High-throughput annotation of full-length long noncoding RNAs with Capture Long-Read Sequencing (CLS)

Lagarde, J.; Uszczynska-Ratajczak, B.; Carbonell, S.; Davis, C.; Gingeras, T. R.; Frankish, A.; Harrow, J.; Guigo, R.; Johnson, R.

doi:10.1101/105064

bioRxiv · 10.1101/105064

High-throughput annotation of full-length long noncoding RNAs with Capture Long-Read Sequencing (CLS)

Lagarde, J.·Uszczynska-Ratajczak, B.·Carbonell, S.·Davis, C.·Gingeras, T. R.·Frankish, A.·Harrow, J.·Guigo, R.·Johnson, R.

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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, reference gene collections remain incomplete: many gene 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, outperforming existing short-read techniques. 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.\n\nAbbreviations

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Lagarde, J., Uszczynska-Ratajczak, B., Carbonell, S., Davis, C., Gingeras, T. R., Frankish, A., Harrow, J., Guigo, R., Johnson, R.. 2017-02-01. High-throughput annotation of full-length long noncoding RNAs with Capture Long-Read Sequencing (CLS). https://doi.org/10.1101/105064

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