PreprintCited by 45Epigenetics and DNA MethylationGenomics and Chromatin DynamicsGenetic Syndromes and Imprinting

Frequent lack of repressive capacity of promoter DNA methylation identified through genome-wide epigenomic manipulation

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Ford, Ethan, Grimmer, Matthew R., Stolzenburg, Sabine, Bogdanovic, Ozren, Mendoza, Alex de, Farnham, Peggy J., Blancafort, Pilar, Lister, Ryan·2017·bioRxiv (Cold Spring Harbor Laboratory)

Abstract

It is widely assumed that the addition of DNA methylation at CpG rich gene promoters silences gene transcription. However, this conclusion is largely drawn from the observation that promoter DNA methylation inversely correlates with gene expression in natural conditions. The effect of induced DNA methylation on endogenous promoters has yet to be comprehensively assessed. Here, we induced the simultaneous methylation of thousands of promoters in the genome of human cells using an engineered zinc finger-DNMT3A fusion protein, enabling assessment of the effect of forced DNA methylation upon transcription, histone modifications, and DNA methylation persistence after the removal of the fusion protein. We find that DNA methylation is frequently insufficient to transcriptionally repress promoters. Furthermore, DNA methylation deposited at promoter regions associated with H3K4me3 is rapidly erased after removal of the zinc finger-DNMT3A fusion protein. Finally, we demonstrate that induced DNA methylation can exist simultaneously on promoter nucleosomes that possess the active histone modification H3K4me3, or DNA bound by the initiated form of RNA polymerase II. These findings suggest that promoter DNA methylation is not generally sufficient for transcriptional inactivation, with implications for the emerging field of epigenome engineering. One Sentence Summary: Genome-wide epigenomic manipulation of thousands of human promoters reveals that induced promoter DNA methylation is unstable and frequently does not function as a primary instructive biochemical signal for gene silencing and chromatin reconfiguration.

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  • A recent methylation editing study demonstrated that deposition of 5mC at thousands of gene promoters led to only moderate transcriptional alterations.

    “For example, a recent methylation editing study demonstrating that deposition of 5mC at thousands of gene promoters led to only moderate transcriptional alterations (65, 66).”

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  1. J. Feng, T. Liu, Y. Zhang, Curr. Protoc. Bioinformatics , in press.

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Authors
Ford, E., Grimmer, M. R., Stolzenburg, S., Bogdanovic, O., Mendoza, A. D., Farnham, P. J., Blancafort, P., & Lister, R.
Affiliations
  • The University of Western Australia (AU)
  • University of Southern California (US)
Corresponding author
Lister, Ryan
Venue
bioRxiv (Cold Spring Harbor Laboratory)
Publisher
openRxiv
Published
2017-08-16
OpenAlex
W2749986987
Cited by
45
References
78
Citations by year
2026: 1 · 2025: 2 · 2022: 2 · 2021: 8 · 2020: 5 · 2019: 15 · 2018: 11 · 2017: 1
Type
posted content
Language
en
Open access
Licence
cc-by-nc-nd
Locations
  • bioRxiv (Cold Spring Harbor Laboratory) (acceptedVersion, cc-by-nc-nd)
  • Queen Mary Research Online (Queen Mary University of London) (submittedVersion)
Funders
  • Raine Medical Research Foundation
  • National Institutes of Health
  • Medical Research Council (GNT1069830)
  • Australian Research Council (CE140100008, FT120100862)
  • National Health and Medical Research Council (1069830)
  • National Human Genome Research Institute (R21HG006761)
  • National Cancer Institute (R01CA170370, P30CA014089)
Topics
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Epigenetics and DNA Methylation
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Chromatin Dynamics
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Genetic Syndromes and Imprinting
Keywords
promoter methylation, transcriptional repression, H3K4me3, histone modifications, RNA polymerase II, nucleosome, gene silencing, human cells

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