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Series GSE55659 Query DataSets for GSE55659
Status Public on Feb 10, 2015
Title Single base resolution analysis of 5-formyl and 5-carboxyl cytosine reveals the actual promoter DNA methylation dynamics in embryonic stem cells [RRBS]
Organism Mus musculus
Experiment type Methylation profiling by high throughput sequencing
Summary DNA methylation is catalysed by DNA methyltransferases (DNMTs) and is necessary for a correct embryonic development. On the other hand, the DNA demethylation is mediated by the Ten Eleven Translocation (Tet) proteins through oxidation of 5-methyl cytosine (5mC) to 5-hydroxyl (5hmC), 5-formyl (5fC) and 5-carboxyl (5caC) cytosine, and by the Thymine-DNA glycosylase (TDG) that excises the 5fC and 5caC. In embryonic stem cells (ESCs), gene promoters are maintained in an hypomethylated state, but the dynamics of this phenomenon still remains unknown. Here we present a genome-wide approach, named methylation-assisted bisulfite sequencing (MAB-Seq) that enables single-base resolution mapping of 5fC and 5caC and measuring of their relative abundance. Application of this method to mouse ESCs exposed the presence of 5fcaC residues on the hypomethylated promoters of the expressed genes, revealing an active DNA demethylation mechanism since the loss of TDG leads to an increase of 5fC/5caC. We also show that TDG is actually bound on these regions and that co-localizes and interacts with Tet1. We moreover demonstrate, by reduced representation of bisulfite sequencing (RRBS), that active promoters are actually demethylated by a Tet-dependent mechanism and that Dnmt1 and Dnmt3a are responsible of this DNA methylation. Our work shows the whole-genome map of 5fC and 5caC at single base resolution in ESCs, it demonstrates in detail the DNA methylation dynamics occurring on expressed gene promoters and identifies the key players of this mechanism. Furthermore, we provide a new tool (MAB-Seq) that can be broadly used in all biological contexts for epigenetics study involving identification and quantification of 5fC and 5caC at single base resolution.
 
Overall design Methylation-assisted bisulfite sequencing (MAB-Seq) of E14 embryonic stem cells (ESCs), Biotag ChIP-Seq of Tdg and Reduced representation Bisulfite Sequencing (RRBS) in E14 ESCs.
 
Contributor(s) Neri F, Incarnato D, Oliviero S
Citation(s) 25660018
Submission date Mar 06, 2014
Last update date Aug 09, 2017
Contact name Francesco Neri
E-mail francesco.neri@hugef-torino.org
Organization name HuGeF
Street address Via Nizza 52
City Torino
State/province Italy
ZIP/Postal code 10126
Country Italy
 
Platforms (1)
GPL16173 Illumina HiScanSQ (Mus musculus)
Samples (6)
GSM1341316 RRBS_shCtr
GSM1341317 RRBS_shTet1/2
GSM1341318 RRBS_shDnmt1a
This SubSeries is part of SuperSeries:
GSE55660 Single base resolution analysis of 5-formyl and 5-carboxyl cytosine reveals the actual promoter DNA methylation dynamics in embryonic stem cells
Relations
BioProject PRJNA240311
SRA SRP039505

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
GSE55659_RAW.tar 27.3 Mb (http)(custom) TAR (of BED)
Raw data are available in SRA
Processed data provided as supplementary file

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