Caught in conspiracy: cooperation between DNA methylation and histone H3K9 methylation in the establishment and maintenance of heterochromatin

2005 ◽  
Vol 83 (3) ◽  
pp. 385-395 ◽  
Author(s):  
Irina Stancheva
Keyword(s):  
Gene Expression ◽  
Dna Methylation ◽  
Rna Interference ◽  
Histone Methylation ◽  
Functional Relationship ◽  
Histone H3 ◽  
H3k9 Methylation ◽  
Complex Interactions ◽  
Histone H3 Methylation ◽  
Intensive Investigation

Heritable patterns of gene expression and gene silencing are determined by chromatin states that either permit or restrict transcription. Restrictive heterochromatin in most eukaryotes is characterized by high levels of DNA methylation and histone H3 methylation at lysine 9. The functional relationship between these two modifications is the focus of intensive investigation in various organisms from fungi to mammals. Complex interactions have been discovered among various components of DNA methylation and histone methylation pathways, proteins involved in the formation of higher-order chromatin structure, chromatin remodelling activities, and RNA interference. This review discusses some aspects of this crosstalk and the cooperation between DNA methylation and histone H3K9 methylation in the establishment and maintenance of heterochromatin.Key words: DNA methylation, H3K9 methylation, heterochromatin.

Nuclear SET Domain (NSD) Protein Lysine Methyltransferases (KMT) Family Members Expression in Acute Myeloid Leukemia

Blood ◽  
2016 ◽  
Vol 128 (22) ◽  
pp. 5097-5097
Author(s):  
Virginia Mara De Deus Wagatsuma ◽  
Luisa C A Koury ◽  
Silvia Elena Sánchez ◽  
Lorena Lobo Figueiredo Pontes ◽  
Fernanda Borges da Silva ◽  
...  
Keyword(s):  
Gene Expression ◽  
Dna Methylation ◽  
Bone Marrow ◽  
Overall Survival ◽  
Histone Methylation ◽  
Histone H3 ◽  
Set Domain ◽  
Genetic Abnormalities ◽  
Leukocyte Counts ◽  
Lysine Methyltransferases

Abstract The Nuclear SET Domain (NSD) Protein Lysine Methyltransferases (KMT) family is composed of three members: NSD1/KMT3B, NSD2/WHSC1/MMSET and NSD3/WHSC1L1 which regulate gene expression through methylation of lysine 36 of histone H3 (H3K36). NSD2 overexpression was reported in multiple myeloma with t(4;14)/IgH-MMSET. NSDs gene expression profile is unknown in acute leukemias, however NSD1 and NSD3 were described to be fused with the nucleoporin 98 gene (NUP98) in rare AML and myelodysplastic syndrome cases and, both fusion proteins were associated with poor prognosis. The aims of the present study were to characterize the expression of NSD-KMTs in patients with AML and healthy controls, to determine if this expression is associated with specific genetic abnormalities and/or with treatment outcome.A total of four healthy donors and 45 AML patients (27♀, 18♂) at diagnosis were included in the study. Our cohort included 8 patients with acute promyelocytic leukemia (APL), 8 with core binding factor (CBF) leukemias [4 with t(8;21) and 4 with inv(16)], and 29 patients with non-APL non-CBF AML. NSD family gene expression was evaluated by qPCR using the comparative Ct method for analysis. A higher expression of the NSD1 gene was observed in AML cells compared to normal bone marrow (BM) samples {median [range] = 3.202 [0.6804-0.096] vs. 1.003 [:0.7956-1.265], p=0.0243}. Similarly, the expression of NSD3 was higher in AML, but the difference was significant only for the comparison between healthy BM and CBF-AML groups {median [range] = 1.070 [0.6360-1.410] vs. 2.719 [1.238-8.830], p=0.0265}. No significant differences were detected in the analysis of NSD2 expression. Considering the three groups of AML patients, no correlation was found between NSD1, NSD2 or NSD3 expression levels and age, gender, leukocyte counts at diagnosis, karyotype (normal vs. abnormal), frequency of specific genetic abnormalities (t(15;17)/PML-RARA; t(8;21)/RUNX1-RUNX1T1; inv(16)/CBFB-MYH11) or percentage of blasts in bone marrow. NPM1 mutations and FLT3 internal tandem duplications (FLT3-ITD) were detected in 29.6% (13/44) and 21% (9/43) of the patients with AML, respectively. We observed a significant increase in NSD1, NSD2 and NSD3 expression in blasts from patients with FLT3-ITD (p=0.0177), but not in those with NPM1 mutations. These differences remained significant when APL cases were excluded from the analysis. Next, patients were grouped according to NSD1 or NSD2 expression. Patients with NSD1 or NSD2 expression higher or lower than the median value (3.25 and 3.16, respectively), showed no significant differences regarding age distribution, leukocyte counts or percentage of blasts in bone marrow at diagnosis, or presence of genetic abnormalities. Regarding the analysis of treatment outcome, patients with non-APL AML were stratified into high and low NSD1 or NSD2 expression subgroups using the criteria above. The median overall survival of patients in the low NSD2 expression subgroup was of 333,023 days [95% CI:158,541-507,505 days] whereas patients in the high NSD2 expression subgroup was of 817,629 days [95% CI:238,702-1396,555 days] (p=0,633). No significant difference observed between the overall survival of patients in the high and low NSD1 expression subgroups. In order to determine if NSD-KMT levels were associated with changes at histone H3 lysine 4 (H4K4) and H3K36 (known to activate gene transcription), as well at histone H3 lysine 9 (H3K9), H3K27, H3K79 and H4K29, associated to regulatory repression, we ran an experiment using Illumina Infinium Methylation 450k arrays. The comparison between normal and leukemic cells revealed specific histone methylation profiles. There is experimental evidence that histone methylation is a prerequisite for DNA methylation and transcriptional regulation, suggesting interplay between histone and DNA methylation. Our data correlate overexpression levels of NSD-KMT with histone modifications, suggesting that this modification and not only DNA methylation can contribute for epigenomic changes associated to AML pathogenesis. Disclosures No relevant conflicts of interest to declare.

scholarly journals Early life stress induces age-dependent epigenetic changes in p11 gene expression in male mice

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Mi Kyoung Seo ◽  
Jung Goo Lee ◽  
Sung Woo Park
Keyword(s):  
Gene Expression ◽  
Dna Methylation ◽  
Histone Acetylation ◽  
Histone Methylation ◽  
Life Stress ◽  
Early Life ◽  
Age Groups ◽  
Early Life Stress ◽  
Epigenetic Modifications ◽  
Age Dependent

AbstractEarly life stress (ELS) causes long-lasting changes in gene expression through epigenetic mechanisms. However, little is known about the effects of ELS in adulthood, specifically across different age groups. In this study, the epigenetic modifications of p11 expression in adult mice subjected to ELS were investigated in different stages of adulthood. Pups experienced maternal separation (MS) for 3 h daily from postnatal day 1 to 21. At young and middle adulthood, behavioral test, hippocampal p11 expression levels, and levels of histone acetylation and methylation and DNA methylation at the hippocampal p11 promoter were measured. Middle-aged, but not young adult, MS mice exhibited increased immobility time in the forced swimming test. Concurrent with reduced hippocampal p11 levels, mice in both age groups showed a decrease in histone acetylation (AcH3) and permissive histone methylation (H3K4me3) at the p11 promoter, as well as an increase in repressive histone methylation (H3K27me3). Moreover, our results showed that the expression, AcH3 and H3Kme3 levels of p11 gene in response to MS were reduced with age. DNA methylation analysis of the p11 promoter revealed increased CpG methylation in middle-aged MS mice only. The results highlight the age-dependent deleterious effects of ELS on the epigenetic modifications of p11 transcription.

scholarly journals Dioxin Disrupts Dynamic DNA Methylation Patterns in Genes That Govern Cardiomyocyte Maturation

2020 ◽  
Vol 178 (2) ◽  
pp. 325-337
Author(s):  
Matthew de Gannes ◽  
Chia-I Ko ◽  
Xiang Zhang ◽  
Jacek Biesiada ◽  
Liang Niu ◽  
...  
Keyword(s):  
Gene Expression ◽  
Dna Methylation ◽  
Heart Development ◽  
Expression Patterns ◽  
Embryonic Stem Cell Line ◽  
Molecular Networks ◽  
Unknown Etiology ◽  
Postnatal Maturation ◽  
Complex Interactions ◽  
And Function

Abstract Congenital heart disease (CHD), the leading birth defect worldwide, has a largely unknown etiology, likely to result from complex interactions between genetic and environmental factors during heart development, at a time when the heart adapts to diverse physiological and pathophysiological conditions. Crucial among these is the regulation of cardiomyocyte development and postnatal maturation, governed by dynamic changes in DNA methylation. Previous work from our laboratory has shown that exposure to the environmental toxicant tetrachlorodibenzo-p-dioxin (TCDD) disrupts several molecular networks responsible for heart development and function. To test the hypothesis that the disruption caused by TCDD in the heart results from changes in DNA methylation and gene expression patterns of cardiomyocytes, we established a stable mouse embryonic stem cell line expressing a puromycin resistance selectable marker under control of the cardiomyocyte-specific Nkx2-5 promoter. Differentiation of these cells in the presence of puromycin induces the expression of a large suite of cardiomyocyte-specific markers. To assess the consequences of TCDD treatment on gene expression and DNA methylation in these cardiomyocytes, we subjected them to transcriptome and methylome analyses in the presence of TCDD. Unlike control cardiomyocytes maintained in vehicle, the TCDD-treated cardiomyocytes showed extensive gene expression changes, with a significant correlation between differential RNA expression and DNA methylation in 111 genes, many of which are key elements of pathways that regulate cardiovascular development and function. Our findings provide an important clue toward the elucidation of the complex interactions between genetic and epigenetic mechanisms after developmental TCDD exposure that may contribute to CHD.

scholarly journals Stress-induced gene expression and behavior are controlled by DNA methylation and methyl donor availability in the dentate gyrus

2016 ◽  
Vol 113 (17) ◽  
pp. 4830-4835 ◽  
Author(s):  
Emily A. Saunderson ◽  
Helen Spiers ◽  
Karen R. Mifsud ◽  
Maria Gutierrez-Mecinas ◽  
Alexandra F. Trollope ◽  
...  
Keyword(s):  
Gene Expression ◽  
Dna Methylation ◽  
Dentate Gyrus ◽  
Crucial Role ◽  
Histone H3 ◽  
Behavioral Responses ◽  
Cpg Methylation ◽  
Granule Neurons ◽  
Methyl Donor ◽  
And Behavior

Stressful events evoke long-term changes in behavioral responses; however, the underlying mechanisms in the brain are not well understood. Previous work has shown that epigenetic changes and immediate-early gene (IEG) induction in stress-activated dentate gyrus (DG) granule neurons play a crucial role in these behavioral responses. Here, we show that an acute stressful challenge [i.e., forced swimming (FS)] results in DNA demethylation at specific CpG (5′-cytosine–phosphate–guanine-3′) sites close to the c-Fos (FBJ murine osteosarcoma viral oncogene homolog) transcriptional start site and within the gene promoter region of Egr-1 (early growth response protein 1) specifically in the DG. Administration of the (endogenous) methyl donor S-adenosyl methionine (SAM) did not affect CpG methylation and IEG gene expression at baseline. However, administration of SAM before the FS challenge resulted in an enhanced CpG methylation at the IEG loci and suppression of IEG induction specifically in the DG and an impaired behavioral immobility response 24 h later. The stressor also specifically increased the expression of the de novo DNA methyltransferase Dnmt3a [DNA (cytosine-5-)-methyltransferase 3 alpha] in this hippocampus region. Moreover, stress resulted in an increased association of Dnmt3a enzyme with the affected CpG loci within the IEG genes. No effects of SAM were observed on stress-evoked histone modifications, including H3S10p-K14ac (histone H3, phosphorylated serine 10 and acetylated lysine-14), H3K4me3 (histone H3, trimethylated lysine-4), H3K9me3 (histone H3, trimethylated lysine-9), and H3K27me3 (histone H3, trimethylated lysine-27). We conclude that the DNA methylation status of IEGs plays a crucial role in FS-induced IEG induction in DG granule neurons and associated behavioral responses. In addition, the concentration of available methyl donor, possibly in conjunction with Dnmt3a, is critical for the responsiveness of dentate neurons to environmental stimuli in terms of gene expression and behavior.

The Role of Histone Demethylases in the Transcription Regulation of HOX Genes in PML-RARa+ AML Patients

Blood ◽  
2014 ◽  
Vol 124 (21) ◽  
pp. 876-876
Author(s):  
Katerina Rejlova ◽  
Karolina Kramarzova ◽  
Meritxell Alberich-Jorda ◽  
Karel Fiser ◽  
Marketa Zaliova ◽  
...  
Keyword(s):  
Gene Expression ◽  
Dna Methylation ◽  
Histone Methylation ◽  
Hox Genes ◽  
Histone Demethylases ◽  
Atra Treatment ◽  
Hox Gene ◽  
Genes Expression ◽  
Methylation Mark

Abstract Homeobox genes (HOX) encode transcription factors that are frequently deregulated in leukemias. Our previous findings described that HOX gene expression differs among genetically characterized subtypes of pediatric AML with PML-RARa+ patients having the lowest overall HOX gene expression. We observed that HOX gene expression positively correlated with expression of histone 3 lysine 27 (H3K27) demethylases JMJD3 and UTX and negatively with DNA methyltransferase DNMT3b. Interestingly, it has been shown that JMJD3 is a direct target of PML-RARa protein (Martens, JH et al, 2010, Cancer Cell). These findings led us to postulate the hypothesis that reduced levels of HOX genes in PML-RARa+ AML can be caused by the suppressed expression of histone demethylases, such as JMJD3 and UTX, resulting in increased H3K27 methylation and transcription inhibition. We chose PML-RARa+ NB4 cell line to study the role of PML-RARa fusion gene in the regulation of HOX gene expression. To inhibit the effect of PML-RARa we used all-trans retinoic acid (ATRA; 1 uM, 10 uM) which was described to release the block caused by this fusion protein. Expression of particular HOX genes (e.g., HOXA1, HOXA3, HOXA5, HOXA7) together with that of JMJD3 and UTX assessed by qPCR was significantly elevated after ATRA treatment, while gene expression of DNMT3b was decreased. To test whether the reduction in HOX gene expression is directly related to the levels of JMJD3 and UTX, we cultured NB4 cells with a specific inhibitor of these histone demethylases, GSK-J4 (1 uM, 10 uM), in combination with ATRA. This co-treatment led to inhibition of JMJD3 and UTX proteins, followed by significant reduction of HOX genes expression (e.g., HOXA1, HOXA3, HOXA5, HOXA7). This result supports our hypothesis that HOX genes expression is directly related to JMJD3/UTX activity. To determine the effect of ATRA and GSK-J4 on histone marks we have isolated histones by acid extraction and detected the levels of histones by western blot in NB4 ATRA or GSK-J4/ATRA treated cells. We observed that the level of repressive histone methylation mark (trimethylated H3K27; H3K27me3) was decreased after ATRA treatment (activation of JMJD3/UTX) and increased after GSK-J4/ATRA co-treatment (inhibition of JMJD3/UTX). The opposite effect was observed in active histone methylation marks where di- and tri-methylated H3K4 (H3K4me2, H3K4me3) increased after ATRA treatment and decreased after GSK-J4/ATRA co-treatment. H3K9 dimethylated (another repressive histone methylation mark) levels did not change. Next, to investigate the histone code directly in particular HOX genes regions we performed chromatin immunoprecipitation (ChIP) assays. We studied the presence of H3K27me3 and H3K4me2 in 5´UTR genomic region of particular HOX genes (HOXA1, HOXA2, HOXA3, HOXA5, HOXA7) in cells treated with ATRA alone or in the combination with GSK-J4. Preliminary results showed reduction in repressive marks (H3K27me3) upon ATRA treatment, whereas addition of GSK-J4 prevented this decrease. Accordingly, we observed that ATRA/GSK-J4 co-treatment reduced active histone mark H3K4me2. To evaluate the role of DNA methylation in observed expression changes after ATRA treatment we performed bisulfite sequencing of particular promoter sites of HOX genes (e.g., HOXA7, HOXA5). Although we detected decreased DNMT3b gene expression after ATRA treatment there was no change in DNA methylation of CpGs in studied regions. Our results demonstrate that changes in chromatin activity correspond with changes in HOX gene expression. Moreover, ChIP data show direct binding of the modified histones and HOX 5´UTR sites. Our data implicate histone demethylases in regulation of HOX gene expression in PML-RARa+ leukemic blasts. DNA methylation in these particular HOX genes is not involved in the regulation. Elucidating the mechanism of regulation of HOX genes expression can help to understand their role in the leukemogenic process. Supported by GACR P304/12/2214 and GAUK 568213. Disclosures No relevant conflicts of interest to declare.

scholarly journals Early mammalian erythropoiesis requires the Dot1L methyltransferase

Blood ◽  
2010 ◽  
Vol 116 (22) ◽  
pp. 4483-4491 ◽  
Author(s):  
Yi Feng ◽  
Yanping Yang ◽  
Manoela M. Ortega ◽  
Jessica N. Copeland ◽  
Mingcai Zhang ◽  
...  
Keyword(s):  
Histone Methylation ◽  
Histone H3 ◽  
Mutant Mice ◽  
Myeloid Differentiation ◽  
Wild Type ◽  
Erythroid Progenitors ◽  
Small Vessels ◽  
Histone H3 Methylation ◽  
Important Regulator ◽  
Steady State Levels

Histone methylation is an important regulator of gene expression; its coordinated activity is critical in complex developmental processes such as hematopoiesis. Disruptor of telomere silencing 1-like (DOT1L) is a unique histone methyltransferase that specifically methylates histone H3 at lysine 79. We analyzed Dot1L-mutant mice to determine influence of this enzyme on embryonic hematopoiesis. Mutant mice developed more slowly than wild-type embryos and died between embryonic days 10.5 and 13.5, displaying a striking anemia, especially apparent in small vessels of the yolk sac. Further, a severe, selective defect in erythroid, but not myeloid, differentiation was observed. Erythroid progenitors failed to develop normally, showing retarded progression through the cell cycle, accumulation during G0/G1 stage, and marked increase in apoptosis in response to erythroid growth factors. GATA2, a factor essential for early erythropoiesis, was significantly reduced in Dot1L-deficient cells, whereas expression of PU.1, a transcription factor that inhibits erythropoiesis and promotes myelopoiesis, was increased. These data suggest a model whereby DOT1L-dependent lysine 79 of histone H3 methylation serves as a critical regulator of a differentiation switch during early hematopoiesis, regulating steady-state levels of GATA2 and PU.1 transcription, thus controlling numbers of circulating erythroid and myeloid cells.

scholarly journals Stability and Lability of Parental Methylation Imprints in Development and Disease

Genes ◽  
2019 ◽  
Vol 10 (12) ◽  
pp. 999 ◽  
Author(s):  
Sabina Farhadova ◽  
Melisa Gomez-Velazquez ◽  
Robert Feil
Keyword(s):  
Gene Expression ◽  
Dna Methylation ◽  
Histone Methylation ◽  
Histone Variants ◽  
Dna Demethylation ◽  
Congenital Disorders ◽  
Epigenetic Mechanisms ◽  
Allelic Gene ◽  
The Stability ◽  
Covalent Histone Modifications

DNA methylation plays essential roles in mammals. Of particular interest are parental methylation marks that originate from the oocyte or the sperm, and bring about mono-allelic gene expression at defined chromosomal regions. The remarkable somatic stability of these parental imprints in the pre-implantation embryo—where they resist global waves of DNA demethylation—is not fully understood despite the importance of this phenomenon. After implantation, some methylation imprints persist in the placenta only, a tissue in which many genes are imprinted. Again here, the underlying epigenetic mechanisms are not clear. Mouse studies have pinpointed the involvement of transcription factors, covalent histone modifications, and histone variants. These and other features linked to the stability of methylation imprints are instructive as concerns their conservation in humans, in which different congenital disorders are caused by perturbed parental imprints. Here, we discuss DNA and histone methylation imprints, and why unravelling maintenance mechanisms is important for understanding imprinting disorders in humans.

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

2005 ◽  
Vol 25 (11) ◽  
pp. 4650-4661 ◽  
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.

scholarly journals Characterization of histone modifications associated with DNA damage repair genes upon exposure to gamma rays in Arabidopsis seedlings

2016 ◽  
Vol 57 (6) ◽  
pp. 646-654 ◽  
Author(s):  
Suvendu Mondal ◽  
Young Sam Go ◽  
Seung Sik Lee ◽  
Byung Yeoup Chung ◽  
Jin-Hong Kim
Keyword(s):  
Gene Expression ◽  
Dna Methylation ◽  
Gamma Irradiation ◽  
Histone Modifications ◽  
Gamma Rays ◽  
Regulation Of Gene Expression ◽  
Chromatin Modification ◽  
Histone H3 ◽  
Marker Genes ◽  
Transcription Start Sites

Abstract Dynamic histone modifications play an important role in controlling gene expression in response to various environmental cues. This mechanism of regulation of gene expression is important for sessile organisms, like land plants. We have previously reported consistent upregulation of various marker genes in response to gamma rays at various post-irradiation times. In the present study, we performed various chromatin modification analyses at selected loci using the standard chromatin immunoprecipitation procedure, and demonstrate that upregulation of these genes is associated with histone H3 lysine 4 tri-methylation (H3K4me3) at the gene body or transcription start sites of these loci. Further, at specific AtAgo2 loci, both H3K4me3 and histone H3 lysine 9 acetylation (H3K9ac) are important in controlling gene expression in response to gamma irradiation. There was no change in DNA methylation in these selected loci. We conclude that specific histone modification such as H3K4me3 and H3K9ac may be more important in activating gene expression in these selected loci in response to gamma irradiation than a change in DNA methylation.

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