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In vivo probing of promoter overlapping between σ-factors in Escherichia coli (ChIP-Seq)

ABSTRACT: An alternative sigma factor (σ32) recognizes the unique set of promoters upon heat shock. Here, we determined 54 σ32 promoters at nucleotide resolution using ChIP-exo, enabling us to compare those with housekeeping σ70 promoters. The results elucidated the overarching principles of promoter overlapping between the two σ-factors, which are sequence-specific non-, half-, and full-shared modes with a perfect sequence conservativeness of −35 element as a key determinant of full-shared mode.

ORGANISM(S): Escherichia coli str. K-12 substr. MG1655

PROVIDER: GSE60668 | GEO | 2020/08/12

REPOSITORIES: GEO

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Project description:Background: In prokaryotes, sigma factors are essential for the targeting of the transcription machinery to promoters. Various sigma factors have been described that recognize and bind to specific DNA sequence motifs in promoter sequences. The canonical sigma factor σ70 is commonly involved in transcription of the cell's general housekeeping genes, which is mediated by the conserved σ70 promoter sequence motifs. This study detects and predicts the general σ70-promoter sequences in Lactobacillus plantarum WCFS1 using genome-wide analysis. The accuracy of the transcriptionally-active part of this promoter prediction was subsequently evaluated by correlating locations of predicted promoters with experimentally detected transcription starts sites (TSSs) using high-resolution tiling array transcriptome datasets. Results: To identify σ70-related promoter sequences, we performed a genome-wide sequence motif scan of the L. plantarum WCFS1 genome focusing on the regions upstream of protein-encoding genes. We obtained several highly conserved motifs including those resembling the conserved σ70-promoter consensus. Position weight matrices-based models of the recovered σ70-promoter sequence motif were employed to identify 4746 motifs with significant similarity (p-value < 10-4) to the model-motif in the L. plantarum genome. Genome-wide transcription start site information deduced from whole genome tiling-array transcriptome datasets revealed 936 TSSs that were employed to validate the transcriptionally active fraction of these predicted promoters. In total, 578 predicted promoters were found in proximity (≤ 100 nucleotides) of the identified TSSs, showing a highly significant co-occurrence of predicted promoter and measured TSS (p-value < 10-23). An additional 224 predicted promoters was validated when the significant similarity to the model-motif was applied less strictly (10-4 ≤ p-value < 10-3). Conclusions: High-resolution tiling arrays provide a suitable source for TSS detection at a genome-wide level, and allow experimental verification of in silico-predicted promoter sequence motifs.

Dataset Information

In vivo probing of promoter overlapping between σ-factors in Escherichia coli (ChIP-Seq)

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