Figure 1

Molecular basis of transcription and a reconstruction of σ-factor-transcription unit gene ( σ-TUG) network from multi-omic experimental datasets. (a) Diagram shows bacterial transcription process by an RNA polymerase (RNAP) core enzyme and an associated σ-factor. (b) Four-step process of multi-omic data integration to reconstruct the σ-TUG network. First, we identified RNAP-binding regions (RNAP map) and σ-factor binding regions (σ map) from RpoB and σ-factor chromatin immunoprecipitation and microarray (ChIP-chip) data (the missing σ²⁴ binding information was taken from a public database [6]), resulting in the genome-wide holoenzyme binding map (Eσ map). The Eσ map was then combined with experimental transcription start site (TSS) information (TSS map), resulting in he strand-specific promoter map (P-map), which was integrated with previously reported TU information [7], resulting in the σ-network. With this σ-network, we then performed further analysis, such as network reprogramming, motif analysis, promoter overlapping, and alternative TSS usage. Subfigure I: IOPR, intensively overlapped promoter region; OPR, overlapped promoter region; SPR, single promoter region; Orphan, orphan promoter region. Subfigure III and IV: green and brown circles represent σ⁷⁰ and σ³⁸, yellow circles represent TUs, and red dots represent genes. Edges show regulatory interactions between elements. (c) Datasets used for σ-TUG network reconstruction: ChIP-chip dataset with RNAP and six σ-factors, and the TSS dataset. The TSS dataset for exponential phase was taken from a previous study [9].TSS subpanel: exp, exponential phase; stat, stationary phase; heat, heat shock; gln, alternative nitrogen source with glutamine. (d) Magnified examples of rpoD (left panel, genomic region ranging from 3,196 to 3,214 kbp), fecI and fecRAB (right panel, genomic region ranging from 4,494 to 4,517 kbp).