The N-terminus of histone H3 is required for de novo DNA methylation in chromatin

DNA methylation (DNAme) profiling is used to establish specific biomarkers to improve the diagnosis of patients with inherited neurodevelopmental disorders and to guide mutation screening. In the specific case of mendelian disorders of the epigenetic machinery, it also provides the basis to infer mechanistic aspects with regard to DNAme determinants and interplay between histone and DNAme that apply to humans. Here, we present comparative methylomes from patients with mutations in the de novo DNA methyltransferases DNMT3A and DNMT3B, in their catalytic domain or their N-terminal parts involved in reading histone methylation, or in histone H3 lysine (K) methylases NSD1 or SETD2 (H3 K36) or KMT2D/MLL2 (H3 K4). We provide disease-specific DNAme signatures and document the distinct consequences of mutations in enzymes with very similar or intertwined functions, including at repeated sequences and imprinted loci. We found that KMT2D and SETD2 germline mutations have little impact on DNAme profiles. In contrast, the overlapping DNAme alterations downstream of NSD1 or DNMT3 mutations underlines functional links, more specifically between NSD1 and DNMT3B at heterochromatin regions or DNMT3A at regulatory elements. Together, these data indicate certain discrepancy with the mechanisms described in animal models or the existence of redundant or complementary functions unforeseen in humans.

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DNA Hypermethylation in Drosophila melanogaster Causes Irregular Chromosome Condensation and Dysregulation of Epigenetic Histone Modifications

Molecular and Cellular Biology ◽

10.1128/mcb.23.7.2577-2586.2003 ◽

2003 ◽

Vol 23 (7) ◽

pp. 2577-2586 ◽

Cited By ~ 28

Author(s):

Frank Weissmann ◽

Inhua Muyrers-Chen ◽

Tanja Musch ◽

Dirk Stach ◽

Manfred Wiessler ◽

...

Keyword(s):

Dna Methylation ◽

Drosophila Melanogaster ◽

Genomic Dna ◽

Cell Cycle Progression ◽

De Novo ◽

Histone H3 ◽

Experimental System ◽

Chromosome Condensation ◽

Dna Hypermethylation ◽

Developmental Defects

ABSTRACT The level of genomic DNA methylation plays an important role in development and disease. In order to establish an experimental system for the functional analysis of genome-wide hypermethylation, we overexpressed the mouse de novo methyltransferase Dnmt3a in Drosophila melanogaster. These flies showed severe developmental defects that could be linked to reduced rates of cell cycle progression and irregular chromosome condensation. In addition, hypermethylated chromosomes revealed elevated rates of histone H3-K9 methylation and a more restricted pattern of H3-S10 phosphorylation. The developmental and chromosomal defects induced by DNA hypermethylation could be rescued by mutant alleles of the histone H3-K9 methyltransferase gene Su(var)3-9. This mutation also resulted in a significantly decreased level of genomic DNA methylation. Our results thus uncover the molecular consequences of genomic hypermethylation and demonstrate a mutual interaction between DNA methylation and histone methylation.

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Dynamic Evolution of De Novo DNA Methyltransferases in Rodent and Primate Genomes

Molecular Biology and Evolution ◽

10.1093/molbev/msaa044 ◽

2020 ◽

Vol 37 (7) ◽

pp. 1882-1892 ◽

Cited By ~ 3

Author(s):

Antoine Molaro ◽

Harmit S Malik ◽

Deborah Bourc’his

Keyword(s):

Dna Methylation ◽

De Novo ◽

Mammalian Species ◽

Dna Methyltransferases ◽

Functional Domain ◽

Last Common Ancestor ◽

Diversifying Selection ◽

Evolutionary Forces ◽

N Terminus ◽

Muroid Rodents

Abstract Transcriptional silencing of retrotransposons via DNA methylation is paramount for mammalian fertility and reproductive fitness. During germ cell development, most mammalian species utilize the de novo DNA methyltransferases DNMT3A and DNMT3B to establish DNA methylation patterns. However, many rodent species deploy a third enzyme, DNMT3C, to selectively methylate the promoters of young retrotransposon insertions in their germline. The evolutionary forces that shaped DNMT3C’s unique function are unknown. Using a phylogenomic approach, we confirm here that Dnmt3C arose through a single duplication of Dnmt3B that occurred ∼60 Ma in the last common ancestor of muroid rodents. Importantly, we reveal that DNMT3C is composed of two independently evolving segments: the latter two-thirds have undergone recurrent gene conversion with Dnmt3B, whereas the N-terminus has instead evolved under strong diversifying selection. We hypothesize that positive selection of Dnmt3C is the result of an ongoing evolutionary arms race with young retrotransposon lineages in muroid genomes. Interestingly, although primates lack DNMT3C, we find that the N-terminus of DNMT3A has also evolved under diversifying selection. Thus, the N-termini of two independent de novo methylation enzymes have evolved under diversifying selection in rodents and primates. We hypothesize that repression of young retrotransposons might be driving the recurrent innovation of a functional domain in the N-termini on germline DNMT3s in mammals.

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Dynamic evolution of de novo DNA methyltransferases in rodent and primate genomes

10.1101/786863 ◽

2019 ◽

Author(s):

Antoine Molaro ◽

Harmit S. Malik ◽

Deborah Bourc’his

Keyword(s):

Dna Methylation ◽

Gene Conversion ◽

De Novo ◽

Mammalian Species ◽

Dna Methyltransferases ◽

Functional Domain ◽

Last Common Ancestor ◽

Diversifying Selection ◽

Evolutionary Forces ◽

N Terminus

AbstractTranscriptional silencing of retrotransposons via DNA methylation is paramount for mammalian fertility and reproductive fitness. During germ cell development, most mammalian species utilize the de novo DNA methyltransferases DNMT3A and DNMT3B to establish DNA methylation patterns. However, many rodent species deploy a third enzyme, DNMT3C, to selectively methylate the promoters of young retrotransposon insertions in their germline. The evolutionary forces that shaped DNMT3C’s unique function are unknown. Using a phylogenomic approach, we confirm here that Dnmt3C arose through a single duplication of Dnmt3B that occurred between 45-71Mya in the last common ancestor of muroid rodents. Most importantly, we reveal that DNMT3C is composed of two independently evolving segments: the latter two-thirds has undergone recurrent gene conversion with Dnmt3B, whereas the N-terminus has not undergone gene conversion and has evolved under strong diversifying selection. We hypothesize that positive selection of Dnmt3C is the result on an ongoing evolutionary arms race with young retrotransposon lineages in muroid genomes. Interestingly, although primates lack DNMT3C, we find that the N-terminus of DNMT3A has also evolved under diversifying selection. Thus, the N-termini of two independent de novo DNMT enzymes have evolved under diversifying selection in rodents and primates. We hypothesize that repression of young retrotransposons might be driving the recurrent innovation of a functional domain in the N-termini on germline DNMTs in mammals.

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Chromatin Inactivation Precedes De Novo DNA Methylation during the Progressive Epigenetic Silencing of the RASSF1A Promoter

Molecular and Cellular Biology ◽

10.1128/mcb.25.10.3923-3933.2005 ◽

2005 ◽

Vol 25 (10) ◽

pp. 3923-3933 ◽

Cited By ~ 96

Author(s):

Maria Strunnikova ◽

Undraga Schagdarsurengin ◽

Astrid Kehlen ◽

James C. Garbe ◽

Martha R. Stampfer ◽

...

Keyword(s):

Dna Methylation ◽

Tumor Suppressor ◽

Epithelial Cells ◽

Dna Methyltransferase ◽

De Novo ◽

Mammary Epithelial Cells ◽

Time Window ◽

Cpg Island ◽

Histone H3 ◽

Mammary Epithelial

ABSTRACT Epigenetic inactivation of the RASSF1A tumor suppressor by CpG island methylation was frequently detected in cancer. However, the mechanisms of this aberrant DNA methylation are unknown. In the RASSF1A promoter, we characterized four Sp1 sites, which are frequently methylated in cancer. We examined the functional relationship between DNA methylation, histone modification, Sp1 binding, and RASSF1A expression in proliferating human mammary epithelial cells. With increasing passages, the transcription of RASSF1A was dramatically silenced. This inactivation was associated with deacetylation and lysine 9 trimethylation of histone H3 and an impaired binding of Sp1 at the RASSF1A promoter. In mammary epithelial cells that had overcome a stress-associated senescence barrier, a spreading of DNA methylation in the CpG island promoter was observed. When the RASSF1A-silenced cells were treated with inhibitors of DNA methyltransferase and histone deacetylase, binding of Sp1 and expression of RASSF1A reoccurred. In summary, we observed that histone H3 deacetylation and H3 lysine 9 trimethylation occur in the same time window as gene inactivation and precede DNA methylation. Our data suggest that in epithelial cells, histone inactivation may trigger de novo DNA methylation of the RASSF1A promoter and this system may serve as a model for CpG island inactivation of tumor suppressor genes.

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Epigenetic Mechanism of rRNA Gene Silencing: Temporal Order of NoRC-Mediated Histone Modification, Chromatin Remodeling, and DNA Methylation

Molecular and Cellular Biology ◽

10.1128/mcb.25.7.2539-2546.2005 ◽

2005 ◽

Vol 25 (7) ◽

pp. 2539-2546 ◽

Cited By ~ 115

Author(s):

Raffaella Santoro ◽

Ingrid Grummt

Keyword(s):

Dna Methylation ◽

Histone Modification ◽

Chromatin Remodeling ◽

Temporal Order ◽

De Novo ◽

Histone H3 ◽

Gene Promoter ◽

Rrna Gene ◽

Histone H4 ◽

Epigenetic Events

ABSTRACT Epigenetic control mechanisms silence about half of the rRNA genes in eukaryotes. Previous studies have demonstrated that recruitment of NoRC, a SNF2h-containing remodeling complex, silences rRNA gene transcription. NoRC mediates histone H4 deacetylation, histone H3-Lys9 dimethylation, and de novo DNA methylation, thus establishing heterochromatic features at the rRNA gene promoter. Here we show that inhibition of any of these activities alleviates NoRC-dependent silencing, indicating that these processes are intimately linked. We have studied the temporal order of epigenetic events at the rRNA gene promoter during gene silencing and demonstrate that recruitment of NoRC by TTF-I is a prerequisite for the deacetylation of histone H4 and the dimethylation of histone H3-Lys9. Inhibition of histone deacetylation prevents DNA methylation, while inhibition of DNA methylation does not affect histone modification. Importantly, ATP-dependent chromatin remodeling is required for methylation of a specific CpG dinucleotide within the upstream control element of the rRNA gene promoter, and this modification impairs preinitiation complex formation. The results of this study reveal a clear hierarchy of epigenetic events that control de novo DNA methylation and lead to silencing of RNA genes.

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