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Series GSE102395 Query DataSets for GSE102395
Status Public on Aug 10, 2017
Title Lack of Repressive Capacity of Human Promoter DNA Methylation identified through Genome-Wide Epigenomic Manipulation
Organism Homo sapiens
Experiment type Methylation profiling by high throughput sequencing
Genome binding/occupancy profiling by high throughput sequencing
Expression profiling by high throughput sequencing
Summary It is widely assumed that the addition of DNA methylation at gene promoters silences gene transcription. However, this conclusion is largely drawn from the observation that promoter DNA methylation inversely correlates with gene expression. The effect of forced DNA methylation on endogenous promoters has yet to be comprehensively assessed. Here, we conducted artificial methylation of thousands of human promoters in human cells using an artificial zinc finger-DNMT3A fusion protein, enabling assessment of the effect of forced DNA methylation upon transcription and histone modifications, and the durability of DNA methylation after the removal of the fusion protein. We find that DNA methylation is insufficient to transcriptionally repress most 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. These findings suggest that promoter DNA methylation is not generally sufficient for transcriptional inactivation suggesting important implications for the emerging field of epigenome engineering.
Overall design The response of MCF-7 cells to enforced DNA methylation by ZF-DNMT3A as measured by MethylC-seq, RNA-seq, ChIP-seq and ChIP-BS-seq. ZF-DNMT3A expression was induced the addition of doxycycline to the growth media for 3 days. Doxycycline was then withdrawn for 9 days. DNA, RNA and/or chrmatin was extracted from the cells before and after doxycycline induction as well as after doxycycline withdrawl. WGBS, RNA-seq, ChIP-seq and ChIP-BS-seq libraries were constructed for sequencing on the Illumina HiSeq1500.
Contributor(s) Ford E, Grimmer MR, Stolzenburg S, Bogdanovic O, de Mendoza A, Farnham PJ, Blancafort P, Lister R
Citation(s) 35883107
Submission date Aug 09, 2017
Last update date Aug 03, 2022
Contact name Ethan Edward Ford
Phone 0061 416 525 900
Organization name University of Western Australia
Department Plant Energy Biology
Lab Ryan Lister
Street address 35 Stirling Highway
City Crawley
State/province WA
ZIP/Postal code 6009
Country Australia
Platforms (1)
GPL18460 Illumina HiSeq 1500 (Homo sapiens)
Samples (40)
GSM2735962 MCF7_emptyVector_doxInduced_rep1_WGBS
GSM2735963 MCF7_empytVector_doxWithdrawn_rep1_WGBS
GSM2735964 MCF7_ZF_DNMT3A_doxInduced_rep1_WGBS
BioProject PRJNA397651
SRA SRP115074

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
GSE102395_MCF7_ZF_DNMT3A_countstable.txt.gz 700.2 Kb (ftp)(http) TXT
GSE102395_RAW.tar 44.0 Gb (http)(custom) TAR (of BED, BIGWIG, TXT)
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Raw data are available in SRA
Processed data provided as supplementary file
Processed data are available on Series record

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