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Series GSE123110 Query DataSets for GSE123110
Status Public on Sep 23, 2019
Title TET3 regulates cellular identity and DNA methylation in neural progenitor cells
Organism Mus musculus
Experiment type Methylation profiling by high throughput sequencing
Summary TET enzymes oxidize 5-methylcytosine (5mC) into 5-hydroxymethylcytosine (5hmC), a process thought to be intermediary in an active DNA demethylation mechanism. Notably, 5hmC is highly abundant in the brain and in neuronal cells. Here we show that Tet3 is highly upregulated during neuronal differentiation and necessary to maintain silencing of pluripotency-associated genes in neural precursor cells (NPCs). Indeed, Tet3 knockdown (KD) in NPCs led to a significant increase in Oct4 and Nanog gene expression, with OCT4-positive cells appearing as cellular aggregates. Moreover, Tet3 KD led to a genome-scale loss of DNA methylation and hypermethylation of a small number of CpGs that are notably located at neurogenesis-related genes and at imprinting control regions (ICRs) of three imprinted genes (Peg10, Zrsr1 and Mcts2). Our results suggest that TET3 plays a pivotal role in maintaining neural stem cell identity and DNA methylation levels in neural precursor cells, and point to a non-catalytic role for TET3 in neural differentiation.
Overall design Mouse embryonic stem cells containing inducible shRNAs for Tet3 or a non-targetting control were differentiated to neural precursor cells. Knockdown was induced with doxyxycline for 5 days. Genomic DNA was extracted to generate oxRRBS libraries.
Contributor(s) Santiago M, Antunes C, Guedes M, Iacovino M, Kyba M, Reik W, Sousa N, Pinto L, Branco MR, Marques CJ
Citation(s) 31646359
Submission date Nov 29, 2018
Last update date Nov 04, 2019
Contact name Miguel R Branco
Organization name Blizard Institute
Street address 4 Newark Street
City London
ZIP/Postal code E1 2AT
Country United Kingdom
Platforms (1)
GPL19057 Illumina NextSeq 500 (Mus musculus)
Samples (8)
GSM3495886 NPC_shScr_BS-1
GSM3495887 NPC_shScr_BS-2
GSM3495888 NPC_shScr_oxBS-1
BioProject PRJNA507587
SRA SRP171135

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Supplementary file Size Download File type/resource
GSE123110_RAW.tar 68.4 Mb (http)(custom) TAR (of TXT)
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Raw data are available in SRA
Processed data provided as supplementary file

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