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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

Probability densities of genes and ncRNAs per 1 Mb bin.NcRNAs have similar genomic densities compared to protein coding genes, but with fewer extreme density regions. The colour coding is consistent with Figure 2.
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pone-0042638-g003: Probability densities of genes and ncRNAs per 1 Mb bin.NcRNAs have similar genomic densities compared to protein coding genes, but with fewer extreme density regions. The colour coding is consistent with Figure 2.

Mentions: To understand the distribution of predicted ncRNAs in the genome, our 23,060 predicted ncRNAs mapped onto BosTau4 were compared to the mapped locations of 24,373 bovine RefSeqs. Figure 2 shows the density distributions of ncRNAs and RefSeqs in 30 bovine chromosomes (29 autosomes and X). Together with the relative frequencies of the densities of ncRNAs and RefSeqs, which are shown in Figure 3, it is obvious that the “gene poor regions” (with fewer than 10 genes in 1 Mb) are more abundant than “ncRNA poor regions” (less than 10 ncRNA s in 1 Mb) in the bovine genome. Furthermore, 288 gene deserts (no gene in 1 Mb) were identified compared to 156 ncRNA deserts (no ncRNA in 1 Mb). At the other end of the gene density spectrum, 21 regions were found with more than 50 genes/Mb, but no comparable regions were found for ncRNAs. These results showed that ncRNAs were more evenly distributed than protein-coding genes across the genome. A correlation analysis of the densities of protein-coding genes and ncRNAs per 1 Mb revealed only a moderate correlation between these two transcriptome sets at the whole genome level (r = 0.5528816, p<2.2e-16).


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

Qu Z, Adelson DL - PLoS ONE (2012)

Probability densities of genes and ncRNAs per 1 Mb bin.NcRNAs have similar genomic densities compared to protein coding genes, but with fewer extreme density regions. The colour coding is consistent with Figure 2.
© Copyright Policy
Related In: Results  -  Collection

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

pone-0042638-g003: Probability densities of genes and ncRNAs per 1 Mb bin.NcRNAs have similar genomic densities compared to protein coding genes, but with fewer extreme density regions. The colour coding is consistent with Figure 2.
Mentions: To understand the distribution of predicted ncRNAs in the genome, our 23,060 predicted ncRNAs mapped onto BosTau4 were compared to the mapped locations of 24,373 bovine RefSeqs. Figure 2 shows the density distributions of ncRNAs and RefSeqs in 30 bovine chromosomes (29 autosomes and X). Together with the relative frequencies of the densities of ncRNAs and RefSeqs, which are shown in Figure 3, it is obvious that the “gene poor regions” (with fewer than 10 genes in 1 Mb) are more abundant than “ncRNA poor regions” (less than 10 ncRNA s in 1 Mb) in the bovine genome. Furthermore, 288 gene deserts (no gene in 1 Mb) were identified compared to 156 ncRNA deserts (no ncRNA in 1 Mb). At the other end of the gene density spectrum, 21 regions were found with more than 50 genes/Mb, but no comparable regions were found for ncRNAs. These results showed that ncRNAs were more evenly distributed than protein-coding genes across the genome. A correlation analysis of the densities of protein-coding genes and ncRNAs per 1 Mb revealed only a moderate correlation between these two transcriptome sets at the whole genome level (r = 0.5528816, p<2.2e-16).

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