GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
Series GSE141227 Query DataSets for GSE141227
Status Public on Mar 18, 2020
Title Myc-mediated SDHA Acetylation Triggers Epigenetic Regulation of Gene Expression and Tumorigenesis.
Organism Homo sapiens
Experiment type Expression profiling by high throughput sequencing
Genome binding/occupancy profiling by high throughput sequencing
Summary Trimethylated H3K4 (H3K4me3), which is often found surrounding the transcriptional start site of active genes, is strongly enriched in the promoter regions of Myc-targeted genes. Succinate, which inhibits JmjC domain-containing histone demethylases (JHDMs), can induce H3K4me3 level of the promoter regions. It's interesting to ask whether Myc can mediate H3K4me3 by regulating cellular succinate level. Here, We used ChIP-seq to study Myc modulates H3K4me3 by altering succinate levels, dimethyl succinate (DMS), a membrane-permeable succinate analog, was introduced to treat CA46 cells with high or depleted Myc expression. And we also performed RNA-seq assays in Myc expressed or depleted CA46 cells with or without DMS treatment.
Overall design CA46 cells were infected with viruses expressing non-targeting control (NTC) or Myc shRNA for 48h in presence of methyl succinate (DMS) and followed by H3K4me3 ChIP-seq to address whether succinate can induce H3K4me3 level of the promoter regions in CA46 cells with depleted Myc expression. For the CA46 cells’ ChIP-seq experiments with spike-in control, Drosophila chromatin (Active Motif 53083) and a Drosophila-specific antibody (Active Motif 61686) were used for each reaction. The D. melanogaster-specific antibody is used to immunoprecipitate D. melanogaster chromatin from each reaction, which is then used as a reference for normalization during data analysis. And ChIP-seq was sequenced at Novogene (Tianjin, China) on the Illumina novaseq6000 platform. Meanwhile, we also performed RNA extraction from these cell samples and sequenced on Illumina novaseq6000 platform.
Contributor(s) Li S, Shen S, Gao P, Zhang H
Citation Li S, Huang D, Shen S, Cai Y, Xing S, et al. Myc-mediated SDHA acetylation triggers epigenetic regulation of gene expression and tumorigenesis. Nat Metab 2020;2:256-269. doi:10.1038/s42255-020-0179-8
Submission date Dec 01, 2019
Last update date Mar 18, 2020
Contact name Shi-Ting Li
Phone 15956951752
Organization name University of Science and Technology of China
Department Innovation Center for Cell Biology
Lab 447 Room
Street address No.443, Huangshan Road
City He Fei
State/province An Hui
ZIP/Postal code 230027
Country China
Platforms (1)
GPL24676 Illumina NovaSeq 6000 (Homo sapiens)
Samples (9)
GSM4198774 spike-in_ChIP-seq_NTC-DMS
GSM4198775 spike-in_ChIP-seq_NTC+DMS
GSM4198776 spike-in_ChIP-seq_shMyc-DMS
BioProject PRJNA592816
SRA SRP234173

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
GSE141227_RAW.tar 415.3 Mb (http)(custom) TAR (of BW, XLSX)
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