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The global RNA-RNA interactome of Klebsiella pneumoniae unveils a small RNA regulator of cell division (RIL-Seq)

ABSTRACT: The global RNA-RNA interactome of Klebsiella pneumoniae unveils a small RNA regulator of cell division (RIL-Seq)

PROVIDER: PRJNA1023942 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR26281961_1.fastq.gz	Fastqsanger.gz
	SRR26281961_2.fastq.gz	Fastqsanger.gz
	SRR26281962_1.fastq.gz	Fastqsanger.gz
	SRR26281962_2.fastq.gz	Fastqsanger.gz
	SRR26281963_1.fastq.gz	Fastqsanger.gz

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The global RNA-RNA interactome of Klebsiella pneumoniae unveils a small RNA regulator of cell division

Project description:The global RNA-RNA interactome of Klebsiella pneumoniae unveils a small RNA regulator of cell division

| PRJNA1023936 | ENA

The global RNA-RNA interactome of Klebsiella pneumoniae unveils a small RNA regulator of cell division (RIL-Seq)

Project description:The ubiquitous RNA chaperone Hfq is involved in the regulation of key biological processes in many species across the bacterial kingdom. In the opportunistic human pathogen Klebsiella pneumoniae, deletion of the hfq gene affects the global transcriptome, virulence, and stress-resistance, however, the ligands of the major RNA-binding protein in this species have remained elusive. In this study, we have combined transcriptomic, co-immunoprecipitation and global RNA interactome analyses to compile an inventory of conserved and species-specific RNAs bound by Hfq, and to monitor Hfq-mediated RNA-RNA interactions. In addition to dozens of previously unknown RNA-RNA pairs, our study revealed an Hfq-dependent sRNA, DinR, which is processed from the 3’ terminal portion of dinI mRNA. Transcription of dinI is controlled by the master regulator of the SOS response, LexA. As DinR accumulates in K. pneumoniae in response to DNA damage, the sRNA represses translation of the ftsZ transcript by occupation of the ribosome binding site. Ectopic overexpression of DinR causes depletion of ftsZ mRNA and inhibition of cell division, while deletion of dinR antagonizes cell elongation in the presence of DNA damage. Collectively, our work highlights the important role of RNA-based gene regulation in K. pneumoniae and uncovers the central role of DinR in LexA-controlled cell cycle inhibition during the SOS response.

2024-02-05 | GSE244638 | GEO

The global RNA-RNA interactome of Klebsiella pneumoniae unveils a small RNA regulator of cell division (RIP-Seq)

Project description:The global RNA-RNA interactome of Klebsiella pneumoniae unveils a small RNA regulator of cell division (RIP-Seq)

| PRJNA1023944 | ENA

The global RNA-RNA interactome of Klebsiella pneumoniae unveils a small RNA regulator of cell division (dRNA-Seq)

Project description:The global RNA-RNA interactome of Klebsiella pneumoniae unveils a small RNA regulator of cell division (dRNA-Seq)

| PRJNA1023941 | ENA

Hfq RIL-seq in Salmonella

Project description:We have used the RIL-seq technique to map the global RNA-RNA interactome on the sRNA chaperone Hfq in Salmonella enterica.

2021-12-07 | GSE163336 | GEO

The global RNA-RNA interactome of Klebsiella pneumoniae unveils a small RNA regulator of cell division (RIP-Seq)

2024-02-05 | GSE244639 | GEO

The global RNA-RNA interactome of Klebsiella pneumoniae unveils a small RNA regulator of cell division (dRNA-Seq)

2024-02-05 | GSE244635 | GEO

Hfq RIL-seq analysis

Project description:In this study we used RIL-seq (RNA interaction by ligation and sequencing) to identify Hfq-mediated RNA-RNA interactions in V. cholerae.

2022-11-15 | GSE198671 | GEO

The global RNA-RNA interactome of <i>Klebsiella pneumoniae</i> unveils a small RNA regulator of cell division.

Project description:The ubiquitous RNA chaperone Hfq is involved in the regulation of key biological processes in many species across the bacterial kingdom. In the opportunistic human pathogen Klebsiella pneumoniae, deletion of the hfq gene affects the global transcriptome, virulence, and stress resistance; however, the ligands of the major RNA-binding protein in this species have remained elusive. In this study, we have combined transcriptomic, co-immunoprecipitation, and global RNA interactome analyses to compile an inventory of conserved and species-specific RNAs bound by Hfq and to monitor Hfq-mediated RNA-RNA interactions. In addition to dozens of RNA-RNA pairs, our study revealed an Hfq-dependent small regulatory RNA (sRNA), DinR, which is processed from the 3' terminal portion of dinI mRNA. Transcription of dinI is controlled by the master regulator of the SOS response, LexA. As DinR accumulates in K. pneumoniae in response to DNA damage, the sRNA represses translation of the ftsZ transcript by occupation of the ribosome binding site. Ectopic overexpression of DinR causes depletion of ftsZ mRNA and inhibition of cell division, while deletion of dinR antagonizes cell elongation in the presence of DNA damage. Collectively, our work highlights the important role of RNA-based gene regulation in K. pneumoniae and uncovers the central role of DinR in LexA-controlled division inhibition during the SOS response.

| S-EPMC10907235 | biostudies-literature

Mapping RNA-RNA interactome and RNA structures in vivo with MARIO

Project description:Many biological processes are regulated by RNA-RNA interactions 1, nonetheless it remains formidable to analyze the entire RNA interactome. We developed a method, MARIO (MApping Rna-rna Interactions in vivO), to map protein-assisted RNA-RNA interactions in vivo. By circumventing the selection for a specific RNA-binding protein 2-5, our approach vastly expands the identifiable portion of the RNA interactome. Using this technology, we mapped the RNA interactome in mouse embryonic stem cells, which was composed of 46,780 RNA-RNA interactions. The RNA interactome was a scale-free network, with several lincRNAs and mRNAs emerging as hubs. We validated an interaction between two hubs, Malat1 and Slc2a3 using single molecule RNA fluorescence in situ hybridization. Base pairing was observed at the interaction sites of long RNAs, and was particularly strong in transposonRNA-mRNA and lincRNA-mRNA interactions. This reveals a new type of regulatory sequences acting in trans. Consistent with their hypothesized roles, the RNA interaction sites were more evolutionarily conserved than other regions of the transcripts. MARIO also provided new information on RNA structures, by simultaneously revealing the footprint of single stranded regions and the spatially proximal sites of each RNA. The unbiased mapping of the protein-assisted RNA interactome with minimum perturbation of cell physiology will greatly expand our capacity to investigate RNA functions. Three (3) ESC samples with different treatment (different digestion size and/or crosslinking method) and one (1) MEF sample were included to test our new approach for RNA-interactome mapping and the different samples were analyzed to show RNA interactome differences between them.

2016-06-23 | E-GEOD-61489 | biostudies-arrayexpress

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