High-throughput annotation of full-length long noncoding RNAs with capture long-read sequencing

• Published in: Nature genetics Vol. 49; no. 12; pp. 1731 - 1740
• Main Authors: Lagarde, Julien, Uszczynska-Ratajczak, Barbara, Carbonell, Silvia, Pérez-Lluch, Sílvia, Abad, Amaya, Davis, Carrie, Gingeras, Thomas R, Frankish, Adam, Harrow, Jennifer, Guigo, Roderic, Johnson, Rory
• Format: Journal Article
• Language: English
• Published: New York Nature Publishing Group US 01.12.2017; Nature Publishing Group; Nature Research
• Subjects: 38; 38/39; 38/90; 38/91; 45; 45/77; 45/88; 631/1647/1888/1891; 631/1647/2017; 631/1647/48; 631/61/514/1949; 631/61/514/2184; Agriculture; Animal Genetics and Genomics; Animal models; Animals; Annotations; Automation; Bioinformatics; Biomedicine; Cancer; Cancer Research; Computational Biology - methods; Consortia; DNA sequencing; Gene expression; Gene expression analysis; Gene Expression Profiling - methods; Gene Function; Gene sequencing; Genetic research; Genomes; Genomics; Genomics - methods; High-Throughput Nucleotide Sequencing - methods; Human Genetics; Humans; Loci; Methods; Mice; Molecular Sequence Annotation - methods; Open Reading Frames - genetics; Properties; Protein structure; Proteins; Reproducibility of Results; Ribonucleic acid; RNA; RNA probes; RNA sequencing; RNA, Long Noncoding - genetics; Sequence annotation; Software quality; Studies; Technology application; Transcription
• ISSN: 1061-4036; 1546-1718; 1546-1718
• DOI: 10.1038/ng.3988

RNA Capture Long Seq (CLS) is a new method for transcript annotation that combines targeted RNA capture with long-read sequencing. CLS reannotates GENCODE lncRNAs and increases the number of validated splice junctions and transcript models for targeted loci. Accurate annotation of genes and their transcripts is a foundation of genomics, but currently no annotation technique combines throughput and accuracy. As a result, reference gene collections remain incomplete—many gene models are fragmentary, and thousands more remain uncataloged, particularly for long noncoding RNAs (lncRNAs). To accelerate lncRNA annotation, the GENCODE consortium has developed RNA Capture Long Seq (CLS), which combines targeted RNA capture with third-generation long-read sequencing. Here we present an experimental reannotation of the GENCODE intergenic lncRNA populations in matched human and mouse tissues that resulted in novel transcript models for 3,574 and 561 gene loci, respectively. CLS approximately doubled the annotated complexity of targeted loci, outperforming existing short-read techniques. Full-length transcript models produced by CLS enabled us to definitively characterize the genomic features of lncRNAs, including promoter and gene structure, and protein-coding potential. Thus, CLS removes a long-standing bottleneck in transcriptome annotation and generates manual-quality full-length transcript models at high-throughput scales.