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A high-resolution view of RNA endonuclease cleavage in Bacillus subtilis [mpra_bc_mapping]

ABSTRACT: A high-resolution view of RNA endonuclease cleavage in Bacillus subtilis [mpra_bc_mapping]

PROVIDER: PRJNA1149079 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR30276731_1.fastq.gz	Fastqsanger.gz
	SRR30276731_2.fastq.gz	Fastqsanger.gz
	SRR30276733_1.fastq.gz	Fastqsanger.gz
	SRR30276733_2.fastq.gz	Fastqsanger.gz
	SRR30276734_1.fastq.gz	Fastqsanger.gz

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Project description:RNA endonucleases are the rate-limiting initiator of decay for many bacterial mRNAs. However, the positions of cleavage and their sequence determinants remain elusive even for the well-studied Bacillus subtilis. Here we present two complementary approaches – transcriptome-wide mapping of endoribonucleolytic activity and deep mutational scanning of RNA cleavage sites – that reveal distinct rules governing the specificity among B. subtilis endoribonucleases. Detection of RNA terminal nucleotides in both 5′- and 3′-exonuclease-deficient cells revealed >103 putative endonucleolytic cleavage sites with single-nucleotide resolution. We found a surprisingly weak consensus for RNase Y targets, a contrastingly strong primary sequence motif for EndoA targets, and long-range intramolecular secondary structures for RNase III targets. Deep mutational analysis of RNase Y cleavage sites showed that the specificity is governed by many disjointed sequence features, each with mild contributions. Our results highlight the delocalized nature of mRNA stability determinants and provide a strategy for elucidating endoribonuclease specificity in vivo.

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