Overexpression of human-derived DNMT3A induced intergenerational inheritance of DNA methylation and gene expression variations in rat brain and testis

ABSTRACT

In mammals, DNA methylation patterns are established by various types of DNA methyltransferases and can be stably passed on during cell division, thus creating a paradigm for epigenetic regulation that can mediate long-lasting changes in gene expression even when the initial triggering signal has disappeared. Although functional deficiency of DNMT3A, one of the methyltransferases, leads to abnormal DNA methylation patterns that result in developmental deficits in mammals, the impacts of its overexpression on tissue gene expression and DNA methylation patterns remain unclear. Here, our previously established hDNMT3A transgenic rat model and mRNA sequencing and bisulphite sequencing PCR were used to analyse the impact of hDNMT3A overexpression on tissue transcriptome and methylome, and whether the impact could be inherited intergenerationally was subsequently investigated. Our results revealed that the overexpression of hDNMT3A could induce notable gene expression variations in rat testis and brain. More importantly, 36.02% and 38.89% of these variations could be intergenerationally inherited to offspring without the transmission of the initial endogenic trigger in the brain and testis, respectively. Furthermore, we found that intergenerationally inherited DNA methylation variations in their promoters and exons could be the underlying mechanism. Compared with inheritable variations that were passively induced by environmental factors, these variations were actively induced by endogenous epigenetic modifiers. This study provided evidence for the epigenetic inheritance of endogenous factors that actively induce gene expression and DNA methylation variations; however, more studies are needed to determine the number of generations that these variations can be stably inherited.

KEYWORDS:

• DNMT3A
• gene expression
• DNA methylation
• intergenerational inheritance
• mRNA-seq

Acknowledgments

We would like to thank Dr. Yu Lin for providing a discussion and critical reading of the manuscript. We thank Shanghai Key Laboratory of Reproductive Medicine, School of Medicine, Shanghai Jiao Tong University for the animal care and equipment support.

Disclosure statement

The authors declare that they have no competing interests.

Author Contributions

FS and XZ designed the work, ZL wrote the manuscript, YM constructed the hDNMT3A transgenic rats, ZL and YZ performed the RNA-seq and BSP assays, GW and HW performed the qPCR assay to analyzed the expression patterns of transgene and differentially expressed genes, YD performed tissue DNA extraction, and XZ and SC analyzed the qPCR data.

Availability of data and materials

All datasets generated in this work have been deposited in the Sequence Read Archive (SRA) database under the accession number GSE128777.

Supplementary material

Supplemental data for this article can be accessed here

Additional information

Funding

This study was supported by the following grants (to F.S.): the National Key Research and Development Program of China [No. 2018YFC1003500] and the National Natural Science Foundation of China No. 81430027, 81671510]; and the following grants (to X.Z.): the Natural Science Foundation of Shanghai, China [No. 17ZR1433100] and the National Natural Science Foundation of China [No. 81801514];