Depletion of TRDMT1 affects 5-methylcytosine modification of mRNA and inhibits HEK293 cell proliferation and migration

Songlei Xue; Hui Xu; Zhen Sun; Hui Shen; Shihao Chen; Juan Ouyang; Qiqi Zhou; Xuming Hu; Hengmi Cui

doi:10.1016/j.bbrc.2019.09.098

Depletion of TRDMT1 affects 5-methylcytosine modification of mRNA and inhibits HEK293 cell proliferation and migration

Biochem Biophys Res Commun. 2019 Nov 26;520(1):60-66. doi: 10.1016/j.bbrc.2019.09.098. Epub 2019 Sep 27.

Authors

Songlei Xue¹, Hui Xu², Zhen Sun², Hui Shen², Shihao Chen², Juan Ouyang², Qiqi Zhou², Xuming Hu¹, Hengmi Cui³

Affiliations

¹ Institute of Epigenetics and Epigenomics and College of Animal Science and Technology, Yangzhou University, Yangzhou, 225009, China; Joint International Research Laboratory of Agricultural & Agri-Product Safety of the Ministry of Education of China, Yangzhou University, Yangzhou, 225009, China.
² Institute of Epigenetics and Epigenomics and College of Animal Science and Technology, Yangzhou University, Yangzhou, 225009, China.
³ Institute of Epigenetics and Epigenomics and College of Animal Science and Technology, Yangzhou University, Yangzhou, 225009, China; Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou, 225009, China; Institute of Comparative Medicine, Yangzhou University, Yangzhou, 225009, China; Joint International Research Laboratory of Agricultural & Agri-Product Safety of the Ministry of Education of China, Yangzhou University, Yangzhou, 225009, China. Electronic address: hmcui@yzu.edu.cn.

PMID: 31570165
DOI: 10.1016/j.bbrc.2019.09.098

Abstract

Human TRDMT1 is a transfer RNA (tRNA) methyltransferase for cytosine-5 methylation and has been suggested to be involved in the regulation of numerous developmental processes. However, little is known about the molecular mechanisms or their biological significance. In this study, we investigated the effects of CRISPR-based TRDMT1 knockdown on phenotypes, mRNA m5C modifications and gene expression changes in HEK293 cells. We found that knockdown of TRDMT1 significantly inhibited cell proliferation and migration but had no effect on clonogenic potential. The inhibitory effects could be attenuated by re-expression of TRDMT1 in HEK293 cells. RNA sequencing (RNA-Seq) and RNA bisulfite sequencing (RNA-BisSeq) were performed in TRDMT1 knockdown and wild-type HEK293 cells. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analyses indicated that the differentially expressed genes were associated with the cell cycle, RNA transport, and RNA degradation and were enriched in cancer and Notch signaling pathways. We also found that TRDMT1 knockdown could change mRNA methylation levels. For the first time, these findings clarify the role of TRDMT1 in regulating mRNA methylation and inhibiting the proliferation and migration of HEK293 cells. These results provide new insights into a new function of TRDMT1 and elucidate the molecular mechanisms of aberrant RNA m5C during tumorigenesis.

Keywords: CRISPR/Cas9; RNA m5C; RNA-BisSeq; RNA-Seq; TRDMT1.

Publication types

Research Support, Non-U.S. Gov't

MeSH terms

5-Methylcytosine / metabolism*
CRISPR-Cas Systems
Carcinogenesis
Cell Movement*
Cell Proliferation*
Computational Biology
DNA (Cytosine-5-)-Methyltransferases / genetics*
DNA (Cytosine-5-)-Methyltransferases / metabolism*
DNA Methylation
Gene Expression Profiling
HEK293 Cells
Humans
Phenotype
RNA, Messenger / metabolism*
RNA-Seq
Signal Transduction

Substances

RNA, Messenger
5-Methylcytosine
DNA (Cytosine-5-)-Methyltransferases
TRDMT1 protein, human