DLAF – a novel method for strand-specific sequencing of RNA (ssRNA-seq)

Massively parallel strand-specific sequencing of RNA (ssRNA-seq) has emerged as a powerful tool for profiling complex transcriptomes. However, many current methods for ssRNA-seq suffer from the underrepresentation of both the 5′ and 3′ ends of RNAs, which can be attributed to second-strand cDNA synthesis. The 5′ and 3′ ends of RNA harbour crucial information for gene regulation; namely, transcription start sites (TSSs) and polyadenylation sites.

Here researchers from the University of Michigan report a novel ssRNA-seq method that does not involve second-strand cDNA synthesis, as they Directly Ligate sequencing Adaptors to the First-strand cDNA (DLAF). This novel method with fewer enzymatic reactions results in a higher quality of the libraries than the conventional method. Sequencing of DLAF libraries followed by a novel analysis pipeline enables the profiling of both 5′ ends and polyadenylation sites at near-base resolution. Therefore, DLAF offers the first genomics tool to obtain the ‘full-length’ transcriptome with a single library.

rna-seq

Agarwal S, Macfarlan TS, Sartor MA, Iwase S. (2015) Sequencing of first-strand cDNA library reveals full-length transcriptomes. Nat Commun 6:6002. [abstract]

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