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Series GSE60316 Query DataSets for GSE60316
Status Public on Aug 10, 2017
Title RUNX1-Mediated Binding Site Directed DNA Demethylation is a Novel Mechanism of Hematopoietic Gene Activation.
Organism Homo sapiens
Experiment type Methylation profiling by genome tiling array
Summary RUNX1 (also known as AML1) is a key transcription factor for definitive hematopoietic stem cell development and following hematopoietic cell linage specifications, in which chromatin- or epigennome-mediated regulation by RUNX1, particularly regulation of DNA methylation status, is proposed to be involved in addition to its direct gene expression regulation. However, how RUNX1 regulates DNA methylation status and its role in the hematopoiesis remain to be elucidated. Here we first demonstrated that RUNX1 induces RUNX1 binding site directed DNA demethylation across the whole genome. HaloTag-based pull-down assay revealed associations of RUNX1 with active DNA demethylation related proteins such as TET, TDG or GADD45A, suggested that the RUNX1-mediated DNA demethylation is active DNA demethylation mechanism. Additional combinatorial overexpression of TET and TDG enlarged the RUNX1-mediated DNA demethylation, supporting what RUNX1-mediated DNA demethylation is active DNA demethylation. These results strongly suggested that RUNX1-mediated DNA demethylation is achieved by recruiting those proteins involved in active DNA demethylation. Finally, we found that the RUNX1-mediated demethylation predominately targets and activates hematopoietic genes whose promoter regions are demethylated during hematopoiesis. Collectively, our insight suggested that RUNX1-mediated binding site directed DNA demethylation is a novel mechanism of hematopoietic gene activation.
Overall design Bisulphite converted DNA from the 6 samples were hybridised to the Illumina Infinium 450k Human Methylation Beadchip
Contributor(s) Suzuki T, Shimizu Y, Furuhata E, Maeda S, Kishima M, Nishimura H, Hayashizaki Y, Suzuki H
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Submission date Aug 11, 2014
Last update date Mar 22, 2019
Contact name Takahiro Suzuki
Phone 81-45-503-9222
Organization name RIKEN
Department Center for Integrative Medical Sciences
Lab Laboratory for Cellular Function Conversion Technologies
Street address 1-7-22 Suehiro-cho, Tsurumi-ku
City Yokohama
State/province Kanagawa
ZIP/Postal code 230-0045
Country Japan
Platforms (1)
GPL13534 Illumina HumanMethylation450 BeadChip (HumanMethylation450_15017482)
Samples (6)
GSM1471623 Genomic DNA from 293T-mock
GSM1471624 Genomc DNA from 293T-RUNX1
GSM2227495 Genomic DNA from 293T-TET2
BioProject PRJNA258014

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
GSE60316_RAW.tar 183.1 Mb (http)(custom) TAR
GSE60316_signal_intensities.txt.gz 14.9 Mb (ftp)(http) TXT
Processed data included within Sample table

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