CRISPR/dCas9-mediated epigenetic modification reveals differential regulation of histone acetylation on Aspergillus niger secondary metabolite

Microbiol Res. 2021 Apr;245:126694. doi: 10.1016/j.micres.2020.126694. Epub 2021 Jan 6.


Epigenetic studies on secondary metabolites (SMs) mainly relied so far on non-selective epigenetic factors deletion or feeding epigenetic inhibitors in Aspergillus niger. Although technologies developed for epigenome editing at specific loci now enable the direct study of the functional relevance of precise gene regulation and epigenetic modification, relevant assays are limited in filamentous fungi. Herein, we show that CRISPR/dCas9-mediated histone epigenetic modification systems efficiently reprogramed the expression of target genes in A. niger. First, we constructed a p300-dCas9 system and demonstrated the activation of a EGFP fluorescent reporter. Second, by precisely locating histone acetylase p300 on ATG adjacent region of secondary metabolic gene breF, the transcription of breF was activated. Third, p300-dCas9 was guided to the native polyketide synthase (PKS) gene fuml, which increased production of the compound fumonisin B2 detected by HPLC and LC-MS. Then, endogenous histone acetylase GcnE-dCas9 and histone deacetylases HosA-dCas9 and RpdA-dCas9 repressed the transcription of breF. Finally, by targeting HosA-dCa9 fusion to pigment gene fwnA, we confirmed that histone deacetylase HosA activated the expression of fwnA, accelerated the synthesis of melanin. Targeted epigenome editing is a promising technology and this study is the first time to apply the epigenetic CRISPR/dCas9 system on regulating the expression of the secondary metabolic genes in A. niger.

Keywords: Aspergillus niger; CRISPR/dCas9; Epigenetic editing; HosA; Secondary metabolic gene cluster; p300.

MeSH terms

  • Acetylation
  • Aspergillus niger / genetics*
  • Clustered Regularly Interspaced Short Palindromic Repeats*
  • Epigenomics / methods*
  • Gene Editing
  • Gene Expression Regulation, Fungal*
  • Histones / genetics*
  • Histones / metabolism*
  • Protein Processing, Post-Translational
  • Secondary Metabolism*


  • Histones