Bioinformatics Approaches to Studying Plant Long Noncoding RNAs (lncRNAs): Identification and Functional Interpretation of lncRNAs from RNA-Seq Data Sets.

Abstract

Long noncoding RNAs (lncRNAs) play important roles in regulating various biological processes including growth and stress responses in plants. RNA-seq data sets provide a good resource to exploring the noncoding transcriptome and studying their comprehensive interactions with the coding transcriptome. Here, we describe computational procedures for studying plant lncRNAs including long intergenic noncoding RNAs (lincRNAs) and long noncoding natural antisense transcripts (lncNATs). Bioinformatics tools for transcriptome assembly, lncRNA identification, and functional interpretations are included. Finally, we also introduce PLncDB, a user-friendly database that provides comprehensive information of plant lncRNAs for researchers to compare their own data sets to those in public database.