Mining mammalian transcript data for functional long non-coding RNAs

Abstract

Background: The role of long non-coding RNAs (lncRNAs) in controlling gene expression has garnered increased interest in recent years. Sequencing projects, such as Fantom3 for mouse and H-InvDB for human, have generated abundant data on transcribed components of mammalian cells, the majority of which appear not to be protein-coding. However, much of the non-protein-coding transcriptome could merely be a consequence of 'transcription noise'. It is therefore essential to use bioinformatic approaches to identify the likely functional candidates in a high throughput manner.

Principal findings: We derived a scheme for classifying and annotating likely functional lncRNAs in mammals. Using the available experimental full-length cDNA data sets for human and mouse, we identified 78 lncRNAs that are either syntenically conserved between human and mouse, or that originate from the same protein-coding genes. Of these, 11 have significant sequence homology. We found that these lncRNAs exhibit: (i) patterns of codon substitution typical of non-coding transcripts; (ii) preservation of sequences in distant mammals such as dog and cow, (iii) significant sequence conservation relative to their corresponding flanking regions (in 50% cases, flanking regions do not have homology at all; and in the remaining, the degree of conservation is significantly less); (iv) existence mostly as single-exon forms (8/11); and, (v) presence of conserved and stable secondary structure motifs within them. We further identified orthologous protein-coding genes that are contributing to the pool of lncRNAs; of which, genes implicated in carcinogenesis are significantly over-represented.

Conclusion: Our comparative mammalian genomics approach coupled with evolutionary analysis identified a small population of conserved long non-protein-coding RNAs (lncRNAs) that are potentially functional across Mammalia. Additionally, our analysis indicates that amongst the orthologous protein-coding genes that produce lncRNAs, those implicated in cancer pathogenesis are significantly over-represented, suggesting that these lncRNAs could play an important role in cancer pathomechanisms.

Figure 1. A schematic representation of the discovery pipeline for conserved expressed long non-protein-coding RNAs (lncRNAs).

Figure 2. A schematic representation of different genomic regions from which lncRNA originate relative to the structure of a protein-coding gene.

Figure 3. A model for antisense regulation of target mRNA transcripts by lncRNAs.

The following lncRNA sequences: HIT000079026.8 and HIT000091723.8, have complementary relationship to UTR of the following protein-coding transcripts: ENST00000393449 and ENST00000383790, respectively.

Figure 4. Assessment for protein-coding ability.

Comparison between Ka/Ks values of long ORFs derived from six-frame conceptual translation for human-mouse lncRNAs and orthologous neighboring protein-coding genes.