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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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Two sequence motifs from intergenic ncRNAs with significant similarity against known DNA motifs.For each comparison, the upper one is the known DNA motif, and the lower one is the intergenic ncRNA sequence motif.
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pone-0042638-g008: Two sequence motifs from intergenic ncRNAs with significant similarity against known DNA motifs.For each comparison, the upper one is the known DNA motif, and the lower one is the intergenic ncRNA sequence motif.

Mentions: Based on the gene expression profiles generated from 95 bovine transcriptome libraries, we identified 21 sequence specific motifs from 5′ intergenic ncRNAs and 29 from 3′ intergenic ncRNAs (Table S8, A & B). By comparison against known DNA motif databases using TOMTOM, we found that 2 motifs, “160_1_5END” from 5′ end intergenic ncRNAs and “086_1_3END” from 3′ end intergenic ncRNAs, showed significant similarity against known DNA motifs “ste11” and “ARF” respectively (p-value<1e-04 and FDR<0.05) (Figure 8 and Table S8). It is interesting to note that the number of “sense” sequence motifs of “ste11” (the motif is the same as the intergenic ncRNA strand) is almost equal to the number of “antisense” “ste11” motifs (the motif is complementary to the intergenic ncRNA strand) (Table S8, A & B). 3 other motifs from 5′ intergenic ncRNAs and 4 from 3′ intergenic ncRNAs also showed strong similarity (p-value<1e-04, FDR<0.5) against known DNA motifs (Figure S3 and Figure S4). The numbers of “sense” and “antisense” sequence sites in intergenic ncRNAs are almost equal for most of the identified motifs (Table S8, A & B and Figure S5).


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

Qu Z, Adelson DL - PLoS ONE (2012)

Two sequence motifs from intergenic ncRNAs with significant similarity against known DNA motifs.For each comparison, the upper one is the known DNA motif, and the lower one is the intergenic ncRNA sequence motif.
© Copyright Policy
Related In: Results  -  Collection

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

pone-0042638-g008: Two sequence motifs from intergenic ncRNAs with significant similarity against known DNA motifs.For each comparison, the upper one is the known DNA motif, and the lower one is the intergenic ncRNA sequence motif.
Mentions: Based on the gene expression profiles generated from 95 bovine transcriptome libraries, we identified 21 sequence specific motifs from 5′ intergenic ncRNAs and 29 from 3′ intergenic ncRNAs (Table S8, A & B). By comparison against known DNA motif databases using TOMTOM, we found that 2 motifs, “160_1_5END” from 5′ end intergenic ncRNAs and “086_1_3END” from 3′ end intergenic ncRNAs, showed significant similarity against known DNA motifs “ste11” and “ARF” respectively (p-value<1e-04 and FDR<0.05) (Figure 8 and Table S8). It is interesting to note that the number of “sense” sequence motifs of “ste11” (the motif is the same as the intergenic ncRNA strand) is almost equal to the number of “antisense” “ste11” motifs (the motif is complementary to the intergenic ncRNA strand) (Table S8, A & B). 3 other motifs from 5′ intergenic ncRNAs and 4 from 3′ intergenic ncRNAs also showed strong similarity (p-value<1e-04, FDR<0.5) against known DNA motifs (Figure S3 and Figure S4). The numbers of “sense” and “antisense” sequence sites in intergenic ncRNAs are almost equal for most of the identified motifs (Table S8, A & B and Figure S5).

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