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Dnmt3L-histone H3 binding is necessary for male fertility and non-CG methylation

ABSTRACT: Patterns of DNA methylation are established during gametogenesis. The catalytically-inactive adaptor Dnmt3L is crucial to ensure this occurs correctly. In vitro, Dnmt3L binds to the N terminal tail of histone H3 but the function of this interaction during development is unknown. Here we show that Dnmt3L-histone H3 interaction is necessary for spermatogenesis. Mutant animals exhibit reduced fertility, defective methylation establishment at retrotransposons coupled with their reactivation and meiotic catastrophe. The spermatogonial stem cell pool is also defective, with mutant cells displaying marked changes in gene expression. Genome-wide methylation analysis reveals reductions in CG methylation as well as severe loss of non-CG methylation suggesting that non-CG methylation is specifically sensitive to the ability of Dnmt3L to bind histone H3.

ORGANISM(S): Mus musculus

PROVIDER: GSE58066 | GEO | 2015/01/14

SECONDARY ACCESSION(S): PRJNA248793

REPOSITORIES: GEO

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Dnmt3L-histone H3 binding is necessary for male fertility and non-CG methylation

Project description:Patterns of DNA methylation are established during gametogenesis. The catalytically-inactive adaptor Dnmt3L is crucial to ensure this occurs correctly. In vitro, Dnmt3L binds to the N terminal tail of histone H3 but the function of this interaction during development is unknown. Here we show that Dnmt3L-histone H3 interaction is necessary for spermatogenesis. Mutant animals exhibit reduced fertility, defective methylation establishment at retrotransposons coupled with their reactivation and meiotic catastrophe. The spermatogonial stem cell pool is also defective, with mutant cells displaying marked changes in gene expression. Genome-wide methylation analysis reveals reductions in CG methylation as well as severe loss of non-CG methylation suggesting that non-CG methylation is specifically sensitive to the ability of Dnmt3L to bind histone H3. MethylC-Seq of wild-type and Dnmt3LA/A 1dpp prospermatagonia

2015-01-14 | E-GEOD-58066 | biostudies-arrayexpress

Combinational effect of the ADD domains of DNMT3A and DNMT3L on DNA methylation landscapes in mouse germ cells [WGBS]

Project description:DNA methyltransferase 3A (DNMT3A) and DNA methyltransferase 3-Like (DNMT3L) form functional heterotetramers and ATRX-DNMT3-DNMT3L (ADD) domains, shared by both DNMT3A and DNMT3L, recognizes histone H3 tail unmethylated at lysine-4 (H3K4me0) to deposit DNA methylation properly in mammalian germ cells. However, the combinational and differential role of ADD domains of DNMT3A and DNMT3L in vivo has not been fully defined. Here we analyze both female and male germ cells derived from mouse with amino-acid substitutions in ADD domains of DNMT3A and/or DNMT3L that impair their domain function. Loss of either DNMT3A-ADD or DNMT3L-ADD domain function shows moderate reduction of global CG methylation level, but in different degree, in both germ cells. However, when both DNMT3A and DNMT3L lost their ADD domain functions, reduction of the global CG methylation level is much more severe and comparable with that of Dnmt3a/3L knockout germ cells. In contrast, such double mutant germ cells have thousands of genomic regions where non-CG methylation is aberrantly accumulated. These results highlight a critical role of the combinational function of ADD domains for the robust CG and non-CG methylation in germ cells.

2024-03-18 | GSE238227 | GEO

Combinational effect of the ADD domains of DNMT3A and DNMT3L on DNA methylation landscapes in mouse germ cells [RNA-seq]

2024-03-18 | GSE238226 | GEO

Non-CG methylation patterns shape the epigenetic landscape in Arabidopsis

Project description:DNA methylation occurs in both CG and non-CG sequence contexts. Non-CG methylation is abundant in plants, and is mediated by CHROMOMETHYLASE (CMT) and DOMAINS REARRANGED METHYLTRANSFERASE (DRM) proteins; however its roles remain poorly understood. Here we characterize the roles of non-CG methylation in Arabidopsis thaliana. We show that a poorly characterized methyltransferase, CMT2, is a functional methyltransferase in vitro and in vivo. CMT2 specifically binds histone H3 lysine 9 (H3K9) dimethylation and methylates non-CG cytosines at sites that are also regulated by H3K9 dimethylation. By generating different combinations of non-CG methylation mutants, we reveal the contributions and redundancies between each methyltransferase in DNA methylation patterning and in regulating transposable elements (TEs) and protein-coding genes. We also demonstrate extensive dependencies of small RNA accumulation and H3K9 methylation patterning on non-CG methylation, suggesting self-reinforcing mechanisms between these epigenetic factors. The results suggest that non-CG methylation patterns are critical in shaping the histone modification and small non-coding RNA landscapes.

2013-12-15 | GSE51304 | GEO

Non-CG methylation patterns shape the epigenetic landscape in Arabidopsis

2013-12-15 | E-GEOD-51304 | biostudies-arrayexpress

Mus musculus

Project description:Dnmt3L-histone H3 binding is necessary for male fertility and non-CG methylation

| PRJNA248793 | ENA

Histone H1 prevents non-CG methylation-mediated small RNA biogenesis in Arabidopsis heterochromatin

Project description:Functional genomic states are maintained by reinforcing chromatin interactions that exclude the components of other states. Plant heterochromatin features methylation of histone H3 at lysine 9 (H3K9me) and extensive DNA methylation. However, DNA methylation is also catalyzed by a mostly euchromatic small RNA-directed pathway (RdDM) thought to seek H3K9me. How RdDM is excluded from H3K9me-rich heterochromatin is unclear. Here we show that without histone H1, RdDM enters heterochromatin, preferentially at nucleosome linker DNA. Surprisingly, this does not require SHH1, the RdDM component that binds H3K9me. Furthermore, H3K9me is dispensable for RdDM, as is CG DNA methylation. Instead, we find that non-CG methylation is specifically required for small RNA biogenesis, and without H1 small RNA production quantitatively expands to non-CG methylated loci. Our results demonstrate that H1 enforces the separation of euchromatic and heterochromatic DNA methylation pathways by excluding the small RNA-generating branch of RdDM from non-CG methylated heterochromatin.

2021-12-01 | GSE179796 | GEO

DNA methylation changes in Dnmt3L-deficient mouse embryonic stem cells (mESCs)

Project description:We used RRBS to analyze DNA methylation in mESC lines deficient for maternal Dnmt3L (Dnmt3L mKO), zygotic Dnmt3L (Dnmt3L KO), and both maternal and zygotic Dnmt3L (Dnmt3L mzKO). Compared to wild-type (WT) mESCs, Dnmt3L mKO mESCs exhibit severe loss of methylation at imprinted loci but no changes in global DNA methylation, Dnmt3L KO mESCs exhibit moderate loss of methylation at many Dnmt3a target regions but do not affect methylation at imprinted loci, and Dnmt3L mzKO mESCs exhibit combined changes of mKO and KO cells, with severe loss of methylation at imprinted loci and moderate loss of methylation at Dnmt3a target regions.

2018-10-04 | GSE116489 | GEO

Ectopic targeting of CG DNA methylation in Arabidopsis with the bacterial SssI methyltransferase.

Project description:Targeting of epigenetic marks like DNA methylation to specific loci to manipulate gene expression is important in both basic research and in crop plant engineering. However, the extent to which targeted DNA methylation can be heritable is unknown. Here, we show that targeting the CG-specific methyltransferase M.SssI (SssI) from Spiroplasma sp. strain MQ1 with an artificial zinc finger (ZF) protein can establish heritable CG methylation and silencing of the targeted loci in Arabidopsis. This occurs even in the absence of a functional RNA-directed DNA methylation pathway, which is usually required for de novo methylation. In addition to the locus-specific targeted CG methylation, we observed widespread ectopic CG methylation throughout the genome that was highly heritable over generations, even in the absence of the effector transgene. A comparison with other epigenetic features showed that this ectopic methylation occurred preferentially at less open chromatin regions that were lacking in positive epigenetic histone marks. Although ectopic CG methylation was highly enriched over gene body regions, it showed little effect on transcription of these genes. However, we observed a mild but significant reduction in the histone variant H2A.Z and H3K27me3 over genes with ectopic CG methylation. These results outline general principals of the interaction of CG methylation with other epigenomic features that should help guide future efforts to engineer epigenomes.

2021-03-22 | GSE158027 | GEO

Dnmt3l-/+ (maternal methylation-deficient) vs normal 8.5dpc embryos

Project description:During oogenesis, DNA methyltransferase 3-like (Dnmt3l) is required for the establishment of the maternal germline DNA methylation imprints that in the offspring, govern the parent-of-origin-specific expression of most known imprinted genes (Science 2001, 294:2536-9). Dnmt3l-deficient dams were crossed with wildtype sires to obtain Dnmt3l-/+ embryos that lack maternal methylation imprints. Gene expression was measured in Dnmt3l-/+ and wildtype embryos and is expected to differ for imprinted genes that are under the control of a maternal methylation mark. Keywords: genetic modification, DNA methylation

2008-04-14 | GSE8756 | GEO

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