Multi-dimensional conservation analysis reveals transcriptional codes ruling the expression of conserved long noncoding RNAs

Although long non-coding RNAs (lncRNAs) encounter weaker evolutionary constraints and exhibit lower sequences conservation than coding genes, lncRNAs can conserve their features at different aspects. Here, we employed multiple approaches to systemically evaluate the conservation between human and mouse lncRNAs from various dimensions including sequences, promoter, global synteny, and local synteny, which led to the identification of 1731 conserved lncRNAs with 427 ultraconserved ones meeting multiple criteria. The conserved lncRNAs, in comparison with non-conserved ones, in generally have longer gene bodies, higher numbers of exons and transcripts, closer connections with human diseases, and are more abundant and widespread across different tissues. The transcriptional factor profile analysis revealed a significant enrichment of TF types and numbers in the promoters of conserved lncRNAs. We further identified a set of TFs that preferentially bind to conserved lncRNAs and exert stronger impacts on their expression than non-conserved lncRNAs’ expression. Thus, our study has revealed a new set of transcriptional “codes” that rules the expression of the conserved lncRNAs. Examination of lncRNA's expression change in 293T cells