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 RNAseq 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 integrative 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 yielded a comprehensive lncRNAs mapping in human brain, allowing discovery of novel lncRNAs and further function annotation.