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Series GSE107204 Query DataSets for GSE107204
Status Public on Nov 28, 2017
Title HydroxyMeDIPseq day 3 differentiated mouse ESCs
Organism Mus musculus
Experiment type Methylation profiling by high throughput sequencing
Summary Graded levels of molecular oxygen (O2) exist within developing mammalian embryos and can differentially regulate cellular specification pathways. During differentiation, cells acquire distinct epigenetic landscapes, which determine their function, however the mechanisms which regulate this are poorly understood. The demethylation of 5-methylcytosine (5mC ) is achieved via successive oxidation reactions catalysed by the Ten-Eleven-Translocation (Tet) enzymes, yielding the 5-hydroxymethylcytosine (5hmC ) intermediate. These require O2 as a co-factor, and hence may link epigenetic processes directly to O2 gradients during development. We demonstrate that the activities of Tet enzymes are differentially dependent upon [O2], and that Tet1 activity, specifically, is inhibited by low levels of O2 which are physiologically relevant in embryogenesis. Further, embryonic stem cells, induced to differentiate, displayed a transient burst of 5hmC, which was both dependent upon Tet1 and inhibited by low (1%) [O2]. A GC-rich promoter region within the Tet3 locus was identified as a significant target of this 5mC-hydroxylation. Further, this region was shown to associate with Tet1, and display the histone epigenetic marks, H3K4me3 and H3K27me3, which are characteristic of a bivalent, developmentally “poised” promoter. We conclude that Tet1 activity, determined by [O2] may play a critical role in regulating cellular differentiation and fate in embryogenesis
Overall design 2 samples (which were pooled biological triplicates), DNA input and 5hmC enrichment were sequenced on an Illumina MiSeq, single read for 50 cycles
Contributor(s) Burr SJ, Brewer AC
Citation(s) 29186571
Submission date Nov 21, 2017
Last update date Jul 31, 2019
Contact name Alison Brewer
Organization name King's College London
Department Cardiology
Street address JBC, 125 Coldharbour Lane
City London
ZIP/Postal code SE5 9NU
Country United Kingdom
Platforms (1)
GPL16417 Illumina MiSeq (Mus musculus)
Samples (2)
GSM2862686 DNA input sequence
GSM2862687 hMeDIP-seq
BioProject PRJNA419308
SRA SRP125389

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Supplementary file Size Download File type/resource
GSE107204_hMeDIP_seq_analysis_gene_list.xlsx 187.8 Kb (ftp)(http) XLSX
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Raw data are available in SRA
Processed data are available on Series record

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