An Integrative Approach Revealing the Landscape of Long Noncoding RNAs in Human Brain

Long noncoding RNAs (lncRNAs) function as regulators and play critical roles in diverse biological processes, however, the majority of lncRNAs are not characterized, and their roles in regulation remain to be elucidated. Present RNA-seq assembly approaches are insufficient to identify complete full-length transcripts and often reveal excessive amount of single-exon lncRNAs, many of them tend to be the fragments of transcripts. Here we developed an integrated approach that combined the results from reference-guided and de novo assembly to systematically identify lncRNAs. Experiments on simulated data and real RNA-seq data showed that our method effectively yielded a more comprehensive set of lncRNAs. We applied the method on 299 human brain RNA-seq samples with a total of 4.5 billion raw reads. The results yield a comprehensive lncRNAs mapping in human brain, allowing discovery of novel lncRNAs and further function annotation.