Abstract
Long non-coding RNAs (lncRNAs) have been reported to play critical roles during pathogen infection and innate immune response in mammals. Such observation inspired us to explore the expression profiles and functions of lncRNAs in invertebrates upon bacterial infection. Here, the lncRNAs of sea cucumber (Apostichopus japonicus) involved in Vibrio splendidus infection were characterized. RNA-seq obtained 2897 differentially expressed lncRNAs from Vibrio splendidus infected coelomocytes of sea cucumbers. The potential functions of the significant differentially expressed lncRNAs were related to immunity and metabolic process based on the gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) databases. Moreover, we identify a lncRNA (XLOC_028509), which is downregulated with Vibrio splendidus challenged, further study indicated that XLOC_028509 adsorb miR-2008 and miR-31 as competing endogenous RNAs (ceRNAs) through base complementarity, which in turn decreased the amount of miRNAs (microRNAs) bound to the 3’UTRs (untranslated regions) of mRNAs to reduce their inhibition of target gene translation. These data demonstrated that the lncRNAs of invertebrates might be important regulators in pathogen-host interactions by sponging miRNAs.
Highlights
In eukaryotic genomes, high-throughput sequencing reveal that only 2% of the nucleic acid sequences are used to encode proteins, and the remaining 98% of the genomes are non-coding protein sequences, suggesting that a large number of transcripts are non-coding RNAs [1, 2]
The results revealed that 983 long non-coding RNAs (lncRNAs) were significantly upregulated while 538 lncRNAs were downregulated in early infected group when compared to uninfected, the later infection resulted in upregulation of 729 lncRNAs while downregulation of 647 lncRNAs than those in uninfected group, indicated the pattern of lncRNA expression in sea cucumber was changed in response to Vibrio splendidus infection (Figure 2A)
It has been reported that lncRNAGAS5 can inhibit HCV infection as a negative regulator of HCV NS3 protein [26], while lncRNA LUCAT1 which is upregulated in response to lipopolysaccharide (LPS) can limit transcription of interferon stimulated genes (ISGs) by interacting with STAT1 [27]
Summary
High-throughput sequencing reveal that only 2% of the nucleic acid sequences are used to encode proteins, and the remaining 98% of the genomes are non-coding protein sequences, suggesting that a large number of transcripts are non-coding RNAs (ncRNAs) [1, 2]. Among ncRNAs, long non-coding RNAs (lncRNAs) are defined as non-coding transcripts greater than 200 nucleotides in length transcribed by RNA polymerase II/III [3]. Classic lncRNAs such as Xist (Xi-specific transcripts) have been discovered many years ago [5]. LncRNAs were ignored by people because of lower expression levels compared to proteincoding transcripts. LncRNAs have been confirmed to play important roles in various
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