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Series GSE74744 Query DataSets for GSE74744
Status Public on Feb 09, 2017
Title Development of DNA demethylation technology in HEK293T cells
Organism Homo sapiens
Experiment type Expression profiling by array
Summary DNA demethylating agents are epigenetic drugs for the therapy of myeloid leukemias. They not only induce DNA demethylation but also have significant cytostatic and cytotoxic effects, however, the relationships between these characteristics have not been established yet due to the lack of method to induce only DNA demethylation. Here we show that a fusion protein comprising the methyl-CpG binding domain (MBD) and the catalytic domain of Ten-eleven translocation protein 1 (TET1-CD) globally demethylates and upregulates a number of methylated genes. Gene expression microarray analyses using human embryonic kidney cell line 293T indicate that cells expressing wild-type (wt) TET1 catalytic domain with MBD (MBD-TET1-CDwt) upregulated more genes than ones expressing TET1-CDwt without MBD or catalytically inactive TET1-CD mutant (mut) with MBD (MBD-TET1-CDmut) and their upregulated genes frequently contained CpG islands (CGIs) within ± 1,000 bp of the transcription start site (TSS). Interestingly, 88% of genes upregulated 5-fold or more by MBD-TET1-CDwt were also reactivated after treatment with DNA demethylating agent, 5-azacytidine, suggesting that gene reactivation by both methods is primarily based on DNA demethylation.
 
Overall design HEK293T cells were transfected with pcDNA6/myc-His vector, pcDNA6-TET1-CDwt, pcDNA-MBD-TET1-CDwt, or pcDNA6-MBD-TET1-CDmut and two independent stable transformants expressing vector, TET1-CDwt, MBD-TET1-CDwt, or MBD-TET1-CDmut were constructed respectively. RNAs from these eight stable cell lines were prepared and analyzed by Agilent Human Gene Expression 4x44K v2 Microarray.
 
Contributor(s) Fukushige S, Mizuguchi Y
Citation(s) 27457352
Submission date Nov 06, 2015
Last update date Jun 30, 2017
Contact name Shinichi Fukushige
E-mail(s) fukushige@med.tohoku.ac.jp
Organization name Tohoku University Graduate School of Medicine
Department Department of Diabetes, Metabolism and Endocrinology
Street address 2-1 Seiryo-machi, Aoba-ku
City Sendai
ZIP/Postal code 980-8575
Country Japan
 
Platforms (1)
GPL10332 Agilent-026652 Whole Human Genome Microarray 4x44K v2 (Feature Number version)
Samples (8)
GSM1931620 293T_Vec1_exp1
GSM1931621 293T_Vec2_exp1
GSM1931622 293T_TET1-CDwt2_exp1
Relations
BioProject PRJNA301398

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
GSE74744_RAW.tar 24.3 Mb (http)(custom) TAR (of TXT)
Processed data included within Sample table
Processed data provided as supplementary file

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