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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

Sequence conservation analysis of ncRNAs.(A, B & C) are based on phastCons score. (D, E & F) are based on GERP++ score. The control line is based on a similar number of randomly selected non-transcribed genomic regions. A & D – ncRNAs compared to RefSeqs, B & E – intergenic ncRNAs compared to intronic and C& F – 5′ vs 3′ ncRNAs and transcriptional orientation with respect to nearest neighbour genes.
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pone-0042638-g007: Sequence conservation analysis of ncRNAs.(A, B & C) are based on phastCons score. (D, E & F) are based on GERP++ score. The control line is based on a similar number of randomly selected non-transcribed genomic regions. A & D – ncRNAs compared to RefSeqs, B & E – intergenic ncRNAs compared to intronic and C& F – 5′ vs 3′ ncRNAs and transcriptional orientation with respect to nearest neighbour genes.

Mentions: To assess whether ncRNAs were under selective constraint, we used two different methods to assess the degree of sequence conservation as shown in Figure 7. Figure 7A shows the degree of conservation based on phastCons score; ncRNAs were clearly conserved compared to control sequences, which were selected at random from un-transcribed regions of the bovine genome, but were less conserved compared to protein-coding genes. When we compared the degree of sequence conservation between intergenic and intronic ncRNAs according to phastCons score (Figure 7B), intergenic ncRNAs were more conserved than intronic ones. When we further refined this to assess the sequence conservation of intergenic ncRNAs according to their relationships with protein-coding genes, we observed that intergenic ncRNAs closest to the 3′ end of genes were more conserved than those closest to the 5′ end of genes. And when we took into the consideration the transcriptional orientation of these ncRNAs with respect to their closest gene, the “sense” intergenic ncRNAs, which are transcribed from the same strand as their neighbour genes, were more conserved than the “antisense” intergenic ncRNAs, regardless of whether they were closest to the 5′ or 3′ end of protein-coding genes (Figure 7C).


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

Qu Z, Adelson DL - PLoS ONE (2012)

Sequence conservation analysis of ncRNAs.(A, B & C) are based on phastCons score. (D, E & F) are based on GERP++ score. The control line is based on a similar number of randomly selected non-transcribed genomic regions. A & D – ncRNAs compared to RefSeqs, B & E – intergenic ncRNAs compared to intronic and C& F – 5′ vs 3′ ncRNAs and transcriptional orientation with respect to nearest neighbour genes.
© Copyright Policy
Related In: Results  -  Collection

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

pone-0042638-g007: Sequence conservation analysis of ncRNAs.(A, B & C) are based on phastCons score. (D, E & F) are based on GERP++ score. The control line is based on a similar number of randomly selected non-transcribed genomic regions. A & D – ncRNAs compared to RefSeqs, B & E – intergenic ncRNAs compared to intronic and C& F – 5′ vs 3′ ncRNAs and transcriptional orientation with respect to nearest neighbour genes.
Mentions: To assess whether ncRNAs were under selective constraint, we used two different methods to assess the degree of sequence conservation as shown in Figure 7. Figure 7A shows the degree of conservation based on phastCons score; ncRNAs were clearly conserved compared to control sequences, which were selected at random from un-transcribed regions of the bovine genome, but were less conserved compared to protein-coding genes. When we compared the degree of sequence conservation between intergenic and intronic ncRNAs according to phastCons score (Figure 7B), intergenic ncRNAs were more conserved than intronic ones. When we further refined this to assess the sequence conservation of intergenic ncRNAs according to their relationships with protein-coding genes, we observed that intergenic ncRNAs closest to the 3′ end of genes were more conserved than those closest to the 5′ end of genes. And when we took into the consideration the transcriptional orientation of these ncRNAs with respect to their closest gene, the “sense” intergenic ncRNAs, which are transcribed from the same strand as their neighbour genes, were more conserved than the “antisense” intergenic ncRNAs, regardless of whether they were closest to the 5′ or 3′ end of protein-coding genes (Figure 7C).

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