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

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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.

Item Type:

Journal Article (Further Contribution)

Division/Institute:

04 Faculty of Medicine > Department of Haematology, Oncology, Infectious Diseases, Laboratory Medicine and Hospital Pharmacy (DOLS) > Clinic of Medical Oncology
04 Faculty of Medicine > Pre-clinic Human Medicine > BioMedical Research (DBMR)

UniBE Contributor:

Johnson, Rory Baldwin

Subjects:

600 Technology > 610 Medicine & health

ISSN:

1940-6029

Publisher:

Springer

Language:

English

Submitter:

Rebeka Gerber

Date Deposited:

11 Feb 2021 11:14

Last Modified:

11 Feb 2021 11:14

Publisher DOI:

10.1007/978-1-0716-1158-6_9

PubMed ID:

33326074

Uncontrolled Keywords:

CaptureSeq GENCODE Genome annotation Long-read RNA sequencing NGS Nanopore Next-generation sequencing PacBio Targeted RNA sequencing lncRNAs

BORIS DOI:

10.48350/150421

URI:

https://boris.unibe.ch/id/eprint/150421

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