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Depletion of DNMT1 in differentiated human cells highlights key classes of sensitive genes and an interplay with

Karla M O'Neill1,2, Rachelle E Irwin1, Sarah-Jayne Mackin1

  • 1Genomic Medicine Research Group, Centre for Molecular Biosciences, School of Biomedical Sciences, Ulster University, Cromore Road, Coleraine, BT52 1SA, UK.

Epigenetics & Chromatin
|March 31, 2018
PubMed
Abstract

Insights

Chronic depletion of DNA methyltransferase 1 (DNMT1) in normal human cells reveals its critical role in maintaining methylation patterns. Loss of DNMT1 impacts neural, fat, and cancer-associated genes, highlighting its importance in cellular identity and disease.

Area of Science:

  • Epigenetics and Gene Regulation
  • Cellular Biology
  • Molecular Oncology

Background:

  • DNA methylation is crucial for cellular function, but DNMT1 loss-of-function mutations are lethal in normal human cells.
  • Existing studies on DNMT1 hypomorphic cell lines used tumor cells, limiting understanding in normal cell contexts.
  • This study generated a hypomorphic series in normal fibroblasts to investigate DNMT1's role.

Purpose of the Study:

  • To investigate the effects of chronic depletion of DNA methyltransferase 1 (DNMT1) in normal human fibroblasts.
  • To identify gene classes and regulatory regions affected by reduced DNMT1 activity.
  • To explore mechanisms of remethylation and their impact on gene expression.

Main Methods:

  • Utilized stably integrated short hairpin RNA (shRNA) to create a hypomorphic DNMT1 series in hTERT-immortalised fibroblasts.
  • Performed enrichment analysis to identify affected gene classes and genomic regions (promoters, gene bodies).
  • Compared results with siRNA-treated cells and assessed the impact of EZH2 inhibition.

Main Results:

  • Approximately two-thirds of DNA methylation sites showed demethylation, while one-third showed hypermethylation.
  • Key affected gene classes included protocadherins, fat homeostasis genes, olfactory receptors, and cancer/testis antigen (CTA) genes.
  • CTA genes exhibited robust derepression, and persistent hypomethylation was linked to polycomb repression, while hypermethylation was associated with poised promoters.

Conclusions:

  • This study provides the first assessment of chronic DNMT1 depletion effects in untransformed human cells.
  • Polycomb marking appears to inhibit remethylation, influencing gene expression.
  • Key neural, adipose, and cancer-associated genes are sensitive to the loss of DNMT1 maintenance methylation activity.
Keywords:
Body massCancer/testis antigenDNMT1EZH2Protocadherin

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