Improved bacterial RNA-seq by Cas9-based depletion of ribosomal RNA reads

A major challenge for RNA-seq analysis of gene expression is to achieve sufficient coverage of informative non-ribosomal transcripts. In eukaryotic samples, this is typically achieved by selective oligo(dT)-priming of messenger RNAs to exclude ribosomal RNA (rRNA) during cDNA synthesis. However, this strategy is not compatible with prokaryotes in which functional transcripts are generally not polyadenylated.

To overcome this, researchers from the Helmholtz Institute for RNA-based Infection Research adopted DASH (Depletion of Abundant Sequences by Hybridization), initially developed for eukaryotic cells, to improve both the sensitivity and depth of bacterial RNA-seq. DASH employs the Cas9 nuclease to remove unwanted cDNA sequences prior to library amplification. The researchers report the design, evaluation, and optimization of DASH experiments for standard bacterial short-read sequencing approaches, including software for automated guide RNA (gRNA) design for Cas9-mediated cleavage in bacterial rDNA sequences. Using these gRNA pools, they effectively removed rRNA reads (56-86%) in RNA-seq libraries from two different model bacteria, the Gram-negative pathogen Salmonella enterica and the anaerobic gut commensal Bacteroides thetaiotaomicron. DASH works robustly, even with sub-nanogram amounts of input cDNA. Its efficiency, high sensitivity, ease of implementation, and low cost (~$5 per sample) render DASH an attractive alternative to rRNA removal protocols, in particular for material-constrained studies where conventional ribodepletion techniques fail.

Overview of the bacterial DASH workflow


Schematic of the principle behind DASH-mediated removal of rRNA-derived cDNA fragments from sequencing libraries. The individual steps in the bacterial DASH pipeline are indicated in the zoom-in at the bottom.

Prezza G, Heckel T, Dietrich S,  Homberger C, Westermann AJ, Vogel J. (2020) Improved bacterial RNA-seq by Cas9-based depletion of ribosomal RNA reads. RNA [Epub ahead of print]. [article]

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