scholarly journals Allelic H3K27me3 to allelic DNA methylation switch maintains noncanonical imprinting in extraembryonic cells

2019 ◽  
Vol 5 (12) ◽  
pp. eaay7246 ◽  
Author(s):  
Zhiyuan Chen ◽  
Qiangzong Yin ◽  
Azusa Inoue ◽  
Chunxia Zhang ◽  
Yi Zhang
Keyword(s):  
Dna Methylation ◽  
De Novo ◽  
Genetic Manipulation ◽  
Paternal Allele ◽  
Gene Promoters ◽  
Maternal Allele ◽  
Mammalian Development ◽  
Placental Development ◽  
Early Embryos ◽  
Allele Specific

Faithful maintenance of genomic imprinting is essential for mammalian development. While germline DNA methylation–dependent (canonical) imprinting is relatively stable during development, the recently found oocyte-derived H3K27me3-mediated noncanonical imprinting is mostly transient in early embryos, with some genes important for placental development maintaining imprinted expression in the extraembryonic lineage. How these noncanonical imprinted genes maintain their extraembryonic-specific imprinting is unknown. Here, we report that maintenance of noncanonical imprinting requires maternal allele–specific de novo DNA methylation [i.e., somatic differentially methylated regions (DMRs)] at implantation. The somatic DMRs are located at the gene promoters, with paternal allele–specific H3K4me3 established during preimplantation development. Genetic manipulation revealed that both maternal EED and zygotic DNMT3A/3B are required for establishing somatic DMRs and maintaining noncanonical imprinting. Thus, our study not only reveals the mechanism underlying noncanonical imprinting maintenance but also sheds light on how histone modifications in oocytes may shape somatic DMRs in postimplantation embryos.

scholarly journals H3K9 methyltransferase EHMT2/G9a controls ERVK-driven noncanonical imprinted genes

Epigenomics ◽  
2021 ◽  
Author(s):  
Tie-Bo Zeng ◽  
Nicholas Pierce ◽  
Ji Liao ◽  
Piroska E Szabó
Keyword(s):  
Dna Methylation ◽  
X Chromosome ◽  
X Chromosome Inactivation ◽  
Paternal Allele ◽  
Imprinted Genes ◽  
Rna Seq ◽  
Maternal Allele ◽  
Specific Expression ◽  
Allele Specific ◽  
Ectoplacental Cone

Aim: Paternal allele-specific expression of noncanonical imprinted genes in the extraembryonic lineages depends on an H3K27me3-based imprint in the oocyte, which is not a lasting mark. We hypothesized that EHMT2, the main euchromatic H3K9 dimethyltransferase, also has a role in controlling noncanonical imprinting. Methods: We carried out allele-specific total RNA-seq analysis in the ectoplacental cone of somite-matched 8.5 days post coitum embryos using reciprocal mouse crosses. Results: We found that the maternal allele of noncanonical imprinted genes was derepressed from its ERVK promoter in the Ehmt2-/- ectoplacental cone. In Ehmt2-/- embryos, loss of DNA methylation accompanied biallelic derepression of the ERVK promoters. Canonical imprinting and imprinted X chromosome inactivation were generally undisturbed. Conclusion: EHMT2 is essential for repressing the maternal allele in noncanonical imprinting.

Transient establishment of imprinted DNA methylation of transgenic human IC1 sequence in mouse during the pre-implantation period

2020 ◽  
Author(s):  
Katsuhiko Hirakawa ◽  
Hitomi Matsuzaki ◽  
Keiji Tanimoto
Keyword(s):  
Dna Methylation ◽  
De Novo ◽  
Blastocyst Stage ◽  
Paternal Allele ◽  
Human Sequence ◽  
Allele Specific ◽  
Imprinting Control Region ◽  
Equivalent Sequence ◽  
Allele Specific Methylation ◽  
Implantation Period

Abstract Monoallelic gene expression at the Igf2/H19 locus is controlled by paternal allele-specific DNA methylation of the imprinting control region (H19 ICR) that is established during spermatogenesis. We demonstrated that the H19 ICR fragment in transgenic mice acquires allele-specific methylation only after fertilization, which is essential for maintaining its allelic methylation during early embryogenesis. We identified a DNA element required for establishing post-fertilization methylation within a 118 bp (m118) region. A previously generated knock-in mouse whose endogenous H19 ICR was substituted with the human H19 ICR (hIC1; 4.8 kb) sequence revealed that the hIC1 sequence was partially methylated in sperm, although this methylation was lost by the blastocyst stage, which we assume is due to a lack of an m118-equivalent sequence in the hIC1 transgene. To identify a cis sequence involved in post-fertilization methylation within the hIC1 region, we generated three transgenic mouse lines (TgM): one carrying an 8.8 kb hIC1 sequence joined to m118 (hIC1+m118), one with the 8.8 kb hIC1, and one with the 5.8 kb hIC1 sequence joined to m118 (hIC1–3′+m118). We found that the hIC1–3′ region was resistant to de novo DNA methylation throughout development. In contrast, the 5′ portion of the hIC1 (hIC1–5′) in both hIC1+m118 and hIC1 TgM were preferentially methylated on the paternal allele only during preimplantation. As DNA methylation levels were higher in hIC1+m118, the m118 sequence could also induce imprinted methylation of the human sequence. Most importantly, the hIC1–5′ sequence appears to possess an activity equivalent to that of m118.

Role of Mammalian DNA Methyltransferases in Development

2020 ◽  
Vol 89 (1) ◽  
pp. 135-158 ◽  
Author(s):  
Zhiyuan Chen ◽  
Yi Zhang
Keyword(s):  
Dna Methylation ◽  
De Novo ◽  
Early Stage ◽  
Dna Methyltransferases ◽  
Structural Studies ◽  
Mammalian Development ◽  
Low Input ◽  
Early Embryos

DNA methylation at the 5-position of cytosine (5mC) plays vital roles in mammalian development. DNA methylation is catalyzed by DNA methyltransferases (DNMTs), and the two DNMT families, DNMT3 and DNMT1, are responsible for methylation establishment and maintenance, respectively. Since their discovery, biochemical and structural studies have revealed the key mechanisms underlying how DNMTs catalyze de novo and maintenance DNA methylation. In particular, recent development of low-input genomic and epigenomic technologies has deepened our understanding of DNA methylation regulation in germ lines and early stage embryos. In this review, we first describe the methylation machinery including the DNMTs and their essential cofactors. We then discuss how DNMTs are recruited to or excluded from certain genomic elements. Lastly, we summarize recent understanding of the regulation of DNA methylation dynamics in mammalian germ lines and early embryos with a focus on both mice and humans.

scholarly journals H3K9 methyltransferase EHMT2/G9a controls ERVK-driven non-canonical imprinted genes

2021 ◽  
Author(s):  
Tie-Bo Zeng ◽  
Nicholas Pierce ◽  
Piroska Szabo
Keyword(s):  
Dna Methylation ◽  
Paternal Allele ◽  
Imprinted Genes ◽  
Rna Seq ◽  
Maternal Allele ◽  
Specific Expression ◽  
Allele Specific Expression ◽  
Methylation Difference ◽  
Allele Specific ◽  
Ectoplacental Cone

Unlike regular imprinted genes, non-canonical imprinted genes are known to not depend on gamete-specific DNA methylation difference. Instead, the paternal allele-specific expression of these genes in the extra-embryonic lineages depends on an H3K27me3-based imprint in the oocyte, but this marking is not maintained beyond pre-implantation development. The maintenance of non-canonical imprinting corresponds to maternal allele-specific DNA methylation and paternal allele-specific H3K4me3 at their somatic DMRs, which occur at ERVK repeats. We hypothesized that EHMT2, the main euchromatic H3K9 methyltransferase, also has a role in this process. Using reciprocal mouse crosses and allele-specific RNA-seq analysis, we found that the maternal allele of each known non-canonical imprinted gene was derepressed from its ERVK promoter in the Ehmt2−/− ectoplacental cone of somite-matched 8.5 dpc embryos. In the Ehmt2−/− embryos, loss of DNA methylation accompanied the derepression of both parental alleles of those ERVK promoters. Our study identifies EHMT2 as an essential player that maintains the repressed chromosomal state in non-canonical imprinting.

scholarly journals Identification of distinct loci for de novo DNA methylation by DNMT3A and DNMT3B during mammalian development

2020 ◽  
Vol 11 (1) ◽  
Author(s):  
Masaki Yagi ◽  
Mio Kabata ◽  
Akito Tanaka ◽  
Tomoyo Ukai ◽  
Sho Ohta ◽  
...  
Keyword(s):  
Dna Methylation ◽  
De Novo ◽  
Mammalian Development

scholarly journals Developmental Genome-Wide DNA Methylation Asymmetry Between Mouse Placenta and Embryo

2019 ◽  
Author(s):  
LM Legault ◽  
K Doiron ◽  
A Lemieux ◽  
M Caron ◽  
D Chan ◽  
...  
Keyword(s):  
Dna Methylation ◽  
De Novo ◽  
Prenatal Development ◽  
Methyltransferase Activity ◽  
Developmental Program ◽  
Genome Wide ◽  
Early Embryos ◽  
Somatic Tissues ◽  
Main Driver ◽  
Methylation Patterns

ABSTRACTIn early embryos, DNA methylation is remodelled to initiate the developmental program but for mostly unknown reasons, methylation marks are acquired unequally between embryonic and placental cells. To better understand this, we generated high-resolution DNA methylation maps of mouse mid-gestation (E10.5) embryo and placenta. We uncovered specific subtypes of differentially methylated regions (DMRs) that contribute directly to the developmental asymmetry existing between mid-gestation embryonic and placental DNA methylation patterns. We show that the asymmetry occurs rapidly during the acquisition of marks in the post-implanted conceptus (E3.5-E6.5), and that these patterns are long-lasting across subtypes of DMRs throughout prenatal development and in somatic tissues. We reveal that at the peri-implantation stages, the de novo methyltransferase activity of DNMT3B is the main driver of methylation marks on asymmetric DMRs, and that DNMT3B can largely compensate for lack of DNMT3A in the epiblast and extraembryonic ectoderm, whereas DNMT3A can only partially compensate in the absence of DNMT3B. However, as development progresses and as DNMT3A becomes the principal de novo methyltransferase, the compensatory DNA methylation mechanism of DNMT3B on DMRs becomes less effective.

scholarly journals Dppa2/4 Counteract De Novo Methylation to Establish a Permissive Epigenome for Development

2020 ◽  
Author(s):  
Kristjan H. Gretarsson ◽  
Jamie A. Hackett
Keyword(s):  
Dna Methylation ◽  
De Novo ◽  
Developmental Competence ◽  
Epigenetic Memory ◽  
Mammalian Development ◽  
Dna Hypomethylation ◽  
Lineage Specification ◽  
Regulatory Pathways ◽  
Genome Wide ◽  
Early Mammalian Development

ABSTRACTEarly mammalian development entails genome-wide epigenome remodeling, including DNA methylation erasure and reacquisition, which facilitates developmental competence. To uncover the mechanisms that orchestrate DNA methylation (DNAme) dynamics, we coupled a single-cell ratiometric DNAme reporter with unbiased CRISPR screening in ESC. We identify key genes and regulatory pathways that drive global DNA hypomethylation, and characterise roles for Cop1 and Dusp6. We also identify Dppa2 and Dppa4 as essential safeguards of focal epigenetic states. In their absence, developmental genes and evolutionary-young LINE1 elements, which DPPA2 specifically binds, lose H3K4me3 and gain ectopic de novo DNA methylation in pluripotent cells. Consequently, lineage-associated genes (and LINE1) acquire a repressive epigenetic memory, which renders them incompetent for activation during future lineage-specification. Dppa2/4 thereby sculpt the pluripotent epigenome by facilitating H3K4me3 and bivalency to counteract de novo methylation; a function co-opted by evolutionary young LINE1 to evade epigenetic decommissioning.

scholarly journals Characterization of Novel Parent-Specific Epigenetic Modifications Upstream of the Imprinted Mouse H19Gene

1998 ◽  
Vol 18 (11) ◽  
pp. 6767-6776 ◽  
Author(s):  
Piroska E. Szabó ◽  
Gerd P. Pfeifer ◽  
Jeffrey R. Mann
Keyword(s):  
Dna Methylation ◽  
Embryonic Stem ◽  
Dnase I ◽  
Epigenetic Modifications ◽  
Monoallelic Expression ◽  
Maternal Allele ◽  
Dnase I Footprinting ◽  
Allele Specific ◽  
Ccaat Box

ABSTRACT Genomic imprinting results in parent-specific monoallelic expression of a small number of genes in mammals. The identity of imprints is unknown, but much evidence points to a role for DNA methylation. The maternal alleles of the imprinted H19 gene are active and hypomethylated; the paternal alleles are inactive and hypermethylated. Roles for other epigenetic modifications are suggested by allele-specific differences in nuclease hypersensitivity at particular sites. To further analyze the possible epigenetic mechanisms determining monoallelic expression of H19, we have conducted in vivo dimethylsulfate and DNase I footprinting of regions upstream of the coding sequence in parthenogenetic and androgenetic embryonic stem cells. These cells carry only maternally and paternally derived alleles, respectively. We observed the presence of maternal-allele-specific dimethylsulfate and DNase I footprints at the promoter indicative of protein-DNA interactions at a CCAAT box and at binding sites for transcription factors Sp1 and AP-2. Also, at the boundary of a region further upstream for which existent differential methylation has been suggested to constitute an imprint, we observed a number of strand-specific dimethylsulfate reactivity differences specific to the maternal allele, along with an unusual chromatin structure in that both strands of maternally derived DNA were strongly hypersensitive to DNase I cutting over a distance of 100 nucleotides. We therefore reveal the existence of novel parent-specific epigenetic modifications, which in addition to DNA methylation, could constitute imprints or maintain monoallelic expression of H19.

QSER1 protects DNA methylation valleys from de novo methylation

Science ◽  
2021 ◽  
Vol 372 (6538) ◽  
pp. eabd0875 ◽  
Author(s):  
Gary Dixon ◽  
Heng Pan ◽  
Dapeng Yang ◽  
Bess P. Rosen ◽  
Therande Jashari ◽  
...  
Keyword(s):  
Dna Methylation ◽  
De Novo ◽  
Embryonic Stem ◽  
Central Question ◽  
Mammalian Development ◽  
Uncharacterized Gene ◽  
Pathological Conditions ◽  
Genome Wide ◽  
A Genome ◽  
De Novo Methylation

DNA methylation is essential to mammalian development, and dysregulation can cause serious pathological conditions. Key enzymes responsible for deposition and removal of DNA methylation are known, but how they cooperate to regulate the methylation landscape remains a central question. Using a knockin DNA methylation reporter, we performed a genome-wide CRISPR-Cas9 screen in human embryonic stem cells to discover DNA methylation regulators. The top screen hit was an uncharacterized gene, QSER1, which proved to be a key guardian of bivalent promoters and poised enhancers of developmental genes, especially those residing in DNA methylation valleys (or canyons). We further demonstrate genetic and biochemical interactions of QSER1 and TET1, supporting their cooperation to safeguard transcriptional and developmental programs from DNMT3-mediated de novo methylation.

Single-cell multiomics sequencing reveals the functional regulatory landscape of early embryos

2019 ◽  
Author(s):  
Yang Wang ◽  
Peng Yuan ◽  
Zhiqiang Yan ◽  
Ming Yang ◽  
Ying Huo ◽  
...  
Keyword(s):  
Gene Expression ◽  
Dna Methylation ◽  
Single Cell ◽  
Regulatory Network ◽  
Chromatin Accessibility ◽  
Epigenetic Reprogramming ◽  
Preimplantation Development ◽  
Rna Expression ◽  
Early Embryos ◽  
Allele Specific

AbstractExtensive epigenetic reprogramming occurs during preimplantation embryo development and is accompanied by zygotic genome activation (ZGA) and first cell fate specification. Recent studies using single-cell epigenome sequencing techniques have provided global views of the dynamics of different epigenetic layers during this period. However, it remains largely unclear how the drastic epigenetic reprogramming contributes to transcriptional regulatory network. Here, we developed a single-cell multiomics sequencing technology (scNOMeRe-seq) that enables profiling of genome-wide chromatin accessibility, DNA methylation and RNA expression in the same individual cell with improved performance compared to that of earlier techniques. We applied this method to analyze the global dynamics of different molecular layers and their associations in mouse preimplantation embryos. We found that global DNA methylation remodeling facilitates the reconstruction of genetic lineages in early embryos and revealed that the gradual increases in heterogeneity among blastomeres are driven by asymmetric cleavage. Allele-specific DNA methylation pattern is maintained throughout preimplantation development and is accompanied by allele-specific associations between DNA methylation and gene expression in the gene body that are inherited from oocytes and sperm. Through integrated analyses of the collective dynamics between gene expression and chromatin accessibility, we constructed a ZGA-associated regulatory network and revealed coordination among multiple epigenetic layers, transcription factors (TFs) and repeat elements that instruct the proper ZGA process. Moreover, we found that inner cell mass (ICM)/trophectoderm (TE) lineage-associated cis-regulatory elements are stepwise activated in blastomeres during post-ZGA embryo stages. TE lineage-specific TFs play dual roles in promoting the TE program while repressing the ICM program, thereby separating the TE lineage from the ICM lineage. Taken together, our findings not only depict the first single-cell triple-omics map of chromatin accessibility, DNA methylation and RNA expression during mouse preimplantation development but also enhance the fundamental understanding of epigenetic regulation in early embryos.

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