GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
Series GSE44942 Query DataSets for GSE44942
Status Public on Mar 08, 2013
Title CG methylated microarrays identify novel methylated sequence bound by the CEBPB|ATF4 heterodimer that are active in vivo
Organism Mus musculus
Experiment type Expression profiling by high throughput sequencing
Genome binding/occupancy profiling by high throughput sequencing
Methylation profiling by high throughput sequencing
Summary To evaluate the effect of CG methylation on DNA binding of sequence-specific B-ZIP transcription factors (TFs) in a high-throughput manner, we enzymatically methylated the cytosine in the CG dinucleotide on protein binding microarrays. Using this novel technology, we show that CG methylation enhanced binding for CEBPA and CEBPB and inhibited binding for CREB, ATF4, JUN, JUND, CEBPD and CEBPG. The CEBPB|ATF4 heterodimer bound a novel motif CGAT|GCAA 10-fold better when methylated. EMSA confirmed these results. CEBPB ChIP-seq data using primary female mouse dermal fibroblasts with 50X methylome coverage for each strand indicate that the methylated sequences well-bound on the arrays are also bound in vivo. CEBPB bound 39% of the methylated canonical 10-mers ATTGC|GCAAT in the mouse genome. After ATF4 protein induction by thapsigargin which results in ER stress, CEBPB binds methylated CGAT|GCAA in vivo, recapitulating what was observed on the arrays. mRNA-seq of primary female mouse dermal fibroblasts with and without thapsigargin identified differentially expressed genes. Genes that are commonly bound by CEBPB and ATF4 to TGAT|GCAA (the best-bound 8-mer in the array) at the promoters were highly expressed and up-regulated or remained unchanged in the thapsigargin treated primary female mouse dermal fibroblasts.
Overall design RNA-Seq: Examination of whole genome transcriptome profiles (RNA-seq) of primary mouse dermal fibroblasts with and without Thapsigargin treatment
ChIP-Seq: Examination of transcription factor binding in dermal fibroblasts with and without Thapsigargin teratment
BS-Seq: Determination of whole genome DNA methylation profiles (BS-seq) of primary mouse dermal fibroblasts
Contributor(s) Chatterjee R, Vinson C
Citation(s) 23590861, 25699092
Submission date Mar 07, 2013
Last update date Jul 31, 2019
Contact name Raghunath Chatterjee
Organization name Indian Statistical institute
Department Human Genetics Unit
Street address 203 BT Road, HGU, Indian Statistical Institute
City Kolkata
State/province WB
ZIP/Postal code 700108
Country India
Platforms (2)
GPL9185 Illumina Genome Analyzer (Mus musculus)
GPL13112 Illumina HiSeq 2000 (Mus musculus)
Samples (7)
GSM1094252 Fb_RNA-seq
GSM1094253 Fb+Tg_RNA-seq
GSM1094254 CEBPB_ChIP-seq
BioProject PRJNA192600
SRA SRP019026

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
GSE44942_Percent_Fb_onlyCpG.bed.gz 259.1 Mb (ftp)(http) BED
GSE44942_RAW.tar 1.9 Mb (http)(custom) TAR (of BED, TXT)
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file
Processed data are available on Series record

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