Abstract
Accurate annotations of genes and their transcripts is a foundation of genomics, but no annotation technique presently combines throughput and accuracy. As a result, current reference gene collections remain far from complete: many genes models are fragmentary, while thousands more remain uncatalogued—particularly for long noncoding RNAs (lncRNAs). To accelerate lncRNA annotation, the GENCODE consortium has developed RNA Capture Long Seq (CLS), combining targeted RNA capture with third generation long-read sequencing. We present an experimental re-annotation of the GENCODE intergenic lncRNA population in matched human and mouse tissues, resulting in novel transcript models for 3574/561 gene loci, respectively. CLS approximately doubles the annotated complexity of targeted loci, in terms of validated splice junctions and transcript models, outperforming existing short-read techniques. The full-length transcript models produced by CLS enable us to definitively characterize the genomic features of lncRNAs, including promoter-and gene-structure, and protein-coding potential. Thus CLS removes a longstanding bottleneck of transcriptome annotation, generating manual-quality full-length transcript models at high-throughput scales.
Footnotes
Abbreviations bp: base pair
FL: full length
nt: nucleotide
ROI: read of insert, i.e. PacBio reads
SJ: splice junction
SMRT: single-molecule real-time
TM: transcript model