Comprehensive identification and annotation of non-protein-coding transcriptomes from vertebrates indicates most ncRNAs are regulatory.

Abstract

Non-coding RNAs (ncRNAs), in particular long ncRNAs, represent a significant proportion of the vertebrate transcriptome and probably regulate many biological processes. Initially, I developed a robust pipeline for the genome wide identification and annotation of ncRNAs and used publically available bovine ESTs (Expressed Sequence Tags) from many developmental stages and tissues as input. The pipeline yielded 23,060 annotated bovine ncRNAs, the majority of which (57%) were intergenic, and were only moderately correlated with protein coding genes. I then used this pipeline to annotate ncRNAs from human, mouse and zebrafish ESTs. Comparative analysis confirmed some previously described findings about intergenic ncRNAs, such as a positionally biased distribution with respect to regulatory or development related protein-coding genes, and weak but clear sequence conservation across species. Furthermore, comparative analysis of developmental and regulatory genes proximate to long intergenic ncRNAs indicated that the relationship of these genes to neighbor long ncRNAs was not conserved, providing evidence for the rapid evolution of species-specific gene associated long ncRNA. In addition, I built protein-coding and nonprotein-coding gene co-expression networks based on available human transcriptome data. More than 30,000 human protein-coding and non-coding transcripts were annotated into tissue-specific co-expression sub-networks, indicating the possible regulatory connections between ncRNAs and protein-coding genes. In conclusion, I have reconstructed and annotated over 130,000 long ncRNAs, most of which are unannotated, in human, mouse and zebrafish. Together with the annotated bovine ncRNAs, we provide a significantly expanded number of candidates for functional testing by the research community.