Unknown,Transcriptomics,Genomics,Proteomics

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RNAseq of Bacillus subtilis wildtype and cspB-cspD deletion mutant reveals that the lack of the cold shock proteins CspB and CspD affects the expression of about 20% of all genes

ABSTRACT: RNAseq of coding RNA in Bacillus subtilis wildtype and deletion strain GP1971 genotype trpC2 ΔcspB::cat ΔcspD::aphA3 using rRNA depleted mRNA and Illumina TruSeq stranded mRNA libraries, sequenced on Illumina MiSeq system with 2 x 75nt in paired end mode shows that the lack of the cold shock proteins CspB and CspD affects the expression of about 20% of all genes and an increased read-through at transcription terminators suggesting that CspB and CspD might be involved in the control of transcription termination.

INSTRUMENT(S): Illumina MiSeq

ORGANISM(S): Bacillus subtilis subsp. subtilis str. 168

SUBMITTER: Patrick Faßhauer

PROVIDER: E-MTAB-10658 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Project description:The majority of all genes have so far been identified and annotated systematically through in silico gene finding. Here we report the finding of 3,217 strand-specific Transcriptionally Active Regions (TARs) in the genome of Bacillus subtilis by the use of tiling arrays. We have measured the genome-wide expression during mid-exponential growth on rich (LB) and minimal (M9) medium. The identified TARs account for 81.5% of the genes as they are currently annotated and additionally we find 44 novel protein-coding genes, 85 putative non-coding RNAs (ncRNAs) and 184 antisense transcripts. Hybridization of labeled genomic DNA (gDNA) has revealed a few thousand regions giving rise to very low signals. These are mostly caused by sequence errors, as is observed in the highly degenerate trp operon and the folding of stable structures such as the regions containing Rho-independent terminators. Through this work we have discovered a group of membrane-associated genes, among these having a long conserved 3â UnTranslated Region (UTR) predicted to fold into a large and highly stable structure. Among these are YwbN, a target of the twin-arginine translocase (Tat) protein translocation system. The transcriptionally active regions were determined at two different conditions, rich medium (Luria Broth) and minimal medium (M9). Cells were harvested at mid-exponential phase (OD600 = 0.5) and each condition were replicated three times. From each replicate RNA was extracted using FastRNA pro blue kit (Qbiogene) and labelled with Cy3 using a strand-specific protocol. The cDNA was hybridized to 385K NimbleGen tiling arrays 'BaSysBio Bsub T1' covering the entire genome with 45-65 nt isothermal probes, spaced by 22 nt on each strand. Additionally genomic DNA was extracted from 4 replicates at OD600 = 0.5, labelled and hybridized to the tiling arrays. These serve as a reference for the mRNA hybridizations. The normalized RNA hybridization signals were used to create segments using a structural change model (Huber et al, 2006) and transcriptionally active regions were identified by a segment joining-scheme.

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RNAseq of Bacillus subtilis wildtype and cspB-cspD deletion mutant reveals that the lack of the cold shock proteins CspB and CspD affects the expression of about 20% of all genes

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