Parental origin of chromatin in human monopronuclear zygotes revealed by asymmetric histone methylation patterns, differs between IVF and ICSI

AbstractDysregulation of epigenetic processes involving histone methylation induces neurodevelopmental impairments and has been implicated in schizophrenia (SCZ) and autism spectrum disorder (ASD). Variants in the gene encoding lysine demethylase 4C (KDM4C) have been suggested to confer a risk for such disorders. However, rare genetic variants in KDM4C have not been fully evaluated, and the functional impact of the variants has not been studied using patient-derived cells. In this study, we conducted copy number variant (CNV) analysis in a Japanese sample set (2605 SCZ and 1141 ASD cases, and 2310 controls). We found evidence for significant associations between CNVs in KDM4C and SCZ (p = 0.003) and ASD (p = 0.04). We also observed a significant association between deletions in KDM4C and SCZ (corrected p = 0.04). Next, to explore the contribution of single nucleotide variants in KDM4C, we sequenced the coding exons in a second sample set (370 SCZ and 192 ASD cases) and detected 18 rare missense variants, including p.D160N within the JmjC domain of KDM4C. We, then, performed association analysis for p.D160N in a third sample set (1751 SCZ and 377 ASD cases, and 2276 controls), but did not find a statistical association with these disorders. Immunoblotting analysis using lymphoblastoid cell lines from a case with KDM4C deletion revealed reduced KDM4C protein expression and altered histone methylation patterns. In conclusion, this study strengthens the evidence for associations between KDM4C CNVs and these two disorders and for their potential functional effect on histone methylation patterns.

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Opposing Histone Methylation Patterns Distinguish the Serca2 Gene in the Pathological and Physiological Hypertrophied Heart

Heart Lung and Circulation ◽

10.1016/j.hlc.2011.05.124 ◽

2011 ◽

Vol 20 ◽

pp. S49

Author(s):

J. Ooi ◽

J. McMullen ◽

X. Du ◽

A. El-Osta

Keyword(s):

Histone Methylation ◽

Hypertrophied Heart ◽

Methylation Patterns

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CpG methylation of an X-linked transgene is determined by somatic events postfertilization and not germline imprinting

Development ◽

10.1242/dev.104.2.235 ◽

1988 ◽

Vol 104 (2) ◽

pp. 235-244

Author(s):

A. Collick ◽

W. Reik ◽

S.C. Barton ◽

A.H. Surani

Keyword(s):

Dna Methylation ◽

X Chromosome ◽

De Novo ◽

Cpg Methylation ◽

Parental Origin ◽

Cpg Dinucleotides ◽

Inactive State ◽

Methylation Of Dna ◽

Methylation Patterns ◽

Extraembryonic Tissues

The process of X-inactivation in mammals requires at least two events, the initiation of inactivation and the maintenance of the inactive state. One possible mechanism of control is by methylation of DNA at CpG dinucleotides to maintain the inactive state. Furthermore, the paternal X-chromosome is frequently inactivated in the extraembryonic membranes. The relationship between the parental origin of the chromosome, nonrandom inactivation and DNA methylation is not clear. In this paper, we report on the CpG methylation of an X-linked transgene, CAT-32. The levels of methylation in embryonic, extraembryonic and germline cells indicates that the modifications of the transgene are broadly similar to those reported for endogenous X-linked genes. Interestingly, the methylation of CAT-32 transgene in extraembryonic tissues displays patterns that could be linked to the germline origin of each allele. Hence, the maternally derived copy of CAT-32 was relatively undermethylated when compared to the paternal one. The changes in DNA methylation were attributed to de novo methylation occurring after fertilization, most probably during differentiation of extraembryonic tissues. In order to determine whether or not the patterns of DNA methylation reflected the germline origin of the X-chromosome, we constructed triploid embryos specifically to introduce two maternal X-chromosomes in the same embryo. In some of these triploid conceptuses, methylation patterns characteristic of the paternally derived transgene were observed. This observation indicates that the methylation patterns are not necessarily dependent on the parental origin of the X-chromosome, but could be changed by somatic events after fertilization. One of the more likely mechanisms is methylation of the transgene following inactivation of the X-chromosome in extraembryonic tissues.

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Erasing genomic imprinting memory in mouse clone embryos produced from day 11.5 primordial germ cells

Development ◽

10.1242/dev.129.8.1807 ◽

2002 ◽

Vol 129 (8) ◽

pp. 1807-1817 ◽

Cited By ~ 3

Author(s):

Jiyoung Lee ◽

Kimiko Inoue ◽

Ryuichi Ono ◽

Narumi Ogonuki ◽

Takashi Kohda ◽

...

Keyword(s):

Dna Methylation ◽

Genomic Imprinting ◽

Nuclear Transfer ◽

Monoallelic Expression ◽

Parental Origin ◽

Imprinted Genes ◽

Specific Expression ◽

Male And Female ◽

Imprinted Gene ◽

Methylation Patterns

Genomic imprinting is an epigenetic mechanism that causes functional differences between paternal and maternal genomes, and plays an essential role in mammalian development. Stage-specific changes in the DNA methylation patterns of imprinted genes suggest that their imprints are erased some time during the primordial germ cell (PGC) stage, before their gametic patterns are re-established during gametogenesis according to the sex of individuals. To define the exact timing and pattern of the erasure process, we have analyzed parental-origin-specific expression of imprinted genes and DNA methylation patterns of differentially methylated regions (DMRs) in embryos, each derived from a single day 11.5 to day 13.5 PGC by nuclear transfer. Cloned embryos produced from day 12.5 to day 13.5 PGCs showed growth retardation and early embryonic lethality around day 9.5. Imprinted genes lost their parental-origin-specific expression patterns completely and became biallelic or silenced. We confirmed that clones derived from both male and female PGCs gave the same result, demonstrating the existence of a common default state of genomic imprinting to male and female germlines. When we produced clone embryos from day 11.5 PGCs, their development was significantly improved, allowing them to survive until at least the day 11.5 embryonic stage. Interestingly, several intermediate states of genomic imprinting between somatic cell states and the default states were seen in these embryos. Loss of the monoallelic expression of imprinted genes proceeded in a step-wise manner coordinated specifically for each imprinted gene. DNA demethylation of the DMRs of the imprinted genes in exact accordance with the loss of their imprinted monoallelic expression was also observed. Analysis of DNA methylation in day 10.5 to day 12.5 PGCs demonstrated that PGC clones represented the DNA methylation status of donor PGCs well. These findings provide strong evidence that the erasure process of genomic imprinting memory proceeds in the day 10.5 to day 11.5 PGCs, with the timing precisely controlled for each imprinted gene. The nuclear transfer technique enabled us to analyze the imprinting status of each PGC and clearly demonstrated a close relationship between expression and DNA methylation patterns and the ability of imprinted genes to support development.

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Mapping Global Histone Methylation Patterns in the Coding Regions of Human Genes

Molecular and Cellular Biology ◽

10.1128/mcb.25.11.4650-4661.2005 ◽

2005 ◽

Vol 25 (11) ◽

pp. 4650-4661 ◽

Cited By ~ 81

Author(s):

Feng Miao ◽

Rama Natarajan

Keyword(s):

Histone Methylation ◽

Histone H3 ◽

Distribution Patterns ◽

Poor Correlation ◽

Histone Marks ◽

Coding Regions ◽

New Information ◽

Human Genes ◽

Histone H3 Methylation ◽

Methylation Patterns

ABSTRACT Histone methylation patterns in the human genome, especially in euchromatin regions, have not been systematically characterized. In this study, we examined the profile of histone H3 methylation (Me) patterns at different lysines (Ks) in the coding regions of human genes by genome-wide location analyses by using chromatin immunoprecipitation linked to cDNA arrays. Specifically, we compared H3-KMe marks known to be associated with active gene expression, namely, H3-K4Me, H3-K36Me, and H3-K79Me, as well as those associated with gene repression, namely, H3-K9Me, H3-K27Me, and H4-K20Me. We further compared these to histone lysine acetylation (H3-K9/14Ac). Our results demonstrated that: first, close correlations are present between active histone marks except between H3-K36Me2 and H3-K4Me2. Notably, histone H3-K79Me2 is closely associated with H3-K4Me2 and H3-K36Me2 in the coding regions. Second, close correlations are present between histone marks associated with gene silencing such as H3-K9Me3, H3-K27Me2, and H4-K20Me2. Third, a poor correlation is observed between euchromatin marks (H3-K9/K14Ac, H3-K4Me2, H3-K36Me2, and H3-K79Me2) and heterochromatin marks (H3-K9Me2, H3-K9Me3, H3-K27Me2, and H4-K20Me2). Fourth, H3-K9Me2 is neither associated with active nor repressive histone methylations. Finally, histone H3-K4Me2, H3-K4Me3, H3-K36Me2, and H3-K79Me2 are associated with hyperacetylation and active genes, whereas H3-K9Me2, H3-K9Me3, H3-K27Me2, and H4-K20Me2 are associated with hypoacetylation. These data provide novel new information regarding histone KMe distribution patterns in the coding regions of human genes.

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Epigenetic Regulation and Therapeutic Targeting in Myeloma

Blood ◽

10.1182/blood-2018-99-109522 ◽

2018 ◽

Vol 132 (Supplement 1) ◽

pp. SCI-37-SCI-37 ◽

Cited By ~ 1

Author(s):

Jonathan D. Licht

Keyword(s):

Cell Adhesion ◽

Histone Methylation ◽

Gene Activation ◽

Genetic Alterations ◽

Major Effect ◽

Cellular Adhesion ◽

Lymphocytic Leukemia ◽

Chromatin Remodelers ◽

Model Cell ◽

Methylation Patterns

Abstract Genetic alterations of epigenetic regulators that alter the repressive trimethylation of lysine 27 on histone H3 (H3K27me3) are a recurrent feature in cancer. The histone demethylase UTX/KDM6A Is mutated in ~5% of multiple myeloma (MM) at diagnosis and is commonly absent in MM cell lines, derived from patients with advanced disease. KDM6A forms a complex containing H3K4 specific methyltransferases KMT2D and KMT2C, the histone acetyltransferase CBP/p300 and SWI/SNF chromatin-remodelers. Collectively the complex adds activation marks on histones and removes the gene repression associated H3K37me mark at enhancers. Removal of KDM6A from MM cells using CRISPR and re-expression of KDM6A in deficient cells showed that KDM6A has tumor suppressor function and regulates genes involved in cell adhesion. ChIP-studies showed that loss of KDM6A lead to decreased H3K27 acetylation and increased H3K27me at specific loci, but at other loci changes in H3K27Ac are the major effect of changes in KDM6A expression. KDM6A loss shifts the balance of gene expression to repression and KDM6A null cells had heightened sensitivity to EZH2 inhibitors. H3K27me/Ac chromatin modifications are also deregulated in MM associated with t(4;14) and overexpression of the NSD2/MMSET histone methyltransferase. NSD2 overexpression leads to a ~10-fold genome wide increase in histone 3 lysine 36 dimethylation (H3K36me2), a chromatin mark associated with gene activation and similar loss of H3K27me3. As a result, many genes are aberrantly activated and NSD2 aberrant stimulates cell growth in part through activation of c-myc. However, some loci are repressed in the presence of high NSD2 due to redistribution of EZH2. These genes may also be important for pathogenesis and growth since NSD2 high cells also show increased sensitivity to EZH2 inhibitors. Nevertheless, the global loss of H3K27me3 makes the chromatin structure of NSD2 overexpressing MM cells more "open" and these cells demonstrated increased DNA damage in response to genotoxic agents. At the same time NSD2 overexpression increased increases DNA repair processes making cells relatively resistant to chemotherapy, potentially explaining the poor prognosis of such patients. A point mutation in NSD2, E1099K is found in some MM patients, the commonly utilized MM.1 model cell line and in up to 15% of cases of relapsed childhood acute lymphocytic leukemia (ALL). This mutation increases the activity of the enzyme and also globally increases H3K36me2 and decreases H3K27me3. Removal of the mutant allele from ALL cells lines reverses of histone methylation patterns, deceased growth, altered cellular adhesion and increased susceptibility to therapy. RNA-seq analysis showed that similar to the UTX mutation, NSD2 mutation activated a program of cell adhesion, motility and signaling. Furthermore in in ALL, the activity of mutant NSD2 blocks glucocorticoid induced expression of pro-apoptotic genes, promoting tumor relapse. In summary deregulation of histone methylation patterns in MM plays an important role in disease pathogenesis and progression. Rebalancing histone modifications using appropriate inhibitors represent a potential therapeutic strategy. Disclosures Licht: Celgene: Research Funding.

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Parental methylation patterns of a transgenic locus in adult somatic tissues are imprinted during gametogenesis

Development ◽

10.1242/dev.116.4.831 ◽

1992 ◽

Vol 116 (4) ◽

pp. 831-839 ◽

Cited By ~ 2

Author(s):

T. Ueda ◽

K. Yamazaki ◽

R. Suzuki ◽

H. Fujimoto ◽

H. Sasaki ◽

...

Keyword(s):

Germ Cells ◽

Developmental Stages ◽

Fusion Gene ◽

Cpg Island ◽

Methylation Status ◽

Gene Promoter ◽

Parental Origin ◽

Chromosome 11 ◽

Somatic Tissues ◽

Methylation Patterns

The methylation status of a mouse metallothionein-I/human transthyretin fusion gene was studied during gametogenesis in transgenic mice. In the adult tissues of this mouse line, the promoter region of the transgene on chromosome 11 is methylated when it is maternally inherited and undermethylated when it is paternally inherited. Germ cells from various developmental stages of gametogenesis were isolated, and their DNAs were assayed using methylation-sensitive restriction endonucleases and the polymerase chain reaction. Only low to nonexistent levels of transgene methylation were detected in germ cells from 14.5-day-old male and female fetuses irrespective of the parental origin of the transgene. This undermethylated state persisted in oocytes from newborn females as well as in testicular spermatogenic cells and sperm. By contrast, the transgene promoter was completely methylated in fully grown oocytes arrested at the first meiotic prophase. The endogenous metallothionein-I gene promoter, located on a different chromosome, remained undermethylated at all stages examined, consistent with previous findings reported for a typical CpG island. Taken together, the results suggest that parental-specific adult patterns of transgene methylation are established during gametogenesis.

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Faculty Opinions recommendation of Mapping global histone methylation patterns in the coding regions of human genes.

Faculty Opinions – Post-Publication Peer Review of the Biomedical Literature ◽

10.3410/f.1026536.325217 ◽

2005 ◽

Author(s):

Janet Stavnezer

Keyword(s):

Histone Methylation ◽

Coding Regions ◽

Human Genes ◽

Methylation Patterns

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Epigenetics Directing Therapy in Acute Lymphocytic Leukemia: Emerging Roles and New Therapies

Blood ◽

10.1182/blood.v126.23.sci-36.sci-36 ◽

2015 ◽

Vol 126 (23) ◽

pp. SCI-36-SCI-36

Author(s):

Kathrin M Bernt

Keyword(s):

Dna Methylation ◽

Clinical Trials ◽

Histone Acetylation ◽

Histone Methylation ◽

Histone Methyltransferase ◽

Demethylating Agents ◽

Early Results ◽

Aberrant Dna Methylation ◽

Epigenetic Modulation ◽

Methylation Patterns

In the last 15 years, our understanding of the contribution of epigenetic mechanisms to ALL leukemogenesis has increased exponentially. Epigenetic alterations are particularly interesting from a therapeutic standpoint, as they are potentially reversible and amenable to pharmacologic modulation. Indeed, inhibitors of DNA methylation, histone deactylation and histone methylation all have entered clinical trials, and early results for several of these agents are encouraging. Incorporating epigenetic modulation into ALL therapy may therefore hold great promise in improving tolerability and outcomes. Specifically, this session will address: - Patterns of aberrant DNA methylation and clinical trials combining "demethylating" agents with standard chemotherapy for relapsed ALL.DNA methylation patterns have been shown to correlate with outcome. Basic studies failed to conclusively link the regulation of specific genes or pathways to aberrant DNA methylation, and upfront methylation patterns poorly predict response to demethylating agents. Nevertheless, several clinical trials combining demethylating agents and chemotherapy in relapsed ALL are ongoing, with encouraging early results. These included responses of patients treated with decitabine and HyperCVAD who had previously failed to respond HyperCVAD alone. - Patterns of aberrant histone acetylation, the biology of histone acetyl transferases (HATs) and histone deacetylases (HDACS) in ALL, and clinical trials modulating histone acetylation. Histone acetylation patterns and a high frequency of deletions of the HAT CBP at relapse suggest that aberrant histone acetylation contributes to relapse and resistance. HDAC inhibitors show efficacy on ALL cells in preclinical studies, and clinical trials are ongoing. - The role of the histone acetylation "reader" protein Brd4 in ALL. In addition to "writers" (HAT) and "erasers" (HDACs), readers of histone acetylation may play a role in leukemia. Inhibition of Brd4 showed activity in several lymphoblastic leukemia models, and two Brd4 inhibitors are currently in clinical trials for relapsed/refractory hematologic malignancies including ALL. - Patterns of aberrant histone methylation, biology and therapeutic possibilities. Aberrant histone methylation is also emerging as a contributor to leukemogenesis, and may offer opportunities for therapeutic intervention. Loss of function mutations of the H3K27 histone methyltransferase EZH2 or other members of its complex (SUZ12, EED) are often found in early T-cell precursor ALL (ETP), and loss of EED or EZH2 contributes to aberrant T-cell development and leukemic transformation in mouse models. Gain of function of the H3K36 histone methyltransferase NSD2 have recently been described in pre-B ALL, raising the obvious question whether these leukemias depend on H3K36 hypermethylation, and NSD2 inhibition would have a therapeutic effect. Finally, aberrant recruitment of the histone methyltransferase DOT1L is observed in MLL-rearranged ALL, and an inhibitor of DOT1L is in clinical trials for MLL-rearranged malignancies, including ALL. Basic and translational studies support a critical role for epigenetic mechanisms in ALL leukemogenesis, drug resistance and relapse. Early results from clinical trials demonstrate that pharmacologic modulation of epigenetic modifiers can produce clinically meaningful responses. The next few years will likely see an increased number of compounds that modulate epigenetics enter clinical trials. Current assignment of patients to studies/compounds is crude, based on tumor type and status (i.e. "relapsed hematologic malignancy") or cytogenetics (i.e. MLL-rearrangement), rather than epigenetic profiling or an understanding of the biology that drives an individual patient's leukemia. As our diagnostic and therapeutic tools improve, epigenetic modulation may become an important component of ALL therapy. Disclosures Off Label Use: This presentation will include discussion of the use of decitabine, azacitidine, vorinostat, rhomidepsin and EPZ-5676 for ALL..

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