摘要
【目的】饥饿是生命体普遍经历的一种胁迫,本文旨在探究饥饿胁迫下黑腹果蝇Drosophila melanogaster长链非编码RNA(lncRNA)的表达变化及其参与的调控网络,揭示lncRNA在饥饿应激反应中的潜在功能。【方法】下载NCBI SRA数据库中黑腹果蝇非生物胁迫相关的RNA-seq文库,进行转录组组装,预测lncRNA基因。利用DEseq2软件分析不同时间饥饿胁迫下lncRNA的差异表达,利用WGCNA共表达分析发现与饥饿胁迫相关的基因模块,构建差异表达lncRNA与蛋白编码基因的调控网路,用clusterProfiler进行GO功能注释和KEGG通路富集分析。【结果】从34个果蝇非生物胁迫转录组中共鉴定得到3612个lncRNA。与正常喂食组相比,在4、12、16和24 h饥饿胁迫下,分别有260、28、200和26个lncRNA表达上调,133、28、148和25个lncRNA表达下调(以下简称为饥饿相关lncRNA)。这些lncRNA分别与790、2950、725、2961个蛋白编码基因表达相关。GO和KEGG富集分析显示,这些蛋白编码基因分别富集于吞噬体和溶酶体通路、糖代谢通路、长寿调节途径、化学刺激和味觉感受及细胞增殖和凋亡等通路中。在饥饿胁迫4、12、16和24 h下,分别有66、1、23和3个lncRNA基因处于调控网络中的核心(hub gene)节点位置(|基因显著性(GS)|>0.4,|模块成员(MM)|>0.8)。这些核心RNA可能具有更为关键的调控作用。【结论】LncRNA参与了果蝇的饥饿应激反应,并与饥饿处理的时间有关。在较短时间饥饿处理下,饥饿相关lncRNA主要参与调控自噬及能量代谢等过程,以保证能量供应;在较长时间饥饿处理下,饥饿相关lncRNA则主要参与觅食、细胞增殖及凋亡以及长寿调节途径等。
[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 3612 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 790,2950,725 and 2961 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.
作者
高丽斌
李美珍
贺康
李飞
GAO Li-Bin;LI Mei-Zhen;HE Kang;LI Fei(Institute of Insect Sciences,Zhejiang University,Hangzhou 310058,China)
出处
《应用昆虫学报》
CAS
CSCD
北大核心
2022年第1期109-123,共15页
Chinese Journal of Applied Entomology
基金
浙江省自然科学基金重点项目(LZ18C060001)。
关键词
黑腹果蝇
饥饿胁迫
lncRNA
WGCNA
Drosophila melanogaster
starvation stress
lncRNA
weighted gene co-expression network analysis
