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Bovine ncRNAs are abundant, primarily intergenic, conserved and associated with regulatory genes.

Qu Z, Adelson DL - PLoS ONE (2012)

Bottom Line: It is apparent that non-coding transcripts are a common feature of higher organisms and encode uncharacterized layers of genetic regulation and information.Many of these intergenic non-coding RNAs mapped close to the 3' or 5' end of thousands of genes and many of these were transcribed from the opposite strand with respect to the closest gene, particularly regulatory-related genes.These results support the hypothesis that ncRNAs are common, transcribed in a regulated fashion and have regulatory functions.

View Article: PubMed Central - PubMed

Affiliation: School of Molecular and Biomedical Science, The University of Adelaide, Adelaide, South Australia, Australia.

ABSTRACT
It is apparent that non-coding transcripts are a common feature of higher organisms and encode uncharacterized layers of genetic regulation and information. We used public bovine EST data from many developmental stages and tissues, and developed a pipeline for the genome wide identification and annotation of non-coding RNAs (ncRNAs). We have predicted 23,060 bovine ncRNAs, 99% of which are un-annotated, based on known ncRNA databases. Intergenic transcripts accounted for the majority (57%) of the predicted ncRNAs and the occurrence of ncRNAs and genes were only moderately correlated (r = 0.55, p-value<2.2e-16). Many of these intergenic non-coding RNAs mapped close to the 3' or 5' end of thousands of genes and many of these were transcribed from the opposite strand with respect to the closest gene, particularly regulatory-related genes. Conservation analyses showed that these ncRNAs were evolutionarily conserved, and many intergenic ncRNAs proximate to genes contained sequence-specific motifs. Correlation analysis of expression between these intergenic ncRNAs and protein-coding genes using RNA-seq data from a variety of tissues showed significant correlations with many transcripts. These results support the hypothesis that ncRNAs are common, transcribed in a regulated fashion and have regulatory functions.

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Related in: MedlinePlus

Flowchart describing the pipeline for ncRNA identification.
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pone-0042638-g001: Flowchart describing the pipeline for ncRNA identification.

Mentions: We identified ncRNAs from bovine ESTs, by developing a computational pipeline based on public software and Perl scripts (Figure 1). A total set of 1,517,143 bovine ESTs (as of 30th September, 2009), extracted from the dbEST of NCBI, was processed as the input dataset for the pipeline. After quality control, repeat filtration and EST assembly, we identified 216,095 unique transcripts. We opted for stringent mapping criteria (coverage ≥90% and identity ≥95%) and as a result, 69,099 unique transcripts were unable to be mapped to the BosTau4 assembly and were therefore discarded. Of the mapped sequences, 3,121 were classified as putative cis-NATs, 74 of which were subsequently manually checked on UCSC genome browser (Materials S1). The remaining 143,875 mapped unique transcripts were further analysed to annotate and characterize the bovine transcriptome.


Bovine ncRNAs are abundant, primarily intergenic, conserved and associated with regulatory genes.

Qu Z, Adelson DL - PLoS ONE (2012)

Flowchart describing the pipeline for ncRNA identification.
© Copyright Policy
Related In: Results  -  Collection

Show All Figures
getmorefigures.php?uid=PMC3412814&req=5

pone-0042638-g001: Flowchart describing the pipeline for ncRNA identification.
Mentions: We identified ncRNAs from bovine ESTs, by developing a computational pipeline based on public software and Perl scripts (Figure 1). A total set of 1,517,143 bovine ESTs (as of 30th September, 2009), extracted from the dbEST of NCBI, was processed as the input dataset for the pipeline. After quality control, repeat filtration and EST assembly, we identified 216,095 unique transcripts. We opted for stringent mapping criteria (coverage ≥90% and identity ≥95%) and as a result, 69,099 unique transcripts were unable to be mapped to the BosTau4 assembly and were therefore discarded. Of the mapped sequences, 3,121 were classified as putative cis-NATs, 74 of which were subsequently manually checked on UCSC genome browser (Materials S1). The remaining 143,875 mapped unique transcripts were further analysed to annotate and characterize the bovine transcriptome.

Bottom Line: It is apparent that non-coding transcripts are a common feature of higher organisms and encode uncharacterized layers of genetic regulation and information.Many of these intergenic non-coding RNAs mapped close to the 3' or 5' end of thousands of genes and many of these were transcribed from the opposite strand with respect to the closest gene, particularly regulatory-related genes.These results support the hypothesis that ncRNAs are common, transcribed in a regulated fashion and have regulatory functions.

View Article: PubMed Central - PubMed

Affiliation: School of Molecular and Biomedical Science, The University of Adelaide, Adelaide, South Australia, Australia.

ABSTRACT
It is apparent that non-coding transcripts are a common feature of higher organisms and encode uncharacterized layers of genetic regulation and information. We used public bovine EST data from many developmental stages and tissues, and developed a pipeline for the genome wide identification and annotation of non-coding RNAs (ncRNAs). We have predicted 23,060 bovine ncRNAs, 99% of which are un-annotated, based on known ncRNA databases. Intergenic transcripts accounted for the majority (57%) of the predicted ncRNAs and the occurrence of ncRNAs and genes were only moderately correlated (r = 0.55, p-value<2.2e-16). Many of these intergenic non-coding RNAs mapped close to the 3' or 5' end of thousands of genes and many of these were transcribed from the opposite strand with respect to the closest gene, particularly regulatory-related genes. Conservation analyses showed that these ncRNAs were evolutionarily conserved, and many intergenic ncRNAs proximate to genes contained sequence-specific motifs. Correlation analysis of expression between these intergenic ncRNAs and protein-coding genes using RNA-seq data from a variety of tissues showed significant correlations with many transcripts. These results support the hypothesis that ncRNAs are common, transcribed in a regulated fashion and have regulatory functions.

Show MeSH
Related in: MedlinePlus