Survey of protein-DNA interactions in Aspergillus oryzae on a genomic scale.
Bottom Line: The resulting map identified overrepresented de novo TF-binding motifs from genomic footprints, and provided the detailed chromatin remodeling patterns and the distribution of digital footprints near transcription start sites.The TFBSs of 19 known Aspergillus TFs were also identified based on DNase I digestion data surrounding potential binding sites in conjunction with TF binding specificity information.We observed that the cleavage patterns of TFBSs were dependent on the orientation of TF motifs and independent of strand orientation, consistent with the DNA shape features of binding motifs with flanking sequences.
Affiliation: School of Bioscience and Bioengineering, South China University of Technology, Guangzhou, Guangdong, 510006, China.Show MeSH
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Mentions: We gathered the available binding motif sequences of 19 known Aspergillus TFs, for which the DNase I cleavage patterns of the orientation-specific motifs were derived from mapping tags to the plus and minus strands based on DNase-seq data (Figure 3A and Supplementary Figure S10). We also plotted heat maps of the typical TFs of five families across all predicted instances of each motif (Figure 3A). The DNase I cleavage patterns of the 19 known TFs showed an imbalance between sense and antisense strands within and outside of the binding-motif sequences derived from the DNA strand-specific alignment information of DNase-seq data (Figure 3A and Supplementary Figure S10). The DNase-seq profiles outside of the binding-motif sequences did not always exhibit a peak/trough/peak footprint shape in the aggregate plots. The cleavage patterns in the 19 known TFs’ binding motifs depended on TF motif orientation-specific information and were independent of the specificity of strand orientation (Figure 3A and Supplementary Figure S10). Each TF contained a distinct DNase cleavage profile visible in aggregate plots derived from different culture conditions. The binding sites of the dimerization of two TF monomers, such as bZIP CpcA and bHLH E-box, had reversely symmetrical patterns between the plus and minus motif sequences (Figure 3A). A marked depression of DNase I cleavage was observed in the opposite 5′-phosphate groups of DNA backbones located in two monomer-overlapping sites of TFs, and high-level DNase I accessible regions occurred in the plus and minus motif sequences near two monomer-overlapping sites (Figure 3A). Similarly, other DNase I cleavage patterns of the dimerization of Zn(II)2Cys6 amyR also showed approximate motif-orientation-specific symmetry, with DNase I inaccessibility between the CGG region and the central zone (Figure 3A). However, the binding sites of monomer GATA TFs and CBCs were obviously asymmetric and imbalanced in plus and minus motif sequences (Figure 3A).
Affiliation: School of Bioscience and Bioengineering, South China University of Technology, Guangzhou, Guangdong, 510006, China.