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Deoxynivalenol globally affects the selection of 3’ splice sites in human cells by suppressing the splicing factors, U2AF1 and SF1

Citation

Sun, Yu et al. (2020), Deoxynivalenol globally affects the selection of 3’ splice sites in human cells by suppressing the splicing factors, U2AF1 and SF1, Dryad, Dataset, https://doi.org/10.5061/dryad.2rbnzs7hq

Abstract

Deoxynivalenol (DON) is one of the most abundant mycotoxins and has adverse effects on several biological processes, posing risks of protein synthesis-disrupting effects and ribotoxic response. Therefore, chronic exposure to DON would fundamentally reshape the global expression pattern. Whether DON causes toxic effects on mRNA splicing, a fundamental biological process, remains unclear. In this study, we found that administration of the relative low dosage of DON dramatically changed the alternative splicing of pre-mRNA in HepG2 cells. The overall number of transcripts with aberrant selection of 3' splice sites was significantly increased in DON-exposed HepG2 cells. This effect was further confirmed in two other human cell lines, HEK293 and Caco-2, suggesting that this DON-induced alteration in splicing pattern is universal in human cells. Among these DON-induced changes in alternative splicing, the expression levels of two related splicing factors, SF1 and U2AF1, which are essential for 3' splice site recognition, were strongly suppressed. The expression of SF1 and U2AF1 in human cells was controlled by DON probably at the transcriptional level by suppressing the promoter activation of these two genes. Overexpression of either of the two splicing factors strongly alleviated the DON-induced 3' splice sites. Moreover, SF1 is required for human cell proliferation in DON exposure, and the restoration of SF1 expression partially reinstated the proliferation potential of DON-treated cells. In conclusion, our study suggests that DON, even at a low dosage, has great potential to change gene expression globally by affecting not only protein synthesis but also mRNA processing in human cells.

Methods

Two biological replicates for DON-treated and untreated control HepG2 cells were collected for RNA-seq. Sequencing library was constructed by NEBNext Ultra RNA Library Prep Kit for Illumina, assessed by gilent 2100 Bioanalyzer and ABI StepOnePlus Real-Time PCR System, and sequenced by Illumina HiSeqTM 2500 platform. The adaptor, ploy-N and low quality reads were removed to obtain clean reads for further analyses. SOAPaligner/SOAP2 were used to assemble the clean reads, and then the gene expression and alternative splicing analyses were conducted based on assembled sequences with homemade perl scripts. GO analysis was conducted on KOBAS 3.0 web server (http://kobas.cbi.pku.edu.cn/index.php). The quantitative analysis and statistics were conducted in R. 

The comprehensive analyses of the transcriptomic data is included.

Funding

National Nature Science Foundation of China, Award: 3147123

Natural Science Foundation of Guangdong Province, Award: 2015A030312005

Department of Education of Guangdong Province, Award: 2017KCXTD001

Department of Education of Guangdong Province, Award: 2018KZDXM015

Science and Technology Program of Guangzhou, Award: 201804020067

Science and Technology Program of Guangzhou, Award: 201607010177