Bovine ncRNAs Are Abundant, Primarily Intergenic, Conserved and Associated with Regulatory Genes

School of Molecular and Biomedical Science, The University of Adelaide, Adelaide, South Australia, Australia.
PLoS ONE (Impact Factor: 3.23). 08/2012; 7(8). DOI: 10.1371/journal.pone.0042638
Source: PubMed


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 39 or 59 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. Copyright: ß 2012 Qu, Adelson. This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.

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    • "Moreover, there are a high number of intergenic ncRNAs which act through cis-regulation of mostly regulatory genes and locate in the 1 kb proximity of UTRs (Qu and Adelson, 2012). As the 3′-UTR associated/proximate ncRNAs are in highly conserved regions (Qu and Adelson, 2012), targeting the 3′-UTR of animal mRNA has been one of the most important pathways for regulation of gene expression (Glazov et al., 2009). "
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    • "Because of the key role of lncRNAs in regulation of gene expression and therefore possible impact on phenotypes, it is important to identify most lncRNAs. Catalogues of lncRNA have been established for many species, including cattle [27–29]. For example, Huang et al. (2012) have identified a total of 449 putative lncRNAs located in 405 intergenic regions using public bovine-specific expressed sequence tags sequences [28]. "
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