RiboRid – A low cost, advanced, and ultra-efficient method to remove ribosomal RNA for bacterial transcriptomics

RNA sequencing techniques have enabled the systematic elucidation of gene expression (RNA-Seq), transcription start sites (differential RNA-Seq), transcript 3′ ends (Term-Seq), and post-transcriptional processes (ribosome profiling). The main challenge of transcriptomic studies is to remove ribosomal RNAs (rRNAs), which comprise more than 90% of the total RNA in a cell.

Researchers at Korea Advanced Institute of Science and Technology have developed a low-cost and robust bacterial rRNA depletion method, RiboRid, based on the enzymatic degradation of rRNA by thermostable RNase H. This method implemented experimental considerations to minimize nonspecific degradation of mRNA and is capable of depleting pre-rRNAs that often comprise a large portion of RNA, even after rRNA depletion. The researchers demonstrated the highly efficient removal of rRNA up to a removal efficiency of 99.99% for various transcriptome studies, including RNA-Seq, Term-Seq, and ribosome profiling, with a cost of approximately $10 per sample. This method is expected to be a robust method for large-scale high-throughput bacterial transcriptomic studies.

Experimental workflow of RiboRid

Fig 1

Anti-rRNA oligonucleotide probes (ArOPs) are chemically synthesized. Short denaturation time, neutral pH, low Mg2+ concentration, and high reaction temperature provides minimal experimental bias.

Choe D, Szubin R, Poudel S, Sastry A, Song Y, Lee Y, et al. (2021) RiboRid: A low cost, advanced, and ultra-efficient method to remove ribosomal RNA for bacterial transcriptomics. PLoS Genet 17(9): e1009821. [article]

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