Profiling of chromatin accessibility across Aspergillus species and identification of transcription factor binding sites in the Aspergillus genome using filamentous fungi ATAC-seq

Abstract

1To identify cis-regulatory elements (CREs) and motifs of TF binding is an important step in understanding the 2 regulatory functions of TF binding and gene expression. The lack of experimentally determined and 3 computationally inferred data means that the genome-wide CREs and TF binding sites (TFBs) in filamentous 4 fungi remain unknown. ATAC-seq is a technique that provides a high-resolution measurement of chromatin 5 accessibility to Tn5 transposase integration. In filamentous fungi, the existence of cell walls and the difficulty 6 in purifying nuclei have prevented the routine application of this technique. Herein, we modified the 7 ATAC-seq protocol in filamentous fungi to identify and map open chromatin and TF-binding sites on a 8 genome-scale. We applied the assay for ATAC-seq among different Aspergillus species, during different 9 culture conditions, and among TF-deficient strains to delineate open chromatin regions and TFBs across each 10 genome. The syntenic orthologues regions and differential changes regions of chromatin accessibility were 11 responsible for functional conservative regulatory elements and differential gene expression in the Aspergillus 12 genome respectively. Importantly, 17 and 15 novel transcription factor binding motifs that were enriched in 13 the genomic footprints identified from ATAC-seq data of A. niger, were verified in vivo by our artificial 14 synthetic minimal promoter system, respectively. Furthermore, we first confirmed the strand-specific patterns 15 of Tn5 transposase around the binding sites of known TFs by comparing ATAC-seq data of TF-deficient 16 strains with the data from a wild-type strain.