GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
Series GSE165891 Query DataSets for GSE165891
Status Public on Jul 04, 2022
Title Large-scale manipulation of promoter DNA methylation reveals context-specific transcriptional responses and stability
Organism Homo sapiens
Experiment type Expression profiling by high throughput sequencing
Genome binding/occupancy profiling by high throughput sequencing
Methylation profiling by high throughput sequencing
Summary Cytosine DNA methylation is widely described as a transcriptional repressive mark with the capacity to silence promoters. Epigenome engineering techniques enable direct testing of the effect of induced DNA methylation on endogenous promoters, however, the downstream effects have not yet been comprehensively assessed. Here, we simultaneously induced methylation at thousands of promoters in human cells using an engineered zinc finger-DNMT3A fusion protein, enabling us to test the effect of forced DNA methylation upon transcription, chromatin accessibility, histone modifications, and DNA methylation persistence after the removal of the fusion protein. We find that DNA methylation is often not sufficient to suppress transcription which appears to be driven by the eviction of methyl-sensitive transcriptional repressors. Furthermore, we find that some regulatory networks can override DNA methylation, and that promoter methylation can cause alternative promoter usage. DNA methylation deposited at promoter and distal regulatory regions is rapidly erased after removal of the zinc finger-DNMT3A fusion protein, in a process combining active and passive demethylation. 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 have important implications for epigenome engineering, and demonstrate that the response of promoters to DNA methylation are more complex than previously appreciated.
Overall design Profiling DNA methylation, chromatin accessibility, and transcription upon conditional ZincFinger-DNMT3A expression in MCF-7 cells, plus additional ChIP-seq of the ZincFinger-DNMT3A.
Contributor(s) de Mendoza A, Nguyen TV, Ford E, Poppe D, Buckberry S, Pflueger J, Lister R
Citation(s) 35883107
Submission date Feb 01, 2021
Last update date Sep 04, 2023
Contact name Ryan Lister
Phone 61864884407
Organization name The University of Western Australia
Street address 35 Stirling Highway
City Perth
State/province WA
ZIP/Postal code 6009
Country Australia
Platforms (1)
GPL24676 Illumina NovaSeq 6000 (Homo sapiens)
Samples (57)
GSM5057382 RL1897_ChIPseq_Dox_HAflag_rep1
GSM5057383 RL1898_ChIPseq_DoxMut_HAflag_rep1
GSM5057384 RL1899_ChIPseq_Dox_HAflag_rep2
BioProject PRJNA698484
SRA SRP304105

Download family Format
SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE165891_RAW.tar 45.3 Gb (http)(custom) TAR (of CGMAP, NARROWPEAK)
GSE165891_ZF_Counts_table_GEO.tsv.gz 787.9 Kb (ftp)(http) TSV
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap