Dataset Information

Computational Analysis Predicts Hundreds of Coding lncRNAs in Zebrafish.

ABSTRACT: Recent studies have demonstrated that numerous long noncoding RNAs (ncRNAs having more than 200 nucleotide base pairs (lncRNAs)) actually encode functional micropeptides, which likely represents the next regulatory biology frontier. Thus, identification of coding lncRNAs from ever-increasing lncRNA databases would be a bioinformatic challenge. Here we employed the Coding Potential Alignment Tool (CPAT), Coding Potential Calculator 2 (CPC2), LGC web server, Coding-Non-Coding Identifying Tool (CNIT), RNAsamba, and MicroPeptide identification tool (MiPepid) to analyze approximately 21,000 zebrafish lncRNAs and computationally to identify 2730-6676 zebrafish lncRNAs with high coding potentials, including 313 coding lncRNAs predicted by all the six bioinformatic tools. We also compared the sensitivity and specificity of these six bioinformatic tools for identifying lncRNAs with coding potentials and summarized their strengths and weaknesses. These predicted zebrafish coding lncRNAs set the stage for further experimental studies.

SUBMITTER: Mishra SK

PROVIDER: S-EPMC8145020 | biostudies-literature | 2021 Apr

REPOSITORIES: biostudies-literature

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Computational Analysis Predicts Hundreds of Coding lncRNAs in Zebrafish.

Mishra Shital Kumar SK Wang Han H

Biology 20210426 5

Recent studies have demonstrated that numerous long noncoding RNAs (ncRNAs having more than 200 nucleotide base pairs (lncRNAs)) actually encode functional micropeptides, which likely represents the next regulatory biology frontier. Thus, identification of coding lncRNAs from ever-increasing lncRNA databases would be a bioinformatic challenge. Here we employed the Coding Potential Alignment Tool (CPAT), Coding Potential Calculator 2 (CPC2), LGC web server, Coding-Non-Coding Identifying Tool (CNI ...[more]

PMID: 33925925

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Project description:Long noncoding RNAs (lncRNAs) have been shown to play crucial roles in various life processes, including circadian rhythms. Although next generation sequencing technologies have facilitated faster profiling of lncRNAs, the resulting datasets require sophisticated computational analyses. In particular, the regulatory roles of lncRNAs in circadian clocks are far from being completely understood. In this study, we conducted RNA-seq-based transcriptome analysis of zebrafish larvae under both constant darkness (DD) and constant light (LL) conditions in a circadian manner, employing state-of-the-art computational approaches to identify approximately 3220 lncRNAs from zebrafish larvae, and then uncovered 269 and 309 lncRNAs displaying circadian rhythmicity under DD and LL conditions, respectively, with 30 of them are coexpressed under both DD and LL conditions. Subsequently, GO, COG, and KEGG pathway enrichment analyses of all these circadianly expressed lncRNAs suggested their potential involvement in numerous biological processes. Comparison of these circadianly expressed zebrafish larval lncRNAs, with rhythmically expressed lncRNAs in the zebrafish pineal gland and zebrafish testis, revealed that nine (DD) and twelve (LL) larval lncRNAs are coexpressed in the zebrafish pineal gland and testis, respectively. Intriguingly, among peptides encoded by these coexpressing circadianly expressed lncRNAs, three peptides (DD) and one peptide (LL) were found to have the known domains from the Protein Data Bank. Further, the conservation analysis of these circadianly expressed zebrafish larval lncRNAs with human and mouse genomes uncovered one lncRNA and four lncRNAs shared by all three species under DD and LL conditions, respectively. We also investigated the conserved lncRNA-encoded peptides and found one peptide under DD condition conserved in these three species and computationally predicted its 3D structure and functions. Our study reveals that hundreds of lncRNAs from zebrafish larvae exhibit circadian rhythmicity and should help set the stage for their further functional studies.

Dataset Information

Computational Analysis Predicts Hundreds of Coding lncRNAs in Zebrafish.

Publications

Computational Analysis Predicts Hundreds of Coding lncRNAs in Zebrafish.

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