title: Survey of protein-DNA interactions in Aspergillus oryzae on a genomic scale.
abstract: The genome-scale delineation of in vivo protein-DNA interactions is key to understanding genome function. Only ∼5% of transcription factors (TFs) in the Aspergillus genus have been identified using traditional methods. Although the Aspergillus oryzae genome contains >600 TFs, knowledge of the in vivo genome-wide TF-binding sites (TFBSs) in aspergilli remains limited because of the lack of high-quality antibodies. We investigated the landscape of in vivo protein-DNA interactions across the A. oryzae genome through coupling the DNase I digestion of intact nuclei with massively parallel sequencing and the analysis of cleavage patterns in protein-DNA interactions at single-nucleotide resolution. 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.
authors.affiliation: School of Bioscience and Bioengineering, South China University of Technology, Guangzhou, Guangdong, 510006, China.
authors.forename: Chao
authors.initials: C
authors.lastname: Wang
authors.affiliation: School of Bioscience and Bioengineering, South China University of Technology, Guangzhou, Guangdong, 510006, China.
authors.forename: Yangyong
authors.initials: Y
authors.lastname: Lv
authors.affiliation: School of Bioscience and Bioengineering, South China University of Technology, Guangzhou, Guangdong, 510006, China.
authors.forename: Bin
authors.initials: B
authors.lastname: Wang
authors.affiliation: School of Bioscience and Bioengineering, South China University of Technology, Guangzhou, Guangdong, 510006, China.
authors.forename: Chao
authors.initials: C
authors.lastname: Yin
authors.affiliation: School of Bioscience and Bioengineering, South China University of Technology, Guangzhou, Guangdong, 510006, China.
authors.forename: Ying
authors.initials: Y
authors.lastname: Lin
authors.affiliation: School of Bioscience and Bioengineering, South China University of Technology, Guangzhou, Guangdong, 510006, China btlipan@scut.edu.cn.
authors.forename: Li
authors.initials: L
authors.lastname: Pan
mesh_terms: D001236:Aspergillus oryzae / Q000235:genetics* / Q000378:metabolism; D001665:Binding Sites; D018983:DNA Footprinting; D004271:DNA, Fungal / Q000737:chemistry* / Q000378:metabolism; D004268:DNA-Binding Proteins / Q000737:chemistry / Q000378:metabolism; D003850:Deoxyribonuclease I; D005656:Fungal Proteins / Q000737:chemistry / Q000378:metabolism*; D016681:Genome, Fungal; D059014:High-Throughput Nucleotide Sequencing; D009690:Nucleic Acid Conformation; D059372:Nucleotide Motifs; D050436:Regulatory Elements, Transcriptional; D017422:Sequence Analysis, DNA; D014157:Transcription Factors / Q000737:chemistry / Q000378:metabolism*; D024363:Transcription Initiation Site
chemical_list: D004271:DNA, Fungal; D004268:DNA-Binding Proteins; D005656:Fungal Proteins; D014157:Transcription Factors; D003850:Deoxyribonuclease I