Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

Strand-specific transcriptome profiles of the oral pathogen Porphyromonas gingivalis using genomic tiling microarray and RNA sequencing

ABSTRACT: High-density tiling microarray and RNA sequencing technologies were used to analyze the transcriptome of Porphyromonas gingivalis. The compiled P. gingivalis transcriptome were based on total RNA samples isolated from three different laboratory culturing conditions and the strand-specific transcription profiles generated covered the entire genome including both protein coding and non-coding regions. The transcription profiles revealed various operon structures, 5' and 3' end untranslated regions (UTRs), differential expression patterns, and several not-yet annotated transcripts within intergenic and antisense regions. Further transcriptome analysis identified the majority of the genes to be expressed within operons and most 5' and 3' ends to be protruding UTRs of which several 3M-CM-"M-BM-^@M-BM-^Y UTRs were extended to overlap genes encoded on the opposite/antisense strand. Extensive antisense RNAs were identified opposite to most of insertion sequence (IS) elements. With the growing realization that non-coding RNAs play important biological functions, the comprehensive transcriptome profiles compiled in this study are of great value for the further understanding of gene regulation and virulence mechanism in this periodontal pathogen. The transcriptome profiles can be viewed at and downloaded from the 'Microbial Transcriptome Database' web site http://bioinformatics.forsyth.org/mtd. 3 total RNA samples from growing P. gingivalis strain W83 under different media conditions subjected to RNA-Seq.

ORGANISM(S): Porphyromonas gingivalis W83

SUBMITTER: Tsute Chen

PROVIDER: E-GEOD-30452 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Publications

Comprehensive transcriptome analysis of the periodontopathogenic bacterium Porphyromonas gingivalis W83.

Høvik Hedda H Yu Wen-Han WH Olsen Ingar I Chen Tsute T

Journal of bacteriology 20111028 1

High-density tiling microarray and RNA sequencing technologies were used to analyze the transcriptome of the periodontopathogenic bacterium Porphyromonas gingivalis. The compiled P. gingivalis transcriptome profiles were based on total RNA samples isolated from three different laboratory culturing conditions, and the strand-specific transcription profiles generated covered the entire genome, including both protein coding and noncoding regions. The transcription profiles revealed various operon s ...[more]

PMID: 22037400

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Project description:Background: With lower manufacturing cost, high spot density, and flexible probe design, genomic tiling microarrays are ideal for comprehensive transcriptome studies. Typically, transcriptome profiling using microarrays involves reverse transcription, which converts RNA to cDNA. The cDNA is then labeled and hybridized to the probes on the arrays, thus the RNA signals are detected indirectly. Reverse transcription is known to generate artifactual cDNA, in particular the synthesis of second-strand cDNA, leading to false discovery of antisense RNA. To address this issue, we have developed an effective method using RNA that is directly labeled, thus by-passing the cDNA generation. This paper describes the development of this method and its application to mapping transcriptome profiles. Results: RNA extracted from laboratory cultures of Porphyromonas gingivalis was fluorescently labeled with an alkylation reagent and hybridized directly to probes on genomic tiling microarrays specifically designed for this periodontal pathogen. The generated transcriptome profile was strand-specific and produced signals close to background level in most antisense regions of the genome. In contrast, high levels of signal were detected in the antisense regions when the hybridization was done with cDNA. In addition, five antisense areas were tested with independent strand-specific RT-PCR and none to negligible amplification was detected, indicating that the strong antisense cDNA signals were artifacts. Conclusions: An efficient method was developed for mapping transcriptome profiles specific to both coding strands of a bacterial genome. This method chemically labels and uses extracted RNA directly in microarray hybridization. The generated transcriptome profile was free of cDNA artifactual signals. In addition, this method requires fewer processing steps and is more sensitive in detecting small amount of RNA compared to end-labeling methods due to the incorporation of more fluorescent molecules per RNA fragment. This serial of experiments were performed to compare the transcriptome profiles revealed between the use of cDNA (converted from RNA) and RNA. Three samples of cDNA-based method were provided and two samples of RNA-based method were included. The signal intensities of these arrays were normalized based on both the in-between array method and the genomic DNA reference arrays (included) using the R 'tilingarray' package and these experiments were referred in the paper.

Dataset Information

Strand-specific transcriptome profiles of the oral pathogen Porphyromonas gingivalis using genomic tiling microarray and RNA sequencing

Publications

Comprehensive transcriptome analysis of the periodontopathogenic bacterium Porphyromonas gingivalis W83.

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