An RNA-seq based comparative approach reveals the transcriptome-wide interplay between 3′-to-5′ exoRNases and RNase Y

Laura Broglia, Anne-Laure Lécrivain, Thibaud T. Renault, Karin Hahnke, Rina Ahmed-Begrich, Anaïs Le Rhun () and Emmanuelle Charpentier ()
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Laura Broglia: Max Planck Unit for the Science of Pathogens
Anne-Laure Lécrivain: Max Planck Unit for the Science of Pathogens
Thibaud T. Renault: Max Planck Unit for the Science of Pathogens
Karin Hahnke: Max Planck Unit for the Science of Pathogens
Rina Ahmed-Begrich: Max Planck Unit for the Science of Pathogens
Anaïs Le Rhun: Max Planck Unit for the Science of Pathogens
Emmanuelle Charpentier: Max Planck Unit for the Science of Pathogens

Nature Communications, 2020, vol. 11, issue 1, 1-12

Abstract: Abstract RNA degradation is an essential process that allows bacteria to control gene expression and adapt to various environmental conditions. It is usually initiated by endoribonucleases (endoRNases), which produce intermediate fragments that are subsequently degraded by exoribonucleases (exoRNases). However, global studies of the coordinated action of these enzymes are lacking. Here, we compare the targetome of endoRNase Y with the targetomes of 3′-to-5′ exoRNases from Streptococcus pyogenes, namely, PNPase, YhaM, and RNase R. We observe that RNase Y preferentially cleaves after guanosine, generating substrate RNAs for the 3′-to-5′ exoRNases. We demonstrate that RNase Y processing is followed by trimming of the newly generated 3′ ends by PNPase and YhaM. Conversely, the RNA 5′ ends produced by RNase Y are rarely further trimmed. Our strategy enables the identification of processing events that are otherwise undetectable. Importantly, this approach allows investigation of the intricate interplay between endo- and exoRNases on a genome-wide scale.

Date: 2020
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DOI: 10.1038/s41467-020-15387-6

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