University, Hangzhou 310058, China;Institute of Insect Sciences, Zhejiang University, Hangzhou 310058, China;Institute of Insect Sciences, Zhejiang University, Hangzhou 310058, China;Institute of Insect Sciences, Zhejiang University, Hangzhou 310058, China
Key Words:Drosophila melanogaster; starvation stress; lncRNA; weighted gene co-expression network analysis
Abstract:
[Objectives] To investigate changes in the expression of long
non-coding RNA (lncRNA) and their associated regulatory networks in D.
melanogaster under starvation stress, and thereby reveal the roles of
lncRNA in the starvation stress response. [Methods] Abiotic stress-related RNA-Seq libraries of D.
melanogaster were downloaded from the NCBI SRA database and transcriptomes
assembled from these data. LncRNAs were identified from the assembled
transcriptomes. The DEseq2 package was used to identify lncRNAs that were
differentially expressed under starvation stress. Using the WGCNA tool, we obtained
co-expression modules related to starvation stress and constructed regulatory
networks of lncRNAs and protein coding genes. Gene ontology (GO) and the Kyoto
Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analysis were
performed using clusterProfiler. [Results] A total of 3 612 lncRNAs were identified from
the assembled transcriptome. After 4, 12, 16, and 24 h of starvation, 260, 28,
200 and 26 lncRNAs were up-regulated and 133, 28, 148, and 25 were
down-regulated, respectively, relative to the control groups. These
lncRNAs are thereafter referred to starvation- related lncRNAs. Expression of
starvation-related lncRNAs was correlated with 790, 2 950, 725 and 2 961
protein-coding genes, respectively. GO and KEGG analysis showed that the enriched
pathways changed with the duration of starvation. Pathways associated with
phagosome and lysosome production, sugar metabolism, longevity regulation,
detection of chemical stimulus, sensory perception of taste, cells signals
related to proliferation and apoptosis, were sequentially enriched as the
duration of starvation increased. After 4, 12, 16, and 24 h of starvation, 66,
1, 23, and 3 hub lncRNAs were found (|gene significance (GS)|>0.4, |module members (MM)
|>0.8). These hub lncRNAs may have key regulatory roles in responding to
starvation stress. [Conclusion] LncRNAs play essential roles in the starvation
stress response in D. melanogaster and the mechanism regulating their
expression is closely related to starvation treatment time. Under short-term
starvation stress, starvation-related lncRNAs are mainly involved in the
regulation of autophagy and energy metabolism and ensuring energy supply,
however, under long-term starvation stress, starvation-related lncRNAs are
mainly involved in foraging, cell proliferation, apoptosis and longevity
regulation.