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Modulation of TET2 expression and 5-methylcytosine oxidation by the CXXC domain protein IDAX

ABSTRACT: Idax/Cxxc4 is the CXXC domain protein that preferentially binds unmethylated CpG sites in vitro. By performing genome-wide mapping of Idax/Cxxc4, we report here that Idax is preferentially enriched in CpG-rich regions in genome including the promoters containing CpG islands. ChIP-seq binding site detection of Myc-Idax and Myc-IdaxDBM over cells expressing an empty vector in stable HEK293T cell lines; two replicates per condition (2x ChIP Myc-Idax, 2x ChIP Myc-IdaxDBM, 2xChIP empty vector)

ORGANISM(S): Homo sapiens

SUBMITTER: Lukas Chavez

PROVIDER: E-GEOD-42958 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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RNA-seq of HEK293T cells overexpressing TET1-FL or TET1-ALT

Project description:TET1 oxidizes methylated cytosine into 5-hydroxymethylcytosine, resulting in regulation of DNA methylation and gene expression. Full length TET1 (TET1-FL) has a CXXC domain that binds to unmethylated stretches of CpG dinucleotides known as CpG islands (CGIs). This CXXC domain allows TET1 to protect CGIs from aberrant methylation but it also limits its ability to regulate genes outside of CGIs. Here we report a novel isoform of TET1 (TET1-ALT) that has a unique transcription start site from an alternate promoter in intron 2, yielding a protein with a unique translation start site. Importantly, TET1-ALT lacks the CXXC domain but retains the catalytic domain. To identify the gene expression targets of TET1-ALT and to compare them to the gene expression targets of TET1-FL, we performed RNA-seq on HEK293T cells that overexpress either Empty Vector (Control), TET1-FL or TET1-ALT.

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Bone morphogenetic protein-7 is a MYC target with pro-survival functions in childhood medulloblastoma

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