Dataset Information

Viruses and long non-coding RNAs: implicating an evolutionary conserved region.

ABSTRACT: Long non-coding RNAs (lncRNAs) are a class of cellular transcripts, which are involved in various biological processes. There is conflicting data regarding to the origin of these non-coding molecules and lncRNAs are thought to be the origin of viral genome. Here we sought to find the homology between human lncRNAs and viruses. For this purpose, the lncRNAdb database was searched for human lncRNAs. The lncRNAs' sequences were aligned with virus taxa using NCBI's BLAST tool. The phylogenic study was performed with maximum-likelihood based algorithm. The database contains 152 human lncRNAs. As a result, 63 (41.44%) of the lncRNAs have homologies with viruses. Of which, 50 (79.36%) have homology with Stealth virus. Other viruses with homology to lncRNAs were nuclear integrating DNA/RNA viruses. Moreover, 35 of 64 (23.03%) of cancer-associated lncRNAs have sequence homology with the same viruses. In phylogenetic analyses, lncRNAs with no homology to viruses were found to be the ancestor of those with homology to viruses and cancer-irrelevant lncRNAs were found to be the ancestor of cancer-related transcripts. In conclusion, lncRNAs could be the origin of nuclear integrating viruses and the nuclear integrating viruses may evolved from the non-coding regions. The results imply the role of lncRNAs with homology to viruses in human cancers.

SUBMITTER: Mohebbi A

PROVIDER: S-EPMC6261887 | biostudies-literature | 2018 Dec

REPOSITORIES: biostudies-literature

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Viruses and long non-coding RNAs: implicating an evolutionary conserved region.

Mohebbi Alireza A Tahamtan Alireza A Eskandarian Samira S Askari Fatemeh Sana FS Shafaei Mahnaz M Lorestani Nazanin N

Virusdisease 20180924 4

Long non-coding RNAs (lncRNAs) are a class of cellular transcripts, which are involved in various biological processes. There is conflicting data regarding to the origin of these non-coding molecules and lncRNAs are thought to be the origin of viral genome. Here we sought to find the homology between human lncRNAs and viruses. For this purpose, the lncRNAdb database was searched for human lncRNAs. The lncRNAs' sequences were aligned with virus taxa using NCBI's BLAST tool. The phylogenic study w ...[more]

PMID: 30539050

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Project description:Background: Long non-coding RNAs (lncRNAs), which are generally less functionally characterized or less annotated, evolve more rapidly than mRNAs and substantially possess fewer sequence conservation patterns than protein-coding genes across divergent species. People assume that the functional inference could be conducted on the evolutionarily conserved long non-coding RNAs as they are most likely to be functional. In the past decades, substantial progress has been made in discussions on the evolutionary conservation of non-coding genomic regions from multiple perspectives. However, understanding their conservation and the functions associated with sequence conservation in relation to further corresponding phenotypic variability or disorders still remains incomplete. Results: Accordingly, we determined a highly conserved region (HCR) to verify the sequence conservation among long non-coding RNAs and systematically profiled homologous long non-coding RNA clusters in humans and mice based on the detection of highly conserved regions. Moreover, according to homolog clustering, we explored the potential function inference via highly conserved regions on representative long non-coding RNAs. On lncRNA XACT, we investigated the potential functional competence between XACT and lncRNA XIST by recruiting miRNA-29a, regulating the downstream target genes. In addition, on lncRNA LINC00461, we examined the interaction relationship between LINC00461 and SND1. This interaction or association may be perturbed during the progression of glioma. In addition, we have constructed a website with user-friendly web interfaces for searching, analyzing, and downloading to present the homologous clusters of humans and mice. Conclusion: Collectively, homolog clustering via the highly conserved region definition and detection on long non-coding RNAs, as well as the functional explorations on representative sequences in our research, would provide new evidence for the potential function of long non-coding RNAs. Our results on the remarkable roles of long non-coding RNAs would presumably provide a new theoretical basis and candidate diagnostic indicators for tumors.

Project description:BackgroundLong non-coding RNAs (lncRNAs) play vital roles in many important biological processes in plants. Currently, a large fraction of plant lncRNA studies center at lncRNA identification and functional analysis. Only a few plant lncRNA studies focus on understanding their evolutionary history, which is crucial for an in-depth understanding of lncRNAs. Therefore, the integration of large volumes of plant lncRNA data is required to deeply investigate the evolution of lncRNAs.ResultsWe present a large-scale evolutionary analysis of lncRNAs in 25 flowering plants. In total, we identified 199,796 high-confidence lncRNAs through data integration analysis, and grouped them into 5497 lncRNA orthologous families. Then, we divided the lncRNAs into groups based on the degree of sequence conservation, and quantified the various characteristics of 756 conserved Arabidopsis thaliana lncRNAs. We found that compared with non-conserved lncRNAs, conserved lncRNAs might have more exons, longer sequence length, higher expression levels, and lower tissue specificities. Functional annotation based on the A. thaliana coding-lncRNA gene co-expression network suggested potential functions of conserved lncRNAs including autophagy, locomotion, and cell cycle. Enrichment analysis revealed that the functions of conserved lncRNAs were closely related to the growth and development of the tissues in which they were specifically expressed.ConclusionsComprehensive integration of large-scale lncRNA data and construction of a phylogenetic tree with orthologous lncRNA families from 25 flowering plants was used to provide an oversight of the evolutionary history of plant lncRNAs including origin, conservation, and orthologous relationships. Further analysis revealed a differential characteristic profile for conserved lncRNAs in A. thaliana when compared with non-conserved lncRNAs. We also examined tissue specific expression and the potential functional roles of conserved lncRNAs. The results presented here will further our understanding of plant lncRNA evolution, and provide the basis for further in-depth studies of their functions.

Dataset Information

Viruses and long non-coding RNAs: implicating an evolutionary conserved region.

Publications

Viruses and long non-coding RNAs: implicating an evolutionary conserved region.

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