GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
Series GSE56821 Query DataSets for GSE56821
Status Public on Dec 31, 2015
Title Genome-wide mapping of Tet3FL in neural progeniter cells
Organism Mus musculus
Experiment type Genome binding/occupancy profiling by high throughput sequencing
Summary We report that the 5-methylcytosine oxidase Tet3 exists as three isoforms and characterized the full-length isoform containing an N-terminal CXXC domain (Tet3FL). Presence of the CXXC domain reduces Tet3’s enzymatic activity. This CXXC domain binds not only to unmethylated CpGs but its highest affinity is towards 5-carboxylcytosine (5caC). We determined the structure of the CXXC domain - 5caC-DNA complex and showed that disruption of the CXXC-5caC interaction leads to enhanced Tet3 activity. Mapping of genomic binding sites of Tet3FL in neuronal cells shows that Tet3FL is targeted to transcription start sites of genes involved in lysosome function, mRNA processing and key genes of the base excision repair pathway. Our data suggest that the CXXC domain of Tet3FL restricts the protein to a set of unmethylated or 5caC-containing CpG islands and that Tet3FL functions both as a reader of 5caC and as a regulator of 5caC removal by base excision repair.
Overall design Examination of genomic binding sites of Tet3FL in neural progeniter cells at day 2 upon neural differentiation and in E15.5 embryonic mouse brain.
Contributor(s) Jin S, Wu X, Pfeifer GP
Citation(s) 26774490
Submission date Apr 15, 2014
Last update date May 15, 2019
Contact name Xiwei Wu
Organization name City of Hope National Medical Center
Department Computational and Quantitative Medicine
Street address 1500 E. Duarte Rd.
City Duarte
State/province CA
ZIP/Postal code 91010
Country USA
Platforms (1)
GPL17021 Illumina HiSeq 2500 (Mus musculus)
Samples (10)
GSM1369880 NP-2d Tet3FL_ChIPSeq
GSM1369881 NP-2d IgG_ChIPSeq
GSM1565736 Brain Tet3FL_ChIPSeq rep1
BioProject PRJNA244682
SRA SRP041193

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
GSE56821_RAW.tar 6.3 Gb (http)(custom) TAR (of BEDGRAPH)
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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