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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

Classification of ncRNAs in relation to protein-coding genes.(A) The entire EST is transcribed from an intergenic region, regardless of the transcription orientation. (B) The entire EST is transcribed from an intron, regardless of the transcription orientation. (C) Single-overlapped ncRNA: EST partially overlapped with a gene; Double-overlapped ncRNA: Both ends of the EST overlapped with two genes and spanned an intergenic region; Single-included ncRNA: The gene was fully included inside the EST; Included-overlapped ncRNA: One gene was fully included within the ncRNA, and the ncRNA spanned the intergenic region and overlapped with a neighbour gene; Double-included ncRNA: More than one genes were fully included within the EST.
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pone-0042638-g004: Classification of ncRNAs in relation to protein-coding genes.(A) The entire EST is transcribed from an intergenic region, regardless of the transcription orientation. (B) The entire EST is transcribed from an intron, regardless of the transcription orientation. (C) Single-overlapped ncRNA: EST partially overlapped with a gene; Double-overlapped ncRNA: Both ends of the EST overlapped with two genes and spanned an intergenic region; Single-included ncRNA: The gene was fully included inside the EST; Included-overlapped ncRNA: One gene was fully included within the ncRNA, and the ncRNA spanned the intergenic region and overlapped with a neighbour gene; Double-included ncRNA: More than one genes were fully included within the EST.

Mentions: We further classified our ncRNAs with respect to neighbour protein-coding genes to analyse the potential transcriptional overlap with RefSeq genes. Our classification scheme for ncRNAs is shown in Figure 4. Excluding 952 ncRNAs mapped to uncharacterized genomic locations, there were three main types of ncRNAs based on this classification and their relative proportions are shown in Figure 5. The majority of the ncRNAs in our dataset were intergenic transcripts (57% intergenic compared to 42% intronic). We also noticed that most ncRNAs were singletons (72.2% out of intergenic, 81.1% out of intronic and 71.3% out of overlapped ncRNAs respectively)(Table 1). The data in Table 1 also showed that the vast majority of ncRNAs (both intergenic and intronic) were apparently unspliced transcripts.


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

Qu Z, Adelson DL - PLoS ONE (2012)

Classification of ncRNAs in relation to protein-coding genes.(A) The entire EST is transcribed from an intergenic region, regardless of the transcription orientation. (B) The entire EST is transcribed from an intron, regardless of the transcription orientation. (C) Single-overlapped ncRNA: EST partially overlapped with a gene; Double-overlapped ncRNA: Both ends of the EST overlapped with two genes and spanned an intergenic region; Single-included ncRNA: The gene was fully included inside the EST; Included-overlapped ncRNA: One gene was fully included within the ncRNA, and the ncRNA spanned the intergenic region and overlapped with a neighbour gene; Double-included ncRNA: More than one genes were fully included within the EST.
© Copyright Policy
Related In: Results  -  Collection

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

pone-0042638-g004: Classification of ncRNAs in relation to protein-coding genes.(A) The entire EST is transcribed from an intergenic region, regardless of the transcription orientation. (B) The entire EST is transcribed from an intron, regardless of the transcription orientation. (C) Single-overlapped ncRNA: EST partially overlapped with a gene; Double-overlapped ncRNA: Both ends of the EST overlapped with two genes and spanned an intergenic region; Single-included ncRNA: The gene was fully included inside the EST; Included-overlapped ncRNA: One gene was fully included within the ncRNA, and the ncRNA spanned the intergenic region and overlapped with a neighbour gene; Double-included ncRNA: More than one genes were fully included within the EST.
Mentions: We further classified our ncRNAs with respect to neighbour protein-coding genes to analyse the potential transcriptional overlap with RefSeq genes. Our classification scheme for ncRNAs is shown in Figure 4. Excluding 952 ncRNAs mapped to uncharacterized genomic locations, there were three main types of ncRNAs based on this classification and their relative proportions are shown in Figure 5. The majority of the ncRNAs in our dataset were intergenic transcripts (57% intergenic compared to 42% intronic). We also noticed that most ncRNAs were singletons (72.2% out of intergenic, 81.1% out of intronic and 71.3% out of overlapped ncRNAs respectively)(Table 1). The data in Table 1 also showed that the vast majority of ncRNAs (both intergenic and intronic) were apparently unspliced transcripts.

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