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ABSTRACT:
PROVIDER: PRJNA928391 | ENA |
REPOSITORIES: ENA
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Project description:BACKGROUND: We identified that a putative CzcRS-like two-component system (TCS) in Burkholderia cenocepacia K56-2 is required for heavy metal resistance and virulence. In an attempt to identify genes directly regulated by the CzcR response regulator, we performed ChIP-seq analysis to identify genomic regions bound by CzcR. METHODS. Sequence encoding a FLAG octapeptide (Sigma-Aldrich) was introduced to the 3’ end of the czcR gene at its native chromosomal position in wild-type B. cenocepacia K56-2. Wildtype K56-2 and the CzcR-FLAG strain were grown in 50 ml tryptone soya broth (TSB) in the presence or absence of 1.5 mM zinc chloride. After overnight incubation, anti-FLAG immunoprecipitation of CzcR-bound genomic DNA was performed. Wildtype K56-2 was processed in parallel, to serve as a control against which to assess for enrichment of genomic regions. Illumina sequencing libraries were prepared from the resulting DNA using the Nextflex ChIPseq protocol (Bioo Scientific) with indexed adapters. Libraries were amplified by 18 cycles PCR, purified using 0.8 volumes Ampure XP beads (Beckman Coulter) and quantified with a Bioanalyzer 7500 assay (Agilent). Libraries ranged in size from 150 bp to 800 bp with a average insert size of 310 bp. Libraries were pooled in equimolar concentrations, denatured and diluted to 6.5 pM, clustered on a flowcell using a cBOT (Illumina) and sequenced on a HiSeq2000 (Illumina). Paired-end reads were filtered using the fastq-mcf package from the ea-utils suite to remove reads with less than 90% Q20 scores or above and to trim off adaptor sequence. The reads were then aligned against the B. cenocepacia J2315 genome (NC_011001-NC_011003) using BWA (0.5.9) and converted to BAM format using Samtools. Potential PCR duplicates were removed using the samtools rmdup command. The MACS package (v1.4) was used to compare and contrast the control and sample data using the –call-subpeaks and –w options. RESULTS: Relative to wildtype B. cenocepacia K56-2, the only genomic region that was found to be enriched by the ChIP-seq analysis of the CzcR-FLAG strain mapped to nucleotide coordinates 787809-798988 on chromosome 2. This region includes the czcRS genes and those encoding the associated efflux pump (CzcCBA).
2017-01-01 | GSE61334 | GEO
Project description:Comparative transcriptional profiling of B. cenocepacia K56-2 (wildtype) and K56-2cepR2b (cepR2 mutant of K56-2).
2009-02-10 | E-MEXP-1935 | biostudies-arrayexpress
Project description:Purpose - To establish the response of B. cenocepacia K56-2 to growth in copper, and to characterise the BCAM0442/3 copper-sensing TCS. Methods - RNA-seq of the response WT and Δbcam0442/3 B. cenocepacia K56-2 to mid-log phase growth in LB with or without 1 mM CuCl2 was performed. Results - Characterisation of the overall response of B. cenocepacia K56-2 to copper, as well as establishing that BCAM0442/3 regulates the CopABCDE system in B. cenocepacia
2021-02-18 | GSE166960 | GEO
Project description:FACT is a histone chaperone that can destabilize or assemble nucleosomes. Acetylation of histone H3-K56 weakens a histone:DNA contact that is central to FACT activity, suggesting that this modification could affect FACT functions. We tested this by asking how mutations of H3-K56 and FACT affect nucleosome structure, chromatin integrity, and transcription output. Mimics of unacetylated or permanently acetylated H3-K56 had different effects on FACT in vitro and in vivo as expected, but H3-K56 and FACT mutations caused surprisingly similar changes in transcription of individual genes. Notably, neither the changes in transcript levels nor the effects on nucleosome occupancy resulting from mutations conformed to the model that FACT is needed to overcome nucleosomal barriers during transcription initiation or elongation. Instead, the results suggest that both FACT and H3-K56ac are involved in establishing chromatin architecture prior to transcription and restoring it afterwards. They contribute to a process that optimizes transcription frequency, especially at conditionally expressed genes, and restores chromatin integrity after transcription, especially at the +1 nucleosome to block antisense transcription, but FACT appears to be less involved than expected in directly promoting transcription.
2019-03-06 | GSE118330 | GEO
Project description:Yili Mares Fecal Microbiota Raw sequence reads
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Project description:ChIP-chip assays to determine the occupancy of acetylated histone H3 K56 in wildtype, isw1, chd1, isw1 chd1 and ISW1[K227R] yeast.
2012-07-25 | GSE36405 | GEO
Project description:ChIP-on chip assays to measure the change in histone H3 K56 acetylation over the yeast genome in wild-type YBL574 yeast strains compared to H3K36A mutant strains.
2012-07-25 | GSE37039 | GEO