Identification of AflR binding sites in the genome of Aspergillus flavus by ChIP-Seq

Authors: KONG, QING - Ocean University Of China; Chang, Perng Kuang; LI, CHUNJUAM - Shandong Peanut Research Institute; HU, ZHAORONG - China Agricultural University; ZHENG, MEI - China Agricultural University; SUN, QUANXI - Shandong Peanut Research Institute; SHAN, SHIHUA - Shandong Peanut Research Institute

Submitted to: The Journal of Fungi
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 4/20/2020
Publication Date: 4/21/2020
Citation: Kong, Q., Chang, P.-K., Li, C., Hu, Z., Zheng, M., Sun, Q., Shan, S. 2020. Identification of AflR binding sites in the genome of Aspergillus flavus by ChIP-Seq. The Journal of Fungi. 6:52. https://doi.org/10.3390/jof6020052.
DOI: https://doi.org/10.3390/jof6020052

Interpretive Summary: The fungus Aspergillus flavus infects crops and produces aflatoxins that are carcinogenic. Aflatoxin contamination of food and feed crops is of great importance to the economy and human health. A regulator named AflR is required for aflatoxin production. This research was conducted to better understand functions of AflR in regulating genome-wide gene expression of A. flavus. Via the use of an antibody against AflR that bound to fragmented DNA sequences coupled with massively parallel DNA sequencing, we were able to identify the specific sequence motif to which AflR bound. Further analysis of those targeted genes suggests that AflR is a regulator potentially functioning on genes outside the aflatoxin biosynthetic gene cluster. The current work provides opportunities to examine AflR-related regulatory network on growth and development of A. flavus.

Technical Abstract: The AflR binding motif of Aspergillus flavus was firstly reported by the aid of ChIP-seq analysis. Of the 540 peak sequences associated with AflR binding events 66.8% were located within 2 kb upstream (promoter region) of translational start sites. This identified 18-bp binding motif was a perfect palindromic sequence, predominated by GGGTTCGAACCC in positions 4-15, a thymine in position 8, and an adenine in position 11. On closer examination, we hypothesized that the 18-bp motif sequence identified actually contained two identical parts (here we called motif A and motif B). Motif A was in positions 8-18 on the upper strand, while motif B was in positions 11-1 on the lower bottom strand. The inferred length and sequence of the putative motif identified in A. flavus were similar to previous findings in Aspergillus parasiticus and Aspergillus nidulans. Gene ontology analysis indicated that AflR was a transcriptional regulator potentially functioning outside the aflatoxin biosynthetic gene cluster. Validating the role of AflR outside the aflatoxin gene cluster is an ongoing research goal to understand the comprehensive functions of AflR in aspergilli.