Fig. 8: CcpA regulates gene expression at both the transcriptional and post-transcriptional level. | Nature Communications

Fig. 8: CcpA regulates gene expression at both the transcriptional and post-transcriptional level.

From: The RNA-bound proteome of MRSA reveals post-transcriptional roles for helix-turn-helix DNA-binding and Rossmann-fold proteins

Fig. 8

a Deletion of ccpA causes global changes in gene expression. DESeq2 analyses were performed on RNA-seq data from three independent biological replicates (Supplementary Data 5). The left volcano plot shows the comparison between the USA300 WT strain and the USA300 ΔccpA strain. The right volcano plot shows the comparison between the USA300 WT and the complemented strain. Red dots indicate genes that are significantly enriched in the WT (left side) or the mutant strains (right side). Transcripts with a log-fold change >2 and a −log10 P value of 1.3 or higher were considered enriched in cross-linked data. Benjamini and Hochberg adjusted P-values were calculated using DESeq228 on data from three independent biological replicate RNA-seq samples. b Northern blot validation of selected transcripts highlighted in a. RNA from three independent replicate experiments was used. c Expression of selected transcripts highlighted in a. Shown are the mean and standard deviations of three independent experiments. Statistical significance was measured through two-sided Student’s unpaired t test (uncorrected P values marked above each comparison). Source data from b, c are provided in the Source data file. d Overlap between the genes differentially expressed (DE) in ΔccpA with transcripts enriched in the CcpA CRAC data (top 200 CcpA-bound transcripts) and genes with a CRE-motif in promoter regions (genes with CRE motif). e Violin plot showing the distribution of fold-changes in mRNA target expression (y axis) in the ΔccpA strain for all the differentially expressed genes (all DE genes), transcripts that are strongly bound by CcpA in the CRAC data (Top 200 CcpA-bound) and for all the genes with a CRE motif. The horizontal line in each violin plot indicates the median value. Statistical significance between the groups was calculated using a two-sided Mann–Whitney U test (no P value adjustment). ****P value = 9.96e−05, ******P value = 7.134e−12.

Back to article page