Annotation of Full-Length Long Noncoding RNAs with Capture Long-Read Sequencing (CLS).

Carbonell Sala, Sílvia; Uszczyńska-Ratajczak, Barbara; Lagarde, Julien; Johnson, Rory; Guigó, Roderic (2021). Annotation of Full-Length Long Noncoding RNAs with Capture Long-Read Sequencing (CLS). Methods in molecular biology, 2254, pp. 133-159. Springer 10.1007/978-1-0716-1158-6_9

Text CarbonellSala2021_Protocol_AnnotationOfFull-LengthLongNon.pdf - Published Version Restricted to registered users only Available under License Publisher holds Copyright. Download (744kB)

Metazoan genomes produce thousands of long-noncoding RNAs (lncRNAs), of which just a small fraction have been well characterized. Understanding their biological functions requires accurate annotations, or maps of the precise location and structure of genes and transcripts in the genome. Current lncRNA annotations are limited by compromises between quality and size, with many gene models being fragmentary or uncatalogued. To overcome this, the GENCODE consortium has developed RNA capture long-read sequencing (CLS), an approach combining targeted RNA capture with third-generation long-read sequencing. CLS provides accurate annotations at high-throughput rates. It eliminates the need for noisy transcriptome assembly from short reads, and requires minimal manual curation. The full-length transcript models produced are of quality comparable to present-day manually curated annotations. Here we describe a detailed CLS protocol, from probe design through long-read sequencing to creation of final annotations.

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