TET proteins safeguard bivalent promoters from de novo methylation in human embryonic stem cells

AbstractCoordinated programs of gene expression drive brain development. It is unclear which transcriptional programs, in which cell-types, are affected in neuropsychiatric disorders such as schizophrenia. Here we integrate human genetics with transcriptomic data from differentiation of human embryonic stem cells into cortical excitatory neurons. We identify transcriptional programs expressed during early neurogenesis in vitro and in human foetal cortex that are down-regulated in DLG2−/− lines. Down-regulation impacted neuronal differentiation and maturation, impairing migration, morphology and action potential generation. Genetic variation in these programs is associated with neuropsychiatric disorders and cognitive function, with associated variants predominantly concentrated in loss-of-function intolerant genes. Neurogenic programs also overlap schizophrenia GWAS enrichment previously identified in mature excitatory neurons, suggesting that pathways active during prenatal cortical development may also be associated with mature neuronal dysfunction. Our data from human embryonic stem cells, when combined with analysis of available foetal cortical gene expression data, de novo rare variants and GWAS statistics for neuropsychiatric disorders and cognition, reveal a convergence on transcriptional programs regulating excitatory cortical neurogenesis.

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De novo DNA cytosine methyltransferase activities in mouse embryonic stem cells

Development ◽

10.1242/dev.122.10.3195 ◽

1996 ◽

Vol 122 (10) ◽

pp. 3195-3205 ◽

Cited By ~ 2

Author(s):

H. Lei ◽

S.P. Oh ◽

M. Okano ◽

R. Juttermann ◽

K.A. Goss ◽

...

Keyword(s):

Stem Cells ◽

Embryonic Stem Cells ◽

Mammalian Cells ◽

Dna Methyltransferase ◽

De Novo ◽

Embryonic Stem ◽

Cytosine Methyltransferase ◽

Methyl Cytosine ◽

Methylation Activity ◽

De Novo Methylation

It has been a controversial issue as to how many DNA cytosine methyltransferase mammalian cells have and whether de novo methylation and maintenance methylation activities are encoded by a single gene or two different genes. To address these questions, we have generated a null mutation of the only known mammalian DNA methyltransferase gene through homologous recombination in mouse embryonic stem cells and found that the development of the homozygous embryos is arrested prior to the 8-somite stage. Surprisingly, the null mutant embryonic stem cells are viable and contain low but stable levels of methyl cytosine and methyltransferase activity, suggesting the existence of a second DNA methyltransferase in mammalian cells. Further studies indicate that de novo methylation activity is not impaired by the mutation as integrated provirus DNA in MoMuLV-infected homozygous embryonic stem cells become methylated at a similar rate as in wild-type cells. Differentiation of mutant cells results in further reduction of methyl cytosine levels, consistent with the de novo methylation activity being down regulated in differentiated cells. These results provide the first evidence that an independently encoded DNA methyltransferase is present in mammalian cells which is capable of de novo methylating cellular and viral DNA in vivo.

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A DNA signal from the Thy-1 gene defines de novo methylation patterns in embryonic stem cells.

Molecular and Cellular Biology ◽

10.1128/mcb.10.8.4396 ◽

1990 ◽

Vol 10 (8) ◽

pp. 4396-4400 ◽

Cited By ~ 63

Author(s):

M Szyf ◽

G Tanigawa ◽

P L McCarthy

Keyword(s):

Stem Cells ◽

Embryonic Stem Cells ◽

Dna Sequences ◽

De Novo ◽

Cpg Island ◽

Embryonic Stem ◽

Cpg Dinucleotides ◽

Somatic Tissues ◽

Methylation Patterns ◽

De Novo Methylation

Although DNA can be extensively methylated de novo when introduced into pluripotent cells, the CpG island in the Thy-1 gene does not become methylated either in the mouse embryo or in embryonic stem cells. A 214-base-pair region near the promoter of the Thy-1 gene protects itself as well as heterologous DNA sequences from de novo methylation. We propose that this nucleotide sequence is representative of a class of important signals that limits de novo methylation in the embryo and establishes the pattern of hypomethylated CpG dinucleotides found in somatic tissues.

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A DNA signal from the Thy-1 gene defines de novo methylation patterns in embryonic stem cells

Trends in Genetics ◽

10.1016/0168-9525(90)90223-s ◽

1990 ◽

Vol 6 ◽

pp. 279

Keyword(s):

Stem Cells ◽

Embryonic Stem Cells ◽

De Novo ◽

Embryonic Stem ◽

Methylation Patterns ◽

De Novo Methylation

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DNMT3B shapes the mCA landscape and regulates mCG for promoter bivalency in human embryonic stem cells

Nucleic Acids Research ◽

10.1093/nar/gkz520 ◽

2019 ◽

Vol 47 (14) ◽

pp. 7460-7475 ◽

Cited By ~ 4

Author(s):

Hong Kee Tan ◽

Chan-Shuo Wu ◽

Jia Li ◽

Zi Hui Tan ◽

Jordan R Hoffman ◽

...

Keyword(s):

Stem Cells ◽

Embryonic Stem Cells ◽

Human Embryonic Stem Cells ◽

Dna Methyltransferase ◽

De Novo ◽

Embryonic Stem ◽

Distribution Profile ◽

Pwwp Domain ◽

The Common ◽

On Chip

Abstract DNMT3B is known as a de novo DNA methyltransferase. However, its preferential target sites for DNA methylation are largely unknown. Our analysis on ChIP-seq experiment in human embryonic stem cells (hESC) revealed that DNMT3B, mCA and H3K36me3 share the same genomic distribution profile. Deletion of DNMT3B or its histone-interacting domain (PWWP) demolished mCA in hESCs, suggesting that PWWP domain of DNMT3B directs the formation of mCA landscape. In contrast to the common presumption that PWWP guides DNMT3B-mediated mCG deposition, we found that deleting PWWP does not affect the mCG landscape. Nonetheless, DNMT3B knockout led to the formation of 2985 de novo hypomethylated regions at annotated promoter sites. Upon knockout, most of these promoters gain the bivalent marks, H3K4me3 and H3K27me3. We call them spurious bivalent promoters. Gene ontology analysis associated spurious bivalent promoters with development and cell differentiation. Overall, we found the importance of DNMT3B for shaping the mCA landscape and for maintaining the fidelity of the bivalent promoters in hESCs.

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Novel Cell Lines Isolated From Mouse Embryonic Stem Cells Exhibiting De Novo Methylation of the E-Cadherin Promoter

Stem Cells ◽

10.1002/stem.1790 ◽

2014 ◽

Vol 32 (11) ◽

pp. 2869-2879 ◽

Cited By ~ 4

Author(s):

Kate Hawkins ◽

Maria Keramari ◽

Francesca Soncin ◽

Joe M. Segal ◽

Lisa Mohamet ◽

...

Keyword(s):

Stem Cells ◽

Embryonic Stem Cells ◽

Cell Lines ◽

De Novo ◽

Embryonic Stem ◽

Mouse Embryonic Stem Cells ◽

De Novo Methylation ◽

E Cadherin

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A DNA signal from the Thy-1 gene defines de novo methylation patterns in embryonic stem cells

Molecular and Cellular Biology ◽

10.1128/mcb.10.8.4396-4400.1990 ◽

1990 ◽

Vol 10 (8) ◽

pp. 4396-4400

Author(s):

M Szyf ◽

G Tanigawa ◽

P L McCarthy

Keyword(s):

Stem Cells ◽

Embryonic Stem Cells ◽

Dna Sequences ◽

De Novo ◽

Cpg Island ◽

Embryonic Stem ◽

Cpg Dinucleotides ◽

Somatic Tissues ◽

Methylation Patterns ◽

De Novo Methylation

Although DNA can be extensively methylated de novo when introduced into pluripotent cells, the CpG island in the Thy-1 gene does not become methylated either in the mouse embryo or in embryonic stem cells. A 214-base-pair region near the promoter of the Thy-1 gene protects itself as well as heterologous DNA sequences from de novo methylation. We propose that this nucleotide sequence is representative of a class of important signals that limits de novo methylation in the embryo and establishes the pattern of hypomethylated CpG dinucleotides found in somatic tissues.

Download Full-text