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Issue:ISSN 2095-1353
           CN 11-6020/Q
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Your Position :Home->Past Journals Catalog->2022年59 No.1

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.
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