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Fungal Biol Biotechnol. 2018 Feb 8;5:2. doi: 10.1186/s40694-018-0047-4. eCollection 2018.

Heterologous and endogenous U6 snRNA promoters enable CRISPR/Cas9 mediated genome editing in Aspergillus niger.

Zheng X1,2, Zheng P1,2, Sun J1,2, Kun Z1,2,3, Ma Y1.

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1Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Xiqidao 32, Tianjin Airport Economic Area, Tianjin, 300308 China.
2Key Laboratory of Systems Microbial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308 China.
3University of Chinese Academy of Sciences, Beijing, 100049 China.



U6 promoters have been used for single guide RNA (sgRNA) transcription in the clustered regularly interspaced short palindromic repeats/CRISPR-associated protein (CRISPR/Cas9) genome editing system. However, no available U6 promoters have been identified in Aspergillus niger, which is an important industrial platform for organic acid and protein production. Two CRISPR/Cas9 systems established in A. niger have recourse to the RNA polymerase II promoter or in vitro transcription for sgRNA synthesis, but these approaches generally increase cloning efforts and genetic manipulation. The validation of functional RNA polymerase II promoters is therefore an urgent need for A. niger.


Here, we developed a novel CRISPR/Cas9 system in A. niger for sgRNA expression, based on one endogenous U6 promoter and two heterologous U6 promoters. The three tested U6 promoters enabled sgRNA transcription and the disruption of the polyketide synthase albA gene in A. niger. Furthermore, this system enabled highly efficient gene insertion at the targeted genome loci in A. niger using donor DNAs with homologous arms as short as 40-bp.


This study demonstrated that both heterologous and endogenous U6 promoters were functional for sgRNA expression in A. niger. Based on this result, a novel and simple CRISPR/Cas9 toolbox was established in A. niger, that will benefit future gene functional analysis and genome editing.


Aspergillus niger; CRISPR/Cas9 system; Genome editing; U6 snRNA promoters

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