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Series GSE124384 Query DataSets for GSE124384
Status Public on Apr 20, 2021
Title FoxA-dependent demethylation of DNA initiates epigenetic memory of cellular identity
Organism Mus musculus
Experiment type Genome binding/occupancy profiling by high throughput sequencing
Methylation profiling by high throughput sequencing
Summary Tissue-specific DNA methylation patterns are created by transcription factors that recruit methylation and demethylation enzymes to cis-regulatory elements. To date, it is not known whether transcription factors are needed to continuously maintain methylation profiles in development and mature tissues or whether they only establish these marks during organ development. We queried the role of the pioneer factor FoxA in generating hypomethylated DNA at liver enhancers. We discovered a set of FoxA binding sites that undergo regional, FoxA-dependent demethylation during organ development. Conditional ablation of FoxA genes in the adult liver demonstrated that continued FoxA presence was not required to maintain the hypomethylated state, even when massive cell proliferation was induced. This study provides strong evidence for the stable, epigenetic nature of tissue-specific DNA methylation patterns directed by lineage-determining transcription factors during organ development.
Overall design WGBS, RRBS, and ChIP seq performed on Foxa1/2 mice depleted in liver development or in adulthood
Contributor(s) Reizel Y, Morgan A, Zaret KS, Kaestner KK
Citation(s) 33636105
Submission date Dec 26, 2018
Last update date Apr 23, 2021
Contact name Klaus H Kaestner
Organization name University of Pennsylvania
Department Department of Genetics and Institute for Diabetes Obesity and Metabolism, Perelman School of Medicine
Street address University of Pennsylvania, 12-126 Smilow Center for Translational Research, 3400 Civic Center Boulevard
City Philadelphia
State/province PA
ZIP/Postal code 19104-5156
Country USA
Platforms (3)
GPL17021 Illumina HiSeq 2500 (Mus musculus)
GPL21103 Illumina HiSeq 4000 (Mus musculus)
GPL24247 Illumina NovaSeq 6000 (Mus musculus)
Samples (73)
GSM3530839 WGBS Foxa1L/L;2L/L 1
GSM3530840 WGBS Foxa1L/L;2L/L 2
GSM3530841 WGBS Foxa1L/L;2L/L Alfp Cre 1
BioProject PRJNA511882
SRA SRP174491

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
GSE124384_2705_hyper_methylated_sites.txt.gz 23.3 Kb (ftp)(http) TXT
GSE124384_5005_2_peaks.txt.gz 117.8 Kb (ftp)(http) TXT
GSE124384_5007_1_peaks.txt.gz 83.9 Kb (ftp)(http) TXT 551.1 Mb (ftp)(http) BW 476.1 Mb (ftp)(http) BW 450.9 Mb (ftp)(http) BW 337.6 Mb (ftp)(http) BW
GSE124384_DKO_5222_peaks.txt.gz 76.5 Kb (ftp)(http) TXT
GSE124384_DKO_5227_peaks.txt.gz 29.9 Kb (ftp)(http) TXT 360.1 Mb (ftp)(http) BW 331.6 Mb (ftp)(http) BW
GSE124384_Methylation_scores_FoxA_Alfp.txt.gz 756.3 Kb (ftp)(http) TXT
GSE124384_Methylation_scores_RRBS_samples.txt.gz 52.0 Mb (ftp)(http) TXT
GSE124384_Methylation_scores_at_FoxA_sites_AAV_Cre.txt.gz 647.5 Kb (ftp)(http) TXT
GSE124384_WT_5406_peaks.txt.gz 142.7 Kb (ftp)(http) TXT
GSE124384_WT_5412_peaks.txt.gz 112.8 Kb (ftp)(http) TXT
GSE124384_WT_5868_peaks.txt.gz 43.6 Kb (ftp)(http) TXT
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