High-throughput annotation of full-length long noncoding RNAs using CapTrap-CLS

In the next lightning presentation, Sílvia Carbonell Sala from the Center for Genomic Regulation described a new method for capturing, sequencing, and analysing long noncoding RNAs (lncRNAs). lncRNAs are a type of RNA that are not translated into protein and studies have shown them to be over four times more abundant in the human genome than coding RNA sequences. Although lncRNA perform diverse and important functions, the overwhelming majority of them remain uncharacterised.

Sílvia explained that the ability to assign function to these molecules depends on accurate annotations; however, at present, lncRNA annotations are far from complete. In order to improve lncRNA annotation in human and mouse genomes, the team at the Center for Genomic Regulation had previously developed Capture Long-read Sequencing (CLS) – a method combining targeted RNA capture with long-read sequencing. The utilisation of long read nanopore technology that can sequence entire RNA molecules in single reads offers a significant advantage over short-read approaches, which rely on complex and often inaccurate transcript reconstruction methods. However, despite its benefits, the CLS approach can produce transcripts with incomplete 5’ ends. In order to address this, the team at the Center for Genomic Regulation developed Cap-CLS.

Sílvia shared data revealing how the utilisation of Cap-CLS together with nanopore sequencing resulted in a significantly higher percentage of full-length transcripts (including the 5’ end and poly-A tail) than alternative approaches. In addition, the read coverage of specific targeted loci was also greatly improved. In closing her presentation, Sílvia suggested that this method will help to ‘accurately and exhaustively annotate lncRNA and elucidate their unknown functions’.