Fig. 2
FadRSa interacts with four genomic loci in the Saci_1103-Saci_1126 gene cluster. a Overview of the genomic binding profile of FadRSa as monitored by ChIP-seq (IP = immunoprecipitated sample). A zoomed image of this profile is shown for the genomic region encompassing the Saci_1103-Saci_1126 gene cluster (corresponding to genomic coordinates 903,000–932,000), with indication of the four clearly visible peaks (numbered 1–4). Below the profile, a schematic representation of the genomic organization of the Saci_1103-Saci_1126 gene cluster is shown with indication of the ChIP-seq peak summit locations and of the transcription start sites as detected in the transcriptomic analysis in ref. 37. b ChIP-qPCR experiment with targeted quantification of enrichment for peaks 1 and 2 (given their close proximity to each other, these are assayed within a single fragment representing the Saci_1106/Saci_1107 intergenic region), peak 3 and peak 4. Fold enrichment is expressed relative to a genomic region within the ORF of Saci_1336 that was shown not be bound by FadRSa in the ChIP-seq profile. Error bars represent standard deviations of biological duplicates. c Sequence logo of the FadRSa binding motif representing MEME predictions of ChIP-seq enriched sequences. d Electrophoretic mobility shift assays of FadRSa binding to radiolabeled DNA probes of about 500 bp representing the ChIP-seq peaks identified in the Saci_1103-Saci_1126 gene cluster (see panel (a)). Molar protein concentrations are shown above each autoradiograph, whereas populations of free DNA (F) and FadRSa-bound DNA (B1 and B2) are indicated with an arrowhead. Apparent KD and Hill coefficient (n) calculations are based on densitometric analysis of free DNA bands followed by binding curve analysis (Supplementary Figure 4)
