Genome‐wide identification of target genes for transcription factor BR‐C in the silkworm, Bombyx mori

• Published in: Insect science 2021-12, Vol.28 (6), p.1530-1540
• Main Authors: Guo, Meng‐Pei, Qian, Wen‐Liang, He, Xue‐Chuan, Peng, Jian, Wang, Peng, Wang, Wei‐Na, Xia, Qing‐You, Cheng, Dao‐Jun
• Format: Article
• Language: English
• Subjects: Animals; Annotations; Bombyx - genetics; Bombyx - metabolism; Bombyx mori; BR‐C; ChIP‐seq; Chromatin; direct binding; Ecdysone; Genes; Genomes; Immunoprecipitation; Insect Proteins - genetics; Insect Proteins - metabolism; Insects; Polymerase chain reaction; Promoter Regions, Genetic; silkworm; Silkworms; target genes; Target recognition; Transcription factors; Transcription Factors - genetics; Transcription Factors - metabolism; transcriptional regulation; Transcriptomes
• ISSN: 1672-9609; 1744-7917
• DOI: 10.1111/1744-7917.12893

Transcription factor Broad Complex (BR‐C) is an ecdysone primary response gene in insects and participates in the regulation of insect growth and development. In this study, we performed a genome‐wide identification of BR‐C target genes in silkworm (Bombyx mori) using chromatin immunoprecipitation followed by high‐throughput sequencing (ChIP‐seq). As a result, a total of 1006 BR‐C ChIP peaks were identified, and 15% of peaks were located in the promoter regions of 133 protein‐coding genes. Functional annotation revealed that these ChIP peak‐associated genes, as potential BR‐C targets, were enriched in pathways related to biosynthetic process, metabolic process, and development. Transcriptome analysis and quantitative real‐time polymerase chain reaction (PCR) examination revealed that developmental changes in expression patterns of a portion of potential BR‐C targets, including HR96 and GC‐α1, were similar to those of BR‐C. ChIP‐PCR examination confirmed that BR‐C could directly bind to the promoters of potential targets. Further, dual luciferase assays demonstrated that HR96 promoter activity was significantly upregulated following BR‐C overexpression, and this upregulation was abolished when the binding motif in the promoter was truncated. This study will be helpful for deciphering the regulatory roles of BR‐C during insect growth and development. Transcription factor Broad Complex (BR‐C) is an ecdysone primary response gene in insects and participates in the regulation of insect growth and development. In this study, we performed a genome‐wide identification of BR‐C target genes in silkworm (Bombyx mori) using chromatin immunoprecipitation followed by high‐throughput sequencing (ChIP‐seq). As a result, a total of 1006 BR‐C ChIP peaks were identified, and 15% of peaks were located in the promoter regions of 133 protein‐coding genes. Functional annotation revealed that these ChIP peak‐associated genes, as potential BR‐C targets, were enriched in pathways related to biosynthetic process, metabolic process, and development. Transcriptome analysis and quantitative real‐time polymerase chain reaction (PCR) examination revealed that developmental changes in expression patterns of a portion of potential BR‐C targets, including HR96 and GC‐α1, were similar to those of BR‐C. ChIP‐PCR examination confirmed that BR‐C could directly bind to the promoters of potential targets.