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Genome-Wide Discovery of Long Non-Coding RNAs in Rainbow Trout.

Al-Tobasei R, Paneru B, Salem M - PLoS ONE (2016)

Bottom Line: Transcripts shorter than 200 nt, with more than 83-100 amino acids ORF, or with significant homologies to the NCBI nr-protein database were removed.In addition, a computational pipeline was used to filter the remaining transcripts based on a protein-coding-score test.This study annotates the lncRNA rainbow trout genome and provides a valuable resource for functional genomics research in salmonids.

View Article: PubMed Central - PubMed

Affiliation: Computational Science Program, Middle Tennessee State University, Murfreesboro, TN, 37132, United States of America.

ABSTRACT
The ENCODE project revealed that ~70% of the human genome is transcribed. While only 1-2% of the RNAs encode for proteins, the rest are non-coding RNAs. Long non-coding RNAs (lncRNAs) form a diverse class of non-coding RNAs that are longer than 200 nt. Emerging evidence indicates that lncRNAs play critical roles in various cellular processes including regulation of gene expression. LncRNAs show low levels of gene expression and sequence conservation, which make their computational identification in genomes difficult. In this study, more than two billion Illumina sequence reads were mapped to the genome reference using the TopHat and Cufflinks software. Transcripts shorter than 200 nt, with more than 83-100 amino acids ORF, or with significant homologies to the NCBI nr-protein database were removed. In addition, a computational pipeline was used to filter the remaining transcripts based on a protein-coding-score test. Depending on the filtering stringency conditions, between 31,195 and 54,503 lncRNAs were identified, with only 421 matching known lncRNAs in other species. A digital gene expression atlas revealed 2,935 tissue-specific and 3,269 ubiquitously-expressed lncRNAs. This study annotates the lncRNA rainbow trout genome and provides a valuable resource for functional genomics research in salmonids.

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Related in: MedlinePlus

Distribution of lncRNA expression in various tissues.Proportion of the transcriptome that is contributed by the most abundant lncRNAs is plotted in various tissues. In complex tissues like brain and testis, larger number of lncRNAs were expressed with fairly equal dominance of many transcripts. On the contrary, less complex tissues like white muscle, fat and liver showed that majority of transcriptome is contributed by few dominant lncRNAs.
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pone.0148940.g005: Distribution of lncRNA expression in various tissues.Proportion of the transcriptome that is contributed by the most abundant lncRNAs is plotted in various tissues. In complex tissues like brain and testis, larger number of lncRNAs were expressed with fairly equal dominance of many transcripts. On the contrary, less complex tissues like white muscle, fat and liver showed that majority of transcriptome is contributed by few dominant lncRNAs.

Mentions: Previously, we showed that tissues are different in terms of the protein-coding transcriptome composition and complexity. Brain and testis possess the most complex transcriptomes. These tissues express large numbers of the genes; however, only a small part of the mRNA pool is expressed by the most abundant genes [43]. On the other hand, white muscle and stomach revealed simpler transcriptomes. These tissues express fewer genes and a greater proportion of the transcriptome comes from the most highly expressed genes. Similarly and in this study, complex tissues like brain and testis, expressed a larger number of lncRNAs with equal dominance of many transcripts (Fig 5). Conversely, white muscle, fat and liver showed less complex transcriptomes; a vast majority of the transcriptome included a few dominant lncRNAs. Similar expression patterns between protein-coding genes and lncRNAs may suggest common mechanisms of gene expression regulation and important role of lncRNAs in regulating protein-coding RNAs. Regardless, these data suggest that lncRNAs may be significant in determining tissue complexity.


Genome-Wide Discovery of Long Non-Coding RNAs in Rainbow Trout.

Al-Tobasei R, Paneru B, Salem M - PLoS ONE (2016)

Distribution of lncRNA expression in various tissues.Proportion of the transcriptome that is contributed by the most abundant lncRNAs is plotted in various tissues. In complex tissues like brain and testis, larger number of lncRNAs were expressed with fairly equal dominance of many transcripts. On the contrary, less complex tissues like white muscle, fat and liver showed that majority of transcriptome is contributed by few dominant lncRNAs.
© Copyright Policy
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4764514&req=5

pone.0148940.g005: Distribution of lncRNA expression in various tissues.Proportion of the transcriptome that is contributed by the most abundant lncRNAs is plotted in various tissues. In complex tissues like brain and testis, larger number of lncRNAs were expressed with fairly equal dominance of many transcripts. On the contrary, less complex tissues like white muscle, fat and liver showed that majority of transcriptome is contributed by few dominant lncRNAs.
Mentions: Previously, we showed that tissues are different in terms of the protein-coding transcriptome composition and complexity. Brain and testis possess the most complex transcriptomes. These tissues express large numbers of the genes; however, only a small part of the mRNA pool is expressed by the most abundant genes [43]. On the other hand, white muscle and stomach revealed simpler transcriptomes. These tissues express fewer genes and a greater proportion of the transcriptome comes from the most highly expressed genes. Similarly and in this study, complex tissues like brain and testis, expressed a larger number of lncRNAs with equal dominance of many transcripts (Fig 5). Conversely, white muscle, fat and liver showed less complex transcriptomes; a vast majority of the transcriptome included a few dominant lncRNAs. Similar expression patterns between protein-coding genes and lncRNAs may suggest common mechanisms of gene expression regulation and important role of lncRNAs in regulating protein-coding RNAs. Regardless, these data suggest that lncRNAs may be significant in determining tissue complexity.

Bottom Line: Transcripts shorter than 200 nt, with more than 83-100 amino acids ORF, or with significant homologies to the NCBI nr-protein database were removed.In addition, a computational pipeline was used to filter the remaining transcripts based on a protein-coding-score test.This study annotates the lncRNA rainbow trout genome and provides a valuable resource for functional genomics research in salmonids.

View Article: PubMed Central - PubMed

Affiliation: Computational Science Program, Middle Tennessee State University, Murfreesboro, TN, 37132, United States of America.

ABSTRACT
The ENCODE project revealed that ~70% of the human genome is transcribed. While only 1-2% of the RNAs encode for proteins, the rest are non-coding RNAs. Long non-coding RNAs (lncRNAs) form a diverse class of non-coding RNAs that are longer than 200 nt. Emerging evidence indicates that lncRNAs play critical roles in various cellular processes including regulation of gene expression. LncRNAs show low levels of gene expression and sequence conservation, which make their computational identification in genomes difficult. In this study, more than two billion Illumina sequence reads were mapped to the genome reference using the TopHat and Cufflinks software. Transcripts shorter than 200 nt, with more than 83-100 amino acids ORF, or with significant homologies to the NCBI nr-protein database were removed. In addition, a computational pipeline was used to filter the remaining transcripts based on a protein-coding-score test. Depending on the filtering stringency conditions, between 31,195 and 54,503 lncRNAs were identified, with only 421 matching known lncRNAs in other species. A digital gene expression atlas revealed 2,935 tissue-specific and 3,269 ubiquitously-expressed lncRNAs. This study annotates the lncRNA rainbow trout genome and provides a valuable resource for functional genomics research in salmonids.

Show MeSH
Related in: MedlinePlus