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Survey of protein-DNA interactions in Aspergillus oryzae on a genomic scale.

Wang C, Lv Y, Wang B, Yin C, Lin Y, Pan L - Nucleic Acids Res. (2015)

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.

View Article: PubMed Central - PubMed

Affiliation: School of Bioscience and Bioengineering, South China University of Technology, Guangzhou, Guangdong, 510006, China.

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The DNase I cleavage patterns of five family types of TFs parallel the co-crystal structures of protein and DNA interaction. (A) Strand-specific DNase-seq signal for DNase I cleavage imbalance between the plus and minus motif sequences of five family types of the TFs independent of strand orientation. The upper panels show the heat maps of per-nucleotide DNase I cleavage derived from all instances of plus (red) and minus (blue) TFBS motifs within DHSs under DPY conditions ranked according to the probability of MILLIPEDE (FIMO P < 10−4, MILLIPEDE probability > 0.5). The lower panels show the average per-nucleotide DNase I cleavage patterns of plus (red line) and minus (blue line) motif sequences of the TFs and its flanking sequences. (B) The co-crystal structures of the known TFs or yeast homologues bound to the DNA recognition sites are aligned with DNase I cleavage patterns relative to the motif orientation. Upper panels: the shadows of DNA backbones and surfaces of amino acids (red) of TFs that contact with the DNA backbones, the marked depression in DNase I cleavage, are indicated in red on the crystal structure. The green color represents high-level DNase I accessibility in the crystal structure. The plus and minus motif sequences are indicated as red and blue characters, respectively. Bottom panels: the labeled amino acids in the bottom graph contact with the DNA backbones. The deoxyribose sugar rings are indicated as pentagons, and the phosphates are indicated as circles. The colors represent the same indication in upper lanes. L and R represent the binding motif sequences contacted by the left and right monomers of the TF dimer, respectively.
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Figure 3: The DNase I cleavage patterns of five family types of TFs parallel the co-crystal structures of protein and DNA interaction. (A) Strand-specific DNase-seq signal for DNase I cleavage imbalance between the plus and minus motif sequences of five family types of the TFs independent of strand orientation. The upper panels show the heat maps of per-nucleotide DNase I cleavage derived from all instances of plus (red) and minus (blue) TFBS motifs within DHSs under DPY conditions ranked according to the probability of MILLIPEDE (FIMO P < 10−4, MILLIPEDE probability > 0.5). The lower panels show the average per-nucleotide DNase I cleavage patterns of plus (red line) and minus (blue line) motif sequences of the TFs and its flanking sequences. (B) The co-crystal structures of the known TFs or yeast homologues bound to the DNA recognition sites are aligned with DNase I cleavage patterns relative to the motif orientation. Upper panels: the shadows of DNA backbones and surfaces of amino acids (red) of TFs that contact with the DNA backbones, the marked depression in DNase I cleavage, are indicated in red on the crystal structure. The green color represents high-level DNase I accessibility in the crystal structure. The plus and minus motif sequences are indicated as red and blue characters, respectively. Bottom panels: the labeled amino acids in the bottom graph contact with the DNA backbones. The deoxyribose sugar rings are indicated as pentagons, and the phosphates are indicated as circles. The colors represent the same indication in upper lanes. L and R represent the binding motif sequences contacted by the left and right monomers of the TF dimer, respectively.

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).


Survey of protein-DNA interactions in Aspergillus oryzae on a genomic scale.

Wang C, Lv Y, Wang B, Yin C, Lin Y, Pan L - Nucleic Acids Res. (2015)

The DNase I cleavage patterns of five family types of TFs parallel the co-crystal structures of protein and DNA interaction. (A) Strand-specific DNase-seq signal for DNase I cleavage imbalance between the plus and minus motif sequences of five family types of the TFs independent of strand orientation. The upper panels show the heat maps of per-nucleotide DNase I cleavage derived from all instances of plus (red) and minus (blue) TFBS motifs within DHSs under DPY conditions ranked according to the probability of MILLIPEDE (FIMO P < 10−4, MILLIPEDE probability > 0.5). The lower panels show the average per-nucleotide DNase I cleavage patterns of plus (red line) and minus (blue line) motif sequences of the TFs and its flanking sequences. (B) The co-crystal structures of the known TFs or yeast homologues bound to the DNA recognition sites are aligned with DNase I cleavage patterns relative to the motif orientation. Upper panels: the shadows of DNA backbones and surfaces of amino acids (red) of TFs that contact with the DNA backbones, the marked depression in DNase I cleavage, are indicated in red on the crystal structure. The green color represents high-level DNase I accessibility in the crystal structure. The plus and minus motif sequences are indicated as red and blue characters, respectively. Bottom panels: the labeled amino acids in the bottom graph contact with the DNA backbones. The deoxyribose sugar rings are indicated as pentagons, and the phosphates are indicated as circles. The colors represent the same indication in upper lanes. L and R represent the binding motif sequences contacted by the left and right monomers of the TF dimer, respectively.
© Copyright Policy - creative-commons
Related In: Results  -  Collection

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Figure 3: The DNase I cleavage patterns of five family types of TFs parallel the co-crystal structures of protein and DNA interaction. (A) Strand-specific DNase-seq signal for DNase I cleavage imbalance between the plus and minus motif sequences of five family types of the TFs independent of strand orientation. The upper panels show the heat maps of per-nucleotide DNase I cleavage derived from all instances of plus (red) and minus (blue) TFBS motifs within DHSs under DPY conditions ranked according to the probability of MILLIPEDE (FIMO P < 10−4, MILLIPEDE probability > 0.5). The lower panels show the average per-nucleotide DNase I cleavage patterns of plus (red line) and minus (blue line) motif sequences of the TFs and its flanking sequences. (B) The co-crystal structures of the known TFs or yeast homologues bound to the DNA recognition sites are aligned with DNase I cleavage patterns relative to the motif orientation. Upper panels: the shadows of DNA backbones and surfaces of amino acids (red) of TFs that contact with the DNA backbones, the marked depression in DNase I cleavage, are indicated in red on the crystal structure. The green color represents high-level DNase I accessibility in the crystal structure. The plus and minus motif sequences are indicated as red and blue characters, respectively. Bottom panels: the labeled amino acids in the bottom graph contact with the DNA backbones. The deoxyribose sugar rings are indicated as pentagons, and the phosphates are indicated as circles. The colors represent the same indication in upper lanes. L and R represent the binding motif sequences contacted by the left and right monomers of the TF dimer, respectively.
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).

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.

View Article: PubMed Central - PubMed

Affiliation: School of Bioscience and Bioengineering, South China University of Technology, Guangzhou, Guangdong, 510006, China.

Show MeSH
Related in: MedlinePlus