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Cell Stem Cell. 2018 Nov 1;23(5):727-741.e9. doi: 10.1016/j.stem.2018.08.016. Epub 2018 Sep 13.

Transcription Factors Drive Tet2-Mediated Enhancer Demethylation to Reprogram Cell Fate.

Author information

1
Gene Regulation, Stem Cells and Cancer Program, Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology (BIST), Barcelona 08003, Spain. Electronic address: joseluis.sardina@crg.eu.
2
Institut de Biologie de l'Ecole Normale Supérieure (IBENS), Paris Sciences & Lettres Université, CNRS UMR8197, INSERM U1024, Paris 75005, France.
3
Gene Regulation, Stem Cells and Cancer Program, Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology (BIST), Barcelona 08003, Spain.
4
Department of Molecular Biology, Massachusetts General Hospital, Harvard Medical School, 185 Cambridge Street, Boston, MA 02114, USA; Center for Regenerative Medicine, Massachusetts General Hospital, Harvard Medical School, 185 Cambridge Street, Boston, MA 02114, USA; Cancer Center, Massachusetts General Hospital, Harvard Medical School, 185 Cambridge Street, Boston, MA 02114, USA; Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA 02138, USA; Harvard Stem Cell Institute, 1350 Massachusetts Avenue, Cambridge, MA 02138, USA.
5
Universitat Pompeu Fabra (UPF), Barcelona 08003, Spain; CNAG-CRG, Centro Nacional de Análisis Genómico, Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology (BIST), Baldiri i Reixac 4, Barcelona 08028, Spain.
6
Gene Regulation, Stem Cells and Cancer Program, Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology (BIST), Barcelona 08003, Spain; Universitat Pompeu Fabra (UPF), Barcelona 08003, Spain.
7
Gene Regulation, Stem Cells and Cancer Program, Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology (BIST), Barcelona 08003, Spain; Universitat Pompeu Fabra (UPF), Barcelona 08003, Spain. Electronic address: thomas.graf@crg.eu.

Abstract

Here, we report DNA methylation and hydroxymethylation dynamics at nucleotide resolution using C/EBPα-enhanced reprogramming of B cells into induced pluripotent cells (iPSCs). We observed successive waves of hydroxymethylation at enhancers, concomitant with a decrease in DNA methylation, suggesting active demethylation. Consistent with this finding, ablation of the DNA demethylase Tet2 almost completely abolishes reprogramming. C/EBPα, Klf4, and Tfcp2l1 each interact with Tet2 and recruit the enzyme to specific DNA sites. During reprogramming, some of these sites maintain high levels of 5hmC, and enhancers and promoters of key pluripotency factors become demethylated as early as 1 day after Yamanaka factor induction. Surprisingly, methylation changes precede chromatin opening in distinct chromatin regions, including Klf4 bound sites, revealing a pioneer factor activity associated with alternation in DNA methylation. Rapid changes in hydroxymethylation similar to those in B cells were also observed during compound-accelerated reprogramming of fibroblasts into iPSCs, highlighting the generality of our observations.

KEYWORDS:

DNA hydroxymethylation; DNA methylation; Tet enzymes; active demethylation; cell fate decisions; cell reprogramming; epigenetics; iPSCs

PMID:
30220521
DOI:
10.1016/j.stem.2018.08.016

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