Comment[ArrayExpressAccession] E-GEOD-46111 MAGE-TAB Version 1.1 Public Release Date 2013-04-18 Investigation Title Genome-wide analysis reveals TET- and TDG-mediated 5-methylcytosine oxidation dynamics [MeDIP-Seq] Comment[Submitted Name] Genome-wide analysis reveals TET- and TDG-mediated 5-methylcytosine oxidation dynamics [MeDIP-Seq] Experiment Description Ten-eleven translocation (Tet) family of DNA dioxygenases converts 5-methylcytosine (5mC) into 5-hydroxymethylcytosine (5hmC), 5-formylcytosine (5fC), and 5- carboxylcytosine (5caC) through iterative oxidation reactions. While 5mC and 5hmC are relatively abundant, 5fC and 5caC are at very low levels in the mammalian genome. Thymine DNA glycosylase (TDG) and base excision repair (BER) pathways can actively remove 5fC/5caC to regenerate unmethylated cytosine, but it is unclear to what extent and at which part of the genome such active demethylation processes take place. Here, we have performed high-throughput sequencing analysis of 5mC/5hmC/5fC/5caC- enriched DNA using modification-specific antibodies and generated genome-wide distribution maps of these cytosine modifications in wild-type and Tdg-deficient mouse embryonic stem cells (ESCs). We observe that the steady state 5fC and 5caC are preferentially detected at repetitive sequences in wild-type mouse ESCs. Depletion of TDG causes marked accumulation of 5fC and 5caC at a large number of distal gene regulatory elements and transcriptionally repressed/poised gene promoters, suggesting that Tet/TDG-dependent dynamic cycling of 5mC oxidation states may be involved in regulating the function of these regions. Thus, comprehensive mapping of 5mC oxidation and BER pathway activity in the mammalian genome provides a promising approach for better understanding of biological roles of DNA methylation and demethylation dynamics in development and diseases. In this dataset, we include the DIP-seq data of 5mC, 5hmC, 5fC and 5caC in both control and Tdg knockdown mouse embryonic stem cells. Term Source Name ArrayExpress EFO Term Source File http://www.ebi.ac.uk/arrayexpress/ http://www.ebi.ac.uk/efo/efo.owl Person Last Name Zhang Shen Wu Diep Yamaguchi D'Alessio Fung Zhang Zhang Person First Name Yi Li Hao Dinh Shinpei Ana Alan Kun Yi Person Mid Initials C Person Email geo@ncbi.nlm.nih.gov Person Affiliation HHMI/Boston Children's Hospital/Harvard Medical School Person Address HHMI/Boston Children's Hospital/Harvard Medical School, 200 Longwood Ave, Boston, USA Person Roles submitter Protocol Name P-GSE46111-5 P-GSE46111-4 P-GSE46111-1 P-GSE46111-3 P-GSE46111-2 Protocol Description Basecalls were performed using OLB-1.8.0 Sequenced reads were de-multiplexed, trimmed and mapped to mm9 whole genome using bowtie v0.12.7 Peak calling were performed using MACS 1.4.2 Genome_build: mm9 Supplementary_files_format_and_content: wiggle files (IgG signal subtracted; scores represent tag numbers per 10 million reads) Basecalls were performed using CASAVA version v.1.8.2 Sequenced reads were de-multiplexed, trimmed and mapped to mm9 whole genome using bowtie v0.12.7 Peak calling were performed using MACS 1.4.2 Genome_build: mm9 Supplementary_files_format_and_content: wiggle files (IgG signal subtracted; scores represent tag numbers per 10 million reads) Around 1x10^5 ES cells/well in 24-well plates are infected with lentiviral vectors at 10 MOI. 48 hours after transduction, puromycin (2ug/ml) is added to the medium for selecting transduced cells. Libraries were prepared using NEBNext DNA Library Prep Master Mix Set for Illumina (NEB) following manufacture's instructions. E14 mESCs are cultured on the 0.1% gelatin coated plates in the DMEM medium (Sigma) supplemented with 100U/ml penicillin/streptomycin, 15% fetal bovine serum (Sigma), 1x nonessential amino acid, 1x sodium pyruvate, 1x GlutaMax, 1x beta-mercaptoethanol (Invitrogen) and 1000 units/ml leukemia inhibitory factor (ESGRO, EMD Millipore). Protocol Type normalization data transformation protocol normalization data transformation protocol sample treatment protocol nucleic acid library construction protocol growth protocol Experimental Factor Name CHIP ANTIBODY GENOTYPE Experimental Factor Type chip antibody genotype Publication Title Genome-wide analysis reveals TET- and TDG-dependent 5-methylcytosine oxidation dynamics. Publication Author List Shen L, Wu H, Diep D, Yamaguchi S, D'Alessio AC, Fung HL, Zhang K, Zhang Y PubMed ID 23602152 Publication DOI 10.1016/j.cell.2013.04.002 Comment[SecondaryAccession] GSE46111 Comment[GEOReleaseDate] 2013-04-18 Comment[ArrayExpressSubmissionDate] 2013-04-16 Comment[GEOLastUpdateDate] 2013-05-21 Comment[AEExperimentType] methylation profiling by high throughput sequencing Comment[SecondaryAccession] SRP021133 Comment[SequenceDataURI] http://www.ebi.ac.uk/ena/data/view/SRR828756-SRR828779 SDRF File E-GEOD-46111.sdrf.txt