Open Access Research

Global mRNA decay analysis at single nucleotide resolution reveals segmental and positional degradation patterns in a Gram-positive bacterium

Simen M Kristoffersen15, Chad Haase2, M Ryan Weil2, Karla D Passalacqua3, Faheem Niazi4, Stephen K Hutchison4, Brian Desany4, Anne-Brit Kolstø1, Nicolas J Tourasse1, Timothy D Read23* and Ole Andreas Økstad1*

Author Affiliations

1 Laboratory for Microbial Dynamics, Department of Pharmaceutical Biosciences, School of Pharmacy, University of Oslo, PB 1068 Blindern, 0316 Oslo, Norway

2 Department of Human Genetics, Division of Infectious Diseases, Emory University School of Medicine, 615 Michael Street, Atlanta, GA 30322-1013, USA

3 Department of Medicine, Division of Infectious Diseases, Emory University School of Medicine, 615 Michael Street, Atlanta, GA 30322-1013, USA

4 454 Life Sciences, A Roche Company, 1 Commercial Street, Branford, CT 06405, USA

5 PHARMAQ AS, PO Box 267 Skøyen, N-0213 Oslo, Norway

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Genome Biology 2012, 13:R30  doi:10.1186/gb-2012-13-4-r30

Published: 26 April 2012

Additional files

Additional file 1:

Supplementary Tables S1, S3, S4, and S5. Supplementary Table S1: overview of raw data and mapping of sequence reads to the respective genomes. Supplementary Table S3: comparison of half-life values estimated by RNA-Seq (GA-II, 454) and RT-qPCR. Supplementary Table S4: explanation of each of the different factors tested in the PCA analyses. Supplementary Table S5: PCA analysis of gene expression level.

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Additional file 2:

Supplementary Figures S1, S4, S5, S6, S7, S8, and S9. Supplementary Figure S1: distribution of the number of ORFs within operons. Supplementary Figure S4: statistical correlation (Pearson correlation) of calculated mRNA half-lives for the B. cereus ATCC 14579 B series and D series, respectively. Supplementary Figure S5: correlation between the RBS sequence and mRNA half-life. Supplementary Figure S6: correlation between mRNA expression level and selected factors. Supplementary Figure S7: expression of 16S rRNA at 2.5, 5, and 10 minutes after transcriptional arrest by rifampicin, relative to 16S rRNA expression at t(0) (time-point of rifampicin addition). Supplementary Figure S8: distribution of mapped read lengths from RNA sequencing using 454 technology. Supplementary Figure S9: explanation of the normalization procedure for RNA-Seq data using RT-qPCR.

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Additional file 3:

Gene half-lives and expression values. Listing of half-life and expression values for each gene in the genomes of B. cereus strains ATCC 10987 and ATCC 14579, and coordinates for all transcribed units.

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Additional file 4:

mRNA degradation patterns for the rbs (ribose utilization) operon in B. cereus ATCC 10987. Supplementary Figure S3 showing detailed mRNA decay patterns for the rbs operon.

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Additional file 5:

Global mRNA decay patterns at single nucleotide resolution. Detailed mRNA decay patterns of highly expressed operons.

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Additional file 6:

Scripts employed in analyses. Lists the scripts used for TSS, TES, and operon prediction.

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