Abstract
ncRNAs (non-coding RNAs), in particular long ncRNAs, represent a significant proportion of the vertebrate transcriptome and probably regulate many biological processes. We used publically available ESTs (Expressed Sequence Tags) from human, mouse and zebrafish and a previously published analysis pipeline to annotate and analyze the vertebrate non-protein-coding transcriptome. Comparative analysis confirmed some previously described features of 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. Significantly, comparative analysis of developmental and regulatory genes proximate to long ncRNAs indicated that the only conserved relationship of these genes to neighbor long ncRNAs was with respect to genes expressed in human brain, suggesting a conserved, ncRNA cis-regulatory network in vertebrate nervous system development. Most of the relationships between long ncRNAs and proximate coding genes were not conserved, providing evidence for the rapid evolution of species-specific gene associated long ncRNAs. We have reconstructed and annotated over 130,000 long ncRNAs in these three species, providing a significantly expanded number of candidates for functional testing by the research community.
Highlights
Protein-coding genes account for only a small proportion of vertebrate genome complexity, only,2% of the human genome [1]
Many more lincRNAs have been reconstructed from RNA-seq data from multiple sources in human, mouse and zebrafish [12,14,24] and over a thousand long ncRNAs, some of which showed enhancer-like activity, were characterized based on GENCODE annotation [25]
Our long ncRNAs fell into 3 categories based on their genomic coordinates with respect to protein-coding genes; intergenic ncRNAs, intronic ncRNAs and overlapped ncRNAs, which overlapped by a small number of base pairs with exons of protein-coding genes [26]
Summary
Protein-coding genes account for only a small proportion of vertebrate genome complexity, only ,2% of the human genome [1]. Studies of some vertebrate genomes have indicated that there are tens of thousands of ncRNAs (non-coding RNAs) [6,7,8], including structural RNAs, such as ribosomal RNAs, transfer RNAs and small non-coding regulatory transcripts such as siRNAs (small interfering RNAs), miRNAs (micro RNAs) and piRNAs (piwi-interacting RNAs) [9]. In addition to these wellcharacterized ncRNAs, there are a substantial number long ncRNAs, only a few of which have been functionally characterized [10,11,12,13,14]. Many more lincRNAs have been reconstructed from RNA-seq data from multiple sources in human, mouse and zebrafish [12,14,24] and over a thousand long ncRNAs, some of which showed enhancer-like activity, were characterized based on GENCODE annotation [25]
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