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Investigation of transcript 3' ends in Campylobacter jejuni wildtype and ribonuclease mutants

ABSTRACT: Investigation of transcript 3' ends in Campylobacter jejuni wildtype and ribonuclease mutants

PROVIDER: PRJNA962813 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR24332107.fastq.gz	Fastqsanger.gz
	SRR24332108.fastq.gz	Fastqsanger.gz
	SRR24332109.fastq.gz	Fastqsanger.gz
	SRR24332110.fastq.gz	Fastqsanger.gz
	SRR24332111.fastq.gz	Fastqsanger.gz

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Investigation of transcript 3' ends in Campylobacter jejuni wildtype and ribonuclease mutants

Project description:Termination site sequencing (term-seq) (Dar et al., 2016) was used to map transcript 3' ends and potential processing sites in Campylobacter jejuni NCTC11168 wildtype and ribonuclease deletion strains.

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Investigation of RNA 5' ends in Campylobacter jejuni wildtype and an RNase III mutant strain

Project description:differential RNA sequencing (dRNA-seq) (Sharma et al., 2010; Dugar et al., 2013) was used to differentially map 5' ends in Campylobacter jejuni NCTC11168 wildtype and RNase III (rnc, Cj1635c) deletion.

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Mapping of internal monophosphate 5’ ends of Bacillus subtilis messenger RNAs and ribosomal RNAs in wild-type and ribonuclease-mutant strains

Project description:The narrow-specificity endoribonuclease RNase III and the 5’ exonuclease RNase J1 have been recently found to be not essential in the Gram-positive model organism, Bacillus subtilis. In this study, we performed a global analysis of internal 5’ ends that are generated or acted upon by these enzymes. An RNA-Seq protocol known as PARE (Parallel Analysis of RNA Ends) was used to capture 5’ monophosphorylated RNA ends in ribonuclease wild-type and mutant strains. Comparison of PARE peaks in strains with RNase III present or absent showed that, in addition to its well-known role in ribosomal (rRNA) processing, many coding sequences and intergenic regions were direct targets of RNase III. A set of regular RNA-seq experiments were performed to investigate RNA profiles in these strains and used to account for the changes in RNA abundance indirectly caused by the loss of RNase III in PARE. The PARE analysis also revealed an accumulation of 3’-proximal peaks that correlated with the absence of RNase J1, confirming the importance of RNase J1 in degrading RNA fragments that contain the transcription terminator structure. In addition, an endonuclease cleavage just two nucleotides downstream of the 16S rRNA 3’ end was discovered with PARE analysis. This latter observation begins to answer, at least for B. subtilis, a long-standing question on the exonucleolytic vs. endonucleolytic nature of 16S rRNA maturation

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Investigation of the regulon and RNA targets of RNase Y in Campylobacter jejuni

Project description:RNA-seq was used to study gene expression profiles and potential processing sites in Campylobacter jejuni NCTC11168 wildtype and RNase Y (rny, Cj1209) deletion.

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Campylobacter jejuni comparative genome: control strain C. jejuni subsp. jejuni ATCC 700819 (NCTC 11168) vs. 12 other strains

Project description:Gene content comparison of control C. jejuni subsp. jejuni strain 11168 which colonizes and causes disease in C57BL/6 IL-10-/- mice versus C. jejuni strains D6844, D6845, D6846, D6847, D6848, D6849, D0121, D0835, D2586, D2600,33560 and NW in the C57BL/6 IL-10-/- mice. Keywords: DNA/DNA comparison

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Ribonuclease Selection for Ribosome Profiling

Project description:Ribonuclease Selection for Ribosome Profiling

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Campylobacter jejuni Utilization of Fucose

Project description:Transcriptional profile of C. jejuni NCTC11168 while growing in MEM medium containing L-fucose. We hypothesize that certain C. jejuni strains, containing A certain genomic island, have acquired the ability to metabolize fucose. This study demonstrates the transcriptional profile C. jejuni growth while utilizing fucose.

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