E-GEOD-50761 - Targeted DNA demethylation using TALE-TET1 fusion proteins

Status
Released on 23 September 2013, last updated on 25 November 2013
Organism
Homo sapiens
Samples (435)
Protocols (4)
Description
Recent large-scale studies have defined genomewide, cell type-specific patterns of DNA methylation, a modification known to be important for regulating gene expression in both normal development and disease states. However, determining the functional significance of specific methylation events remains a challenging problem due to the current lack of targeted methodologies for removing these modifications. Here we describe an approach for efficient targeted demethylation of specific CpGs in human cells using fusions of engineered transcription activator-like effector (TALE) repeat arrays and the TET1 hydroxylase catalytic domain. Using these TALE-TET1 fusions, we demonstrate that modification of certain critical methylated promoter CpG positions can be associated with substantial increases in endogenous human gene expression. Our results delineate a general strategy for defining the functional significance of specific CpG methylation marks in the context of endogenous gene loci and validate new programmable DNA demethylation reagents with broad utility for research and potential therapeutic applications. Bisulfite sequencing of three different loci in three different cell lines (Klf4 in K562s, HBB in K562s and RHOXF2 in 293s and HeLas. Biological triplicates of all samples and controls (off-target and GFP controls).
Experiment type
methylation profiling by high throughput sequencing 
Contacts
MINSEQE
Exp. designProtocolsVariablesProcessedSeq. reads
Files
Investigation descriptionE-GEOD-50761.idf.txt
Sample and data relationshipE-GEOD-50761.sdrf.txt
Additional data (1)E-GEOD-50761.additional.1.zip
Links