DNA methylation directs genomic localization of Mbd2 and Mbd3 in embryonic stem cells

Cytosine methylation is an epigenetic and regulatory mark that functions in part through recruitment of chromatin remodeling complexes containing methyl-CpG binding domain (MBD) proteins. Two MBD proteins, Mbd2 and Mbd3, were previously shown to bind methylated or hydroxymethylated DNA, respectively; however, both of these findings have been disputed. Here, we investigated this controversy using experimental approaches and re-analysis of published data and find no evidence for methylation-independent functions of Mbd2 or Mbd3. We show that chromatin localization of Mbd2 and Mbd3 is highly overlapping and, unexpectedly, we find Mbd2 and Mbd3 are interdependent for chromatin association. Further investigation reveals that both proteins are required for normal levels of cytosine methylation and hydroxymethylation in murine embryonic stem cells. Furthermore, Mbd2 and Mbd3 regulate overlapping sets of genes that are also regulated by DNA methylation/hydroxymethylation factors. These findings reveal an interdependent regulatory mechanism mediated by the DNA methylation machinery and its readers.

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Reduced Genomic Cytosine Methylation and Defective Cellular Differentiation in Embryonic Stem Cells Lacking CpG Binding Protein

Molecular and Cellular Biology ◽

10.1128/mcb.25.12.4881-4891.2005 ◽

2005 ◽

Vol 25 (12) ◽

pp. 4881-4891 ◽

Cited By ~ 61

Author(s):

Diana L. Carlone ◽

Jeong-Heon Lee ◽

Suzanne R. L. Young ◽

Erika Dobrota ◽

Jill Sergesketter Butler ◽

...

Keyword(s):

Stem Cells ◽

Embryonic Stem Cells ◽

Dna Methyltransferase ◽

Cellular Differentiation ◽

Cytosine Methylation ◽

Epigenetic Modification ◽

Binding Protein ◽

Embryonic Stem ◽

Growth Media ◽

Methyltransferase Activity

ABSTRACT Cytosine methylation at CpG dinucleotides is a critical epigenetic modification of mammalian genomes. CpG binding protein (CGBP) exhibits a unique DNA-binding specificity for unmethylated CpG motifs and is essential for early murine development. Embryonic stem cell lines deficient for CGBP were generated to further examine CGBP function. CGBP − / − cells are viable but show an increased rate of apoptosis and are unable to achieve in vitro differentiation following removal of leukemia inhibitory factor from the growth media. Instead, CGBP − / − embryonic stem cells remain undifferentiated as revealed by persistent expression of the pluripotent markers Oct4 and alkaline phosphatase. CGBP − / − cells exhibit a 60 to 80% decrease in global cytosine methylation, including hypo-methylation of repetitive elements, single-copy genes, and imprinted genes. Total DNA methyltransferase activity is reduced by 30 to 60% in CGBP − / − cells, and expression of the maintenance DNA methyltransferase 1 protein is similarly reduced. However, de novo DNA methyltransferase activity is normal. Nearly all aspects of the pleiotropic CGBP − / − phenotype are rescued by introduction of a CGBP expression vector. Hence, CGBP is essential for normal epigenetic modification of the genome by cytosine methylation and for cellular differentiation, consistent with the requirement for CGBP during early mammalian development.

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DNA methylation on N6-adenine in mammalian embryonic stem cells

Nature ◽

10.1038/nature17640 ◽

2016 ◽

Vol 532 (7599) ◽

pp. 329-333 ◽

Cited By ~ 291

Author(s):

Tao P. Wu ◽

Tao Wang ◽

Matthew G. Seetin ◽

Yongquan Lai ◽

Shijia Zhu ◽

...

Keyword(s):

Dna Methylation ◽

Stem Cells ◽

Embryonic Stem Cells ◽

Embryonic Stem

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DAXX safeguards pericentromeric heterochromatin formation in embryonic stem cells

10.1101/2021.04.28.441827 ◽

2021 ◽

Author(s):

Antoine Canat ◽

Adeline Veillet ◽

Robert Illingworth ◽

Emmanuelle Fabre ◽

Pierre Therizols

Keyword(s):

Dna Methylation ◽

Stem Cells ◽

Dna Damage ◽

Embryonic Stem Cells ◽

Embryonic Stem ◽

Pericentric Heterochromatin ◽

Dna Demethylation ◽

Pericentromeric Heterochromatin ◽

Major Satellite ◽

Heterochromatin Formation

AbstractDNA methylation is essential for heterochromatin formation and repression of DNA repeat transcription, both of which are essential for genome integrity. Loss of DNA methylation is associated with disease, including cancer, but is also required for development. Alternative pathways to maintain heterochromatin are thus needed to limit DNA damage accumulation. Here, we find that DAXX, an H3.3 chaperone, protects pericentromeric heterochromatin and is essential for embryonic stem cells (ESCs) maintenance in the ground-state of pluripotency. Upon DNA demethylation-mediated damage, DAXX relocalizes to pericentromeric regions, and recruits PML and SETDB1, thereby promoting heterochromatin formation. In the absence of DAXX, the 3D-architecture and physical properties of pericentric heterochromatin are disrupted, resulting in derepression of major satellite DNA. Using epigenome editing tools, we demonstrate that H3.3, and specifically H3.3K9 modification, directly contribute to maintaining pericentromeric chromatin conformation. Altogether, our data reveal that DAXX and H3.3 unite DNA damage response and heterochromatin maintenance in ESCs.

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BAF Complex in Embryonic Stem Cells and Early Embryonic Development

Stem Cells International ◽

10.1155/2021/6668866 ◽

2021 ◽

Vol 2021 ◽

pp. 1-7

Author(s):

Heyao Zhang ◽

Xuepeng Wang ◽

Jingsheng Li ◽

Ronghua Shi ◽

Ying Ye

Keyword(s):

Stem Cells ◽

Embryonic Stem Cells ◽

Embryonic Development ◽

Embryonic Stem ◽

Early Embryonic Development ◽

Mouse Escs ◽

Baf Complex ◽

Pluripotency Gene ◽

Chromatin Remodeling Complexes ◽

Gene Regulatory

Embryonic stem cells (ESCs) can self-renew indefinitely and maintain their pluripotency status. The pluripotency gene regulatory network is critical in controlling these properties and particularly chromatin remodeling complexes. In this review, we summarize the research progresses of the functional and mechanistic studies of BAF complex in mouse ESCs and early embryonic development. A discussion of the mechanistic bases underlying the distinct phenotypes upon the deletion of different BAF subunits in ESCs and embryos will be highlighted.

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