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Synergetic effects of DNA methylation and histone modification during mouse induced pluripotent stem cell generation

Guiying Wang1, Rong Weng1, Yuanyuan Lan1

  • 1Clinical and Translational Research Center of Shanghai First Maternity and Infant Health Hospital, Collaborative Innovation Center for Brain Science, Shanghai Key Laboratory of Signaling and Disease Research, School of Life Science and Technology, Tongji University, Shanghai, P.R. China.

Scientific Reports
|February 4, 2017
PubMed

Insights

DNA methylation and histone methylation are barriers to induced pluripotent stem cell (iPSC) generation. Demethylation using miR-29b improves iPSC quality by regulating gene expression and reducing tumorigenesis risk.

Area of Science:

  • Epigenetics and Stem Cell Biology
  • Molecular Biology
  • Genomics

Background:

  • DNA methylation and H3K27me3 modifications impede induced pluripotent stem cell (iPSC) generation using core transcription factors (Oct4, Sox2, Klf4, c-Myc; OSKM).
  • Understanding the precise impact of these epigenetic modifications on gene expression during reprogramming is crucial for improving iPSC derivation efficiency and quality.

Purpose of the Study:

  • To investigate the potential of demethylation strategies for deriving iPSCs.
  • To elucidate the specific roles of DNA methylation and histone modification in regulating gene expression during somatic cell reprogramming.
  • To compare the efficacy of miR-29b and shDnmt3a in demethylation-mediated iPSC generation and assess resulting iPSC quality.

Main Methods:

  • RNA sequencing was employed to profile the transcriptomes of embryonic stem cells (ES cells) and iPSCs generated via demethylation (using miR-29b or shDnmt3a).
  • Integrated bioinformatic analyses were performed to compare transcriptomic profiles and identify differentially expressed genes.
  • Analysis focused on gene ontology (GO) terms and KEGG signaling pathways associated with stem cell pluripotency and tumorigenesis.

Main Results:

  • iPSCs generated with OSKM and miR-29b (OSKM + miR-29b-iPSC) exhibited transcriptomic profiles closer to ES cells compared to other iPSC groups.
  • Upregulated genes in high-quality iPSCs were associated with methylated CpG-dense promoters and H3K27me3-enriched regions.
  • Demethylation-induced gene expression changes during reprogramming primarily affected stem cell-related pathways, potentially reducing iPSC tumorigenesis risk.

Conclusions:

  • DNA and histone methylation exhibit synergistic effects on gene expression regulation during iPSC generation.
  • Demethylation mediated by miR-29b is more effective than shDnmt3a for generating high-quality iPSCs.
  • Integrated analyses are essential for detecting subtle differences in transcriptomic data that may be missed by individual analyses, offering superior insights into reprogramming dynamics.

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