Integrated analysis of lncRNA and mRNA in liver of Megalobrama amblycephala post Aeromonas hydrophila infection

Qianhui Sun,Huanling Wang,Guowen Wang,Hong Liu,Jixiu Wang

doi:10.1186/s12864-021-07969-5

Qianhui Sun, Huanling Wang + Show 3 more

Open Access

https://doi.org/10.1186/s12864-021-07969-5

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Abstract

BackgroundAs non-coding RNA molecules of more than 200 bp in length, long non-coding RNAs (lncRNAs) play a variety of roles in biological processes, including regulating the immune responses to bacterial infections. In recent years, there have been many in-depth studies on mammalian lncRNAs, but the relevant studies in fish are very limited. Meanwhile, since lncRNAs are not conserved among species, it is difficult to apply the existing results directly to unstudied species.ResultsTo obtain the information of lncRNAs in Megalobrama amblycephala, one of the most economically important freshwater fish in China, also to better understand the biological significance of lncRNAs in the immunity system, the fish liver at 0, 4, 12, 24, and 72 h post Aeromonas hydrophila infection (hpi) were obtained for lncRNA-sequencing (lncRNA-seq). A total of 14,849 lncRNAs were identified, and 2196 lncRNAs showed significant differences at different time points post A. hydrophila infection. Gene Ontology (GO) annotation and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analyses showed that the target genes of the differentially expressed lncRNAs were enriched in several pathways related to immune such as apoptosis, inflammation, and immune response. Time-specific modules were then identified, using weighted correlation network analysis (WGCNA), and 28 modules significantly correlated with different time point after infection were found. Furthermore, four immune-related genes and six lncRNAs in the time-specific modules were subsequently verified by RT-qPCR.ConclusionsThe above findings reveal the discovery of widespread differentially expressed lncRNAs in the M. amblycephala liver post A. hydrophila infection, suggesting that lncRNAs might participate in the regulation of host response to bacterial infection, enriching the information of lncRNAs in teleost and providing a resources basis for further studies on the immune function of lncRNAs.

Highlights

As non-coding RNA molecules of more than 200 bp in length, long non-coding RNAs play a variety of roles in biological processes, including regulating the immune responses to bacterial infections
Identification and characterization of mRNA and long non-coding RNAs (lncRNAs) in the M. amblycephala liver To identify lncRNAs expressed in the M. amblycephala liver at different time points after A. hydrophila infection, 15 cDNA libraries (5 time points, 3 repetitions per time point) were constructed and sequenced
This study explored the response of lncRNAs in the M. amblycephala liver to A. hydrophila infection

Summary

Introduction

As non-coding RNA molecules of more than 200 bp in length, long non-coding RNAs (lncRNAs) play a variety of roles in biological processes, including regulating the immune responses to bacterial infections. Long noncoding RNAs (lncRNAs) are operationally defined as non-coding RNA molecules with a length of more than 200 base-pairs (bp) [1]. LncRNAs play important roles in multiple biological processes by interacting with RNA, DNA, or proteins to change the expression of proteincoding genes [3], which can regulate diverse cellular processes, including disease process, development and cell proliferation [4]. LncRNAs regulate gene expression at the epigenetic, transcriptional and posttranscriptional levels [7] and previous studies have shown that they play an important regulatory role in the innate immune system [8, 9]. As miRNA sponges, lncRNAs play a role in immunity by competitively inhibit the ability of miRNAs to interact with their mRNA targets [15, 16]

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