title: Predicting long non-coding RNAs using RNA sequencing.
abstract: The advent of next-generation sequencing, and in particular RNA-sequencing (RNA-seq), technologies has expanded our knowledge of the transcriptional capacity of human and other animal, genomes. In particular, recent RNA-seq studies have revealed that transcription is widespread across the mammalian genome, resulting in a large increase in the number of putative transcripts from both within, and intervening between, known protein-coding genes. Long transcripts that appear to lack protein-coding potential (long non-coding RNAs, lncRNAs) have been the focus of much recent research, in part owing to observations of their cell-type and developmental time-point restricted expression patterns. A variety of sequencing protocols are currently available for identifying lncRNAs including RNA polymerase II occupancy, chromatin state maps and - the focus of this review - deep RNA sequencing. In addition, there are numerous analytical methods available for mapping reads and assembling transcript models that predict the presence and structure of lncRNAs from RNA-seq data. Here we review current methods for identifying lncRNAs using large-scale sequencing data from RNA-seq experiments and highlight analytical considerations that are required when undertaking such projects.
authors.affiliation: CGAT, MRC Functional Genomics Unit, Department of Physiology, Anatomy and Genetics, University of Oxford, UK. Electronic address: nicholas.ilott@dpag.ox.ac.uk.
authors.forename: Nicholas E
authors.initials: NE
authors.lastname: Ilott
authors.forename: Chris P
authors.initials: CP
authors.lastname: Ponting
mesh_terms: D001483:Base Sequence; D002843:Chromatin / Q000235:genetics; D059014:High-Throughput Nucleotide Sequencing / Q000379:methods*; D006801:Humans; D012319:RNA Polymerase II / Q000235:genetics; D062085:RNA, Long Noncoding / Q000235:genetics / Q000302:isolation & purification*; D014158:Transcription, Genetic
chemical_list: D002843:Chromatin; D062085:RNA, Long Noncoding; D012319:RNA Polymerase II
keywords: Long non-coding RNA; Next generation sequencing; RNA-seq; lncRNAs