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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

Positional bias distribution of ncRNAs with respect to neighbour genes.(A) Relative frequencies of ncRNAs with respect to the distance from neighbour genes. 100 kb adjacent to TSS or TTS of genes is shown in these plots. 3′ END means the ncRNA is located in the 3′ flanking region of its neighbour gene. 5′ END means the ncRNA is located in the 5′ flanking region of its neighbour gene. “Gene intervals” refers to the intergenic region of two adjacent genes. (B) Relative frequencies of ncRNAs from neighbour genes partitioned with respect to transcription orientation. The internal boxes represent the zoom in view of the relative frequencies from 5 kb to 20 kb.
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pone-0042638-g006: Positional bias distribution of ncRNAs with respect to neighbour genes.(A) Relative frequencies of ncRNAs with respect to the distance from neighbour genes. 100 kb adjacent to TSS or TTS of genes is shown in these plots. 3′ END means the ncRNA is located in the 3′ flanking region of its neighbour gene. 5′ END means the ncRNA is located in the 5′ flanking region of its neighbour gene. “Gene intervals” refers to the intergenic region of two adjacent genes. (B) Relative frequencies of ncRNAs from neighbour genes partitioned with respect to transcription orientation. The internal boxes represent the zoom in view of the relative frequencies from 5 kb to 20 kb.

Mentions: Most bovine ncRNAs mapped to intergenic regions (Figure 5). To get a better understanding of these intergenic ncRNAs, we plotted the frequency distribution of intergenic ncRNAs as a function of their distance and transcriptional orientation to the nearest neighbour genes (Figure 6). About 67.4% (8,500 out of 12,614) of intergenic ncRNAs had a neighbour gene within 20 kb, with a significant concentration of intergenic ncRNAs in the 5 kb flanking regions of genes. Beyond 10 kb, the number of intergenic ncRNAs decreased very gradually as a function of distance. It was also apparent from Figure 6A that intergenic ncRNAs were more prevalent at the 3′ end of genes than at the 5′ end. The intergenic ncRNAs closest to the 5′ end of a gene also tended to be within 5 kb of the gene, but this localization was not significantly different to the control frequency distribution calculated using gene to gene nearest neighbour distances, where the majority of intergenic distances were less than 5 kb. We were able to determine transcriptional orientation of 10,969 of 12,614 intergenic ncRNAs based on their dbEST annotation. When we compared the transcriptional orientation of these intergenic ncRNAs to their closest gene neighbour, we observed that most of them closest to the 3′ end of genes were transcribed from the same strand as the gene (Figure 6B). There were four times more ncRNAs in the same transcriptional orientation when they were 3′ to the closest gene (6,296 to 1,433). This difference in transcriptional orientation for the ncRNAs 5′ of the closest gene was also observed, but not to the same degree (1,931 same to 1,309 reverse). The intergenic ncRNAs, transcribed from the same strand as the closest gene, might be extensions of the UTRs produced by alternative transcription start or termination sites of protein-coding genes, but many of them were at significant distances from these genes making this an unlikely possibility.


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

Qu Z, Adelson DL - PLoS ONE (2012)

Positional bias distribution of ncRNAs with respect to neighbour genes.(A) Relative frequencies of ncRNAs with respect to the distance from neighbour genes. 100 kb adjacent to TSS or TTS of genes is shown in these plots. 3′ END means the ncRNA is located in the 3′ flanking region of its neighbour gene. 5′ END means the ncRNA is located in the 5′ flanking region of its neighbour gene. “Gene intervals” refers to the intergenic region of two adjacent genes. (B) Relative frequencies of ncRNAs from neighbour genes partitioned with respect to transcription orientation. The internal boxes represent the zoom in view of the relative frequencies from 5 kb to 20 kb.
© Copyright Policy
Related In: Results  -  Collection

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

pone-0042638-g006: Positional bias distribution of ncRNAs with respect to neighbour genes.(A) Relative frequencies of ncRNAs with respect to the distance from neighbour genes. 100 kb adjacent to TSS or TTS of genes is shown in these plots. 3′ END means the ncRNA is located in the 3′ flanking region of its neighbour gene. 5′ END means the ncRNA is located in the 5′ flanking region of its neighbour gene. “Gene intervals” refers to the intergenic region of two adjacent genes. (B) Relative frequencies of ncRNAs from neighbour genes partitioned with respect to transcription orientation. The internal boxes represent the zoom in view of the relative frequencies from 5 kb to 20 kb.
Mentions: Most bovine ncRNAs mapped to intergenic regions (Figure 5). To get a better understanding of these intergenic ncRNAs, we plotted the frequency distribution of intergenic ncRNAs as a function of their distance and transcriptional orientation to the nearest neighbour genes (Figure 6). About 67.4% (8,500 out of 12,614) of intergenic ncRNAs had a neighbour gene within 20 kb, with a significant concentration of intergenic ncRNAs in the 5 kb flanking regions of genes. Beyond 10 kb, the number of intergenic ncRNAs decreased very gradually as a function of distance. It was also apparent from Figure 6A that intergenic ncRNAs were more prevalent at the 3′ end of genes than at the 5′ end. The intergenic ncRNAs closest to the 5′ end of a gene also tended to be within 5 kb of the gene, but this localization was not significantly different to the control frequency distribution calculated using gene to gene nearest neighbour distances, where the majority of intergenic distances were less than 5 kb. We were able to determine transcriptional orientation of 10,969 of 12,614 intergenic ncRNAs based on their dbEST annotation. When we compared the transcriptional orientation of these intergenic ncRNAs to their closest gene neighbour, we observed that most of them closest to the 3′ end of genes were transcribed from the same strand as the gene (Figure 6B). There were four times more ncRNAs in the same transcriptional orientation when they were 3′ to the closest gene (6,296 to 1,433). This difference in transcriptional orientation for the ncRNAs 5′ of the closest gene was also observed, but not to the same degree (1,931 same to 1,309 reverse). The intergenic ncRNAs, transcribed from the same strand as the closest gene, might be extensions of the UTRs produced by alternative transcription start or termination sites of protein-coding genes, but many of them were at significant distances from these genes making this an unlikely possibility.

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