Effects of NSUN2 deficiency on the mRNA 5-methylcytosine modification and gene expression profile in HEK293 cells

Epigenomics. 2019 Feb;11(4):439-453. doi: 10.2217/epi-2018-0169. Epub 2018 Dec 11.

Abstract

Aim: To study the biological function of NSUN2 in regulating gene expression and cell proliferation.

Materials & methods: The NSUN2 gene was knocked down in HEK293 cells via CRISPR/Cas9 system. mRNA m5C modification and gene expression were assessed using RNA-BisSeq and RNA-Seq.

Results: NSUN2 deficiency could inhibit proliferation and migration of HEK293 cells. A total of 1185 differentially methylated genes and 790 differentially expressed genes were identified. Bioinformatics analysis revealed that the differentially methylated genes were mainly involved in regulating gene expression. Some pathways associated with cell proliferation were significantly enriched by the differentially expressed genes. Additionally, GRB2 and CD44 may be key regulators in NSUN2-mediated cell proliferation.

Conclusion: These findings help to elucidate the molecular mechanisms by which NSUN2 affects cell proliferation, migration and other cell phenotypes.

Keywords: RNA m5C modification; RNA-seq; cell proliferation and migration; knockdown.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • 5-Methylcytosine / metabolism*
  • Cell Proliferation
  • Computational Biology / methods
  • Gene Expression Profiling
  • Gene Knockdown Techniques
  • Gene Regulatory Networks
  • Gene Targeting
  • HEK293 Cells
  • Humans
  • Methylation
  • Methyltransferases / deficiency*
  • RNA, Messenger / genetics*
  • Transcriptome*

Substances

  • RNA, Messenger
  • 5-Methylcytosine
  • Methyltransferases
  • NSUN2 protein, human