A Robust Analytical Pipeline for Genome-Wide Identification of the Genes Regulated by a Transcription Factor: Combinatorial Analysis Performed Using gSELEX-Seq and RNA-Seq

• Published in: PloS one Vol. 11; no. 7; p. e0159011
• Main Authors: Kojima, Takaaki, Kunitake, Emi, Ihara, Kunio, Kobayashi, Tetsuo, Nakano, Hideo
• Format: Journal Article
• Language: English
• Published: United States Public Library of Science 13.07.2016; Public Library of Science (PLoS)
• Subjects: Aspergillus nidulans; Aspergillus nidulans - genetics; Aspergillus niger; Base Sequence; Binding; Binding sites; Bioengineering; Bioinformatics; Biological evolution; Biology and Life Sciences; Combinatorial analysis; Deoxyribonucleic acid; DNA; Gene expression; Gene Expression Profiling - methods; Gene mapping; Genes; Genome-wide association studies; Genomes; Genomics; Genomics - methods; High-Throughput Nucleotide Sequencing; Ligands (Biochemistry); Mathematical analysis; Next-generation sequencing; Reliability analysis; Research and Analysis Methods; Ribonucleic acid; RNA; RNA sequencing; SELEX Aptamer Technique - methods; Sequence Analysis, RNA - methods; Transcription factors; Transcription Factors - metabolism; Japan
• ISSN: 1932-6203; 1932-6203
• DOI: 10.1371/journal.pone.0159011

For identifying the genes that are regulated by a transcription factor (TF), we have established an analytical pipeline that combines genomic systematic evolution of ligands by exponential enrichment (gSELEX)-Seq and RNA-Seq. Here, SELEX was used to select DNA fragments from an Aspergillus nidulans genomic library that bound specifically to AmyR, a TF from A. nidulans. High-throughput sequencing data were obtained for the DNAs enriched through the selection, following which various in silico analyses were performed. Mapping reads to the genome revealed the binding motifs including the canonical AmyR-binding motif, CGGN8CGG, as well as the candidate promoters controlled by AmyR. In parallel, differentially expressed genes related to AmyR were identified by using RNA-Seq analysis with samples from A. nidulans WT and amyR deletant. By obtaining the intersecting set of genes detected using both gSELEX-Seq and RNA-Seq, the genes directly regulated by AmyR in A. nidulans can be identified with high reliability. This analytical pipeline is a robust platform for comprehensive genome-wide identification of the genes that are regulated by a target TF.