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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

Scatter plot for the log10 ratio of expressions of intergenic ncRNAs and corresponding neighbour genes.Dots were binned into 80*80 hexagons across the plot area. Different colours represent the dot count in each bin. A represents the expression of 5′ end UTR-related RNAs and neighbour genes. B represents the expression of 5′ end intergenic ncRNAs with UTR-related RNAs removed and neighbour genes. C represents the expression of 3′ end UTR-related RNAs and neighbour genes, and D represent the expression of 3′ end intergenic ncRNAs with UTR-related RNAs removed and corresponding neighbour genes.
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pone-0042638-g009: Scatter plot for the log10 ratio of expressions of intergenic ncRNAs and corresponding neighbour genes.Dots were binned into 80*80 hexagons across the plot area. Different colours represent the dot count in each bin. A represents the expression of 5′ end UTR-related RNAs and neighbour genes. B represents the expression of 5′ end intergenic ncRNAs with UTR-related RNAs removed and neighbour genes. C represents the expression of 3′ end UTR-related RNAs and neighbour genes, and D represent the expression of 3′ end intergenic ncRNAs with UTR-related RNAs removed and corresponding neighbour genes.

Mentions: Most of the identified intergenic ncRNAs reported from other species were directly or indirectly involved in gene regulatory networks. To understand whether there are correlations between the expression of intergenic ncRNAs and corresponding neighbour genes, we identified all intergenic ncRNA and neighbour gene pairs with expression in at least one library based on the 95 bovine MPSS transcriptome data. Globally, there was no clear correlation between the expression of intergenic ncRNAs and corresponding neighbour genes no matter whether intergenic ncRNAs were at the 5′ end or 3′ end of the genes (Figure 9). Because many intergenic ncRNAs containing sequence motifs are also close to regulatory genes, we checked the expression of these “motif and regulatory” intergenic ncRNAs across different libraries (Figure S6). Some of these intergenic ncRNAs showed negative expression correlation with neighbour genes. One of these intergenic ncRNAs is the antisense transcript of protein-coding gene “ZNFX1” (Figure S6). In human, the antisense transcript of “ZNFX1” has been annotated as “ZNFX1-AS1” [33]. This antisense transcript in bovine might be the homolog of the human “ZNFX1-AS1”. This bovine “ZNFX1-AS1” does not show high sequence conservation with 4 different human transcript variants (Figure S7). It is also the host transcript of two possible snoRNAs (SNORD12 and SNORD12B), which is consistent with human “ZNFX1-AS1” (Figure S8) [33].


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

Qu Z, Adelson DL - PLoS ONE (2012)

Scatter plot for the log10 ratio of expressions of intergenic ncRNAs and corresponding neighbour genes.Dots were binned into 80*80 hexagons across the plot area. Different colours represent the dot count in each bin. A represents the expression of 5′ end UTR-related RNAs and neighbour genes. B represents the expression of 5′ end intergenic ncRNAs with UTR-related RNAs removed and neighbour genes. C represents the expression of 3′ end UTR-related RNAs and neighbour genes, and D represent the expression of 3′ end intergenic ncRNAs with UTR-related RNAs removed and corresponding neighbour genes.
© Copyright Policy
Related In: Results  -  Collection

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

pone-0042638-g009: Scatter plot for the log10 ratio of expressions of intergenic ncRNAs and corresponding neighbour genes.Dots were binned into 80*80 hexagons across the plot area. Different colours represent the dot count in each bin. A represents the expression of 5′ end UTR-related RNAs and neighbour genes. B represents the expression of 5′ end intergenic ncRNAs with UTR-related RNAs removed and neighbour genes. C represents the expression of 3′ end UTR-related RNAs and neighbour genes, and D represent the expression of 3′ end intergenic ncRNAs with UTR-related RNAs removed and corresponding neighbour genes.
Mentions: Most of the identified intergenic ncRNAs reported from other species were directly or indirectly involved in gene regulatory networks. To understand whether there are correlations between the expression of intergenic ncRNAs and corresponding neighbour genes, we identified all intergenic ncRNA and neighbour gene pairs with expression in at least one library based on the 95 bovine MPSS transcriptome data. Globally, there was no clear correlation between the expression of intergenic ncRNAs and corresponding neighbour genes no matter whether intergenic ncRNAs were at the 5′ end or 3′ end of the genes (Figure 9). Because many intergenic ncRNAs containing sequence motifs are also close to regulatory genes, we checked the expression of these “motif and regulatory” intergenic ncRNAs across different libraries (Figure S6). Some of these intergenic ncRNAs showed negative expression correlation with neighbour genes. One of these intergenic ncRNAs is the antisense transcript of protein-coding gene “ZNFX1” (Figure S6). In human, the antisense transcript of “ZNFX1” has been annotated as “ZNFX1-AS1” [33]. This antisense transcript in bovine might be the homolog of the human “ZNFX1-AS1”. This bovine “ZNFX1-AS1” does not show high sequence conservation with 4 different human transcript variants (Figure S7). It is also the host transcript of two possible snoRNAs (SNORD12 and SNORD12B), which is consistent with human “ZNFX1-AS1” (Figure S8) [33].

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