Changes in Epigenetic Patterns Related to DNA Replication in Vicia faba Root Meristem Cells under Cadmium-Induced Stress Conditions

Experiments on Vicia faba root meristem cells exposed to 150 µM cadmium chloride (CdCl2) were undertaken to analyse epigenetic changes, mainly with respect to DNA replication stress. Histone modifications examined by means of immunofluorescence labeling included: (1) acetylation of histone H3 on lysine 56 (H3K56Ac), involved in transcription, S phase, and response to DNA damage during DNA biosynthesis; (2) dimethylation of histone H3 on lysine 79 (H3K79Me2), correlated with the replication initiation; (3) phosphorylation of histone H3 on threonine 45 (H3T45Ph), engaged in DNA synthesis and apoptosis. Moreover, immunostaining using specific antibodies against 5-MetC-modified DNA was used to determine the level of DNA methylation. A significant decrease in the level of H3K79Me2, noted in all phases of the CdCl2-treated interphase cell nuclei, was found to correspond with: (1) an increase in the mean number of intranuclear foci of H3K56Ac histones (observed mainly in S-phase), (2) a plethora of nuclear and nucleolar labeling patterns (combined with a general decrease in H3T45Ph), and (3) a decrease in DNA methylation. All these changes correlate well with a general viewpoint that DNA modifications and post-translational histone modifications play an important role in gene expression and plant development under cadmium-induced stress conditions.

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Dynamic Methylation Changes of DNA and H3K4 by RG108 Improve Epigenetic Reprogramming of Somatic Cell Nuclear Transfer Embryos in Pigs

Cellular Physiology and Biochemistry ◽

10.1159/000494598 ◽

2018 ◽

Vol 50 (4) ◽

pp. 1376-1397 ◽

Cited By ~ 5

Author(s):

Yanhui Zhai ◽

Zhiren Zhang ◽

Hao Yu ◽

Li Su ◽

Gang Yao ◽

...

Keyword(s):

Dna Methylation ◽

Somatic Cell ◽

Histone Modifications ◽

Somatic Cell Nuclear Transfer ◽

Nuclear Transfer ◽

Histone H3 ◽

Dna Demethylation ◽

Epigenetic Reprogramming ◽

Expression Levels ◽

Fetal Fibroblasts

Background/Aims: DNA methylation and histone modifications are essential epigenetic marks that can significantly affect the mammalian somatic cell nuclear transfer (SCNT) embryo development. However, the mechanisms by which the DNA methylation affects the epigenetic reprogramming have not been fully elucidated. Methods: In our study, we used quantitative polymerase chain reaction (qPCR), Western blotting, immunofluorescence staining (IF) and sodium bisulfite genomic sequencing to examine the effects of RG108, a DNA methyltransferase inhibitor (DNMTi), on the dynamic pattern of DNA methylation and histone modifications in porcine SCNT embryos and investigate the mechanism by which the epigenome status of donor cells’ affects SCNT embryos development and the crosstalk between epigenetic signals. Results: Our results showed that active DNA demethylation was enhanced by the significantly improving expression levels of TET1, TET2, TET3 and 5hmC, and passive DNA demethylation was promoted by the remarkably inhibitory expression levels of DNMT1, DNMT3A and 5mC in embryos constructed from the fetal fibroblasts (FFs) treated with RG108 (RG-SCNT embryos) compared to the levels in embryos from control FFs (FF-SCNT embryos). The signal intensity of histone H3 lysine 4 trimethylation (H3K4me3) and histone H3 lysine 9 acetylation (H3K9Ac) was significantly increased and the expression levels of H3K4 methyltransferases were more than 2-fold higher expression in RG-SCNT embryos. RG-SCNT embryos had significantly higher cleavage and blastocyst rates (69.3±1.4%, and 24.72±2.3%, respectively) than FF-SCNT embryos (60.1±2.4% and 18.38±1.9%, respectively). Conclusion: Dynamic changes in DNA methylation caused by RG108 result in dynamic alterations in the patterns of H3K4me3, H3K9Ac and histone H3 lysine 9 trimethylation (H3K9me3), which leads to the activation of embryonic genome and epigenetic modification enzymes associated with H3K4 methylation, and contributes to reconstructing normal epigenetic modifications and improving the developmental efficiency of porcine SCNT embryos.

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Variable S-phase duration in Vicia faba root meristem cells

Environmental and Experimental Botany ◽

10.1016/0098-8472(78)90014-x ◽

1978 ◽

Vol 18 (1) ◽

pp. 1-8 ◽

Cited By ~ 10

Author(s):

Morton W. Miller ◽

Annie Brulfert ◽

Gary E. Kaufman

Keyword(s):

Vicia Faba ◽

Root Meristem ◽

S Phase ◽

Phase Duration

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Staying true to yourself: mechanisms of DNA methylation maintenance in mammals

Nucleic Acids Research ◽

10.1093/nar/gkaa1154 ◽

2020 ◽

Author(s):

Nataliya Petryk ◽

Sebastian Bultmann ◽

Till Bartke ◽

Pierre-Antoine Defossez

Keyword(s):

Dna Methylation ◽

Dna Replication ◽

Neurological Disorders ◽

Normal Development ◽

Epigenetic Modification ◽

S Phase ◽

Epigenetic Mark ◽

Chromatin Modifications ◽

Methylated Dna ◽

Cellular Physiology

Abstract DNA methylation is essential to development and cellular physiology in mammals. Faulty DNA methylation is frequently observed in human diseases like cancer and neurological disorders. Molecularly, this epigenetic mark is linked to other chromatin modifications and it regulates key genomic processes, including transcription and splicing. Each round of DNA replication generates two hemi-methylated copies of the genome. These must be converted back to symmetrically methylated DNA before the next S-phase, or the mark will fade away; therefore the maintenance of DNA methylation is essential. Mechanistically, the maintenance of this epigenetic modification takes place during and after DNA replication, and occurs within the very dynamic context of chromatin re-assembly. Here, we review recent discoveries and unresolved questions regarding the mechanisms, dynamics and fidelity of DNA methylation maintenance in mammals. We also discuss how it could be regulated in normal development and misregulated in disease.

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Histone H3 lysine 56 acetylation by Rtt109 is crucial for chromosome positioning

The Journal of Cell Biology ◽

10.1083/jcb.200806065 ◽

2008 ◽

Vol 183 (4) ◽

pp. 641-651 ◽

Cited By ~ 26

Author(s):

Shin-ichiro Hiraga ◽

Sotirios Botsios ◽

Anne D. Donaldson

Keyword(s):

Saccharomyces Cerevisiae ◽

Dna Replication ◽

Histone Acetyltransferase ◽

Nuclear Periphery ◽

Histone H3 ◽

Epigenetic Inheritance ◽

S Phase ◽

Chromosome Localization ◽

Chromosome Domains ◽

H3k56 Acetylation

Correct intranuclear organization of chromosomes is crucial for many genome functions, but the mechanisms that position chromatin are not well understood. We used a layered screen to identify Saccharomyces cerevisiae mutants defective in telomere localization to the nuclear periphery. We find that events in S phase are crucial for correct telomere localization. In particular, the histone chaperone Asf1 functions in telomere peripheral positioning. Asf1 stimulates acetylation of histone H3 lysine 56 (H3K56) by the histone acetyltransferase Rtt109. Analysis of rtt109Δ and H3K56 mutants suggests that the acetylation/deacetylation cycle of the H3K56 residue is required for proper telomere localization. The function of H3K56 acetylation in localizing chromosome domains is not confined to telomeres because deletion of RTT109 also prevents the correct peripheral localization of a newly identified S. cerevisiae “chromosome-organizing clamp” locus. Because chromosome positioning is subject to epigenetic inheritance, H3K56 acetylation may mediate correct chromosome localization by facilitating accurate transmission of chromatin status during DNA replication.

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

Journal of Radiation Research ◽

10.1093/jrr/rrw077 ◽

2016 ◽

Vol 57 (6) ◽

pp. 646-654 ◽

Cited By ~ 9

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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Effect of hydroxyurea on mitotic activity 3H-thymidine and 3H-phenylalanine incorporation in the antheridial filament cells of Chara vulgaris

Acta Societatis Botanicorum Poloniae ◽

10.5586/asbp.1979.016 ◽

2015 ◽

Vol 48 (2) ◽

pp. 179-193 ◽

Cited By ~ 1

Author(s):

Anastazja Bilecka

Keyword(s):

Protein Synthesis ◽

Dna Replication ◽

Helianthus Annuus ◽

Mitotic Activity ◽

Vicia Faba ◽

Root Meristem ◽

Thymidine Incorporation ◽

Chara Vulgaris ◽

Slowing Down ◽

In Cells

Hydroxyurea inhibits mitotic activity in cells of the antheridial filaments of Chara vulgaris by blocking phase S and phase G2. Blocking of cells in phase G2 also occurs in the case of the root meristem cells of Helianthus annuus and Vicia faba var. minor. 3H-thymidine incorporation confirmed autoradiographically the blocking of cells of the antheridial filaments in Chara vulgaris at phase S and slowing down of the rate of DNA replication. Incubation with 3H-phenylalanine demonstrated that hydroxyurea inhibits protein synthesis.

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Epigenetic inheritance uncoupled from sequence-specific recruitment

Science ◽

10.1126/science.1258699 ◽

2014 ◽

Vol 348 (6230) ◽

pp. 1258699 ◽

Cited By ~ 155

Author(s):

Kaushik Ragunathan ◽

Gloria Jih ◽

Danesh Moazed

Keyword(s):

Gene Expression ◽

Dna Methylation ◽

Histone Modifications ◽

Posttranslational Modifications ◽

Histone H3 ◽

Epigenetic Inheritance ◽

Meiotic Cell ◽

Epigenetic Information ◽

Cell Divisions ◽

Jmjc Domain

Changes in histone posttranslational modifications are associated with epigenetic states that define distinct patterns of gene expression. It remains unclear whether epigenetic information can be transmitted through histone modifications independently of specific DNA sequence, DNA methylation, or RNA interference. Here we show that, in the fission yeast Schizosaccharomyces pombe, ectopically induced domains of histone H3 lysine 9 methylation (H3K9me), a conserved marker of heterochromatin, are inherited through several mitotic and meiotic cell divisions after removal of the sequence-specific initiator. The putative JmjC domain H3K9 demethylase, Epe1, and the chromodomain of the H3K9 methyltransferase, Clr4/Suv39h, play opposing roles in maintaining silent H3K9me domains. These results demonstrate how a direct “read-write” mechanism involving Clr4 propagates histone modifications and allows histones to act as carriers of epigenetic information.

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Inheritance of Repressed Chromatin Domains during S-phase Requires the Histone Chaperone NPM1

10.1101/2021.08.31.458436 ◽

2021 ◽

Author(s):

Thelma M. Escobar ◽

Jia-Ray Yu ◽

Sanxiong Liu ◽

Kimberly Lucero ◽

Nikita Vasilyev ◽

...

Keyword(s):

Dna Replication ◽

Expression Profiles ◽

Histone H3 ◽

Gene Expression Profiles ◽

Epigenetic Inheritance ◽

S Phase ◽

Facultative Heterochromatin ◽

Chromatin Domains ◽

Epigenetic Process ◽

Integral Component

AbstractThe epigenetic process safeguards cell identity during cell division through the inheritance of appropriate gene expression profiles. We demonstrated previously that parental nucleosomes are inherited by the same chromatin domains during DNA replication only in the case of repressed chromatin. We now show that this specificity is conveyed by NPM1, a histone H3/H4 chaperone. Proteomic analyses of late S-phase chromatin revealed NPM1 in association with both H3K27me3, an integral component of facultative heterochromatin and MCM2, an integral component of the DNA replication machinery; moreover NPM1 interacts directly with PRC2 and with MCM2. Given that NPM1 is essential, the inheritance of repressed chromatin domains was examined anew using mESCs expressing an auxin-degradable version of endogenous NPM1. Upon NPM1 degradation, cells accumulated in S-phase of the cell-cycle and parental nucleosome inheritance from repressed chromatin domains was markedly compromised. Appropriate inheritance required the NPM1 acidic patches that function in chaperone activity, pointing to NPM1 being integral to the epigenetic process.One-Sentence SummaryThe histone H3/H4 chaperone, NPM1, fosters epigenetic inheritance from parental repressed chromatin during DNA replication.

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Genome duplication in Leishmania major relies on persistent subtelomeric DNA replication

eLife ◽

10.7554/elife.58030 ◽

2020 ◽

Vol 9 ◽

Author(s):

Jeziel Dener Damasceno ◽

Catarina A Marques ◽

Dario Beraldi ◽

Kathryn Crouch ◽

Craig Lapsley ◽

...

Keyword(s):

Cell Division ◽

Dna Replication ◽

Leishmania Major ◽

Genome Duplication ◽

Histone H3 ◽

S Phase ◽

Replication Initiation ◽

G1 Phase ◽

Dna Replication Initiation ◽

Single Region

DNA replication is needed to duplicate a cell’s genome in S phase and segregate it during cell division. Previous work in Leishmania detected DNA replication initiation at just a single region in each chromosome, an organisation predicted to be insufficient for complete genome duplication within S phase. Here, we show that acetylated histone H3 (AcH3), base J and a kinetochore factor co-localise in each chromosome at only a single locus, which corresponds with previously mapped DNA replication initiation regions and is demarcated by localised G/T skew and G4 patterns. In addition, we describe previously undetected subtelomeric DNA replication in G2/M and G1-phase-enriched cells. Finally, we show that subtelomeric DNA replication, unlike chromosome-internal DNA replication, is sensitive to hydroxyurea and dependent on 9-1-1 activity. These findings indicate that Leishmania’s genome duplication programme employs subtelomeric DNA replication initiation, possibly extending beyond S phase, to support predominantly chromosome-internal DNA replication initiation within S phase.

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Structure study of UHRF1, recoginition of epigenetic marks.

Acta Crystallographica Section A Foundations and Advances ◽

10.1107/s2053273314084095 ◽

2014 ◽

Vol 70 (a1) ◽

pp. C1590-C1590

Author(s):

Kyohei Arita ◽

Mariko Ariyoshi ◽

Kazuya Sugita ◽

Hidehito Tochio ◽

Masahiro Shirakawa

Keyword(s):

Crystal Structure ◽

Dna Methylation ◽

Dna Binding ◽

Histone Modifications ◽

Dna Methyltransferase ◽

Histone H3 ◽

Ring Finger ◽

Structural Basis ◽

Epigenetic Marks ◽

Methylated Dna

Two major epigenetic traits, histone modifications and DNA methylation, regulate various chromatin-template processes in mammals. The pattern of these epigenetic traits is cooperatively established in early embryogenesis and cell development, and inherited during the cell cycle. UHRF1 (also known as Np95 or ICBP90) is believed to play an important role in linking the two major epigenetic traits. UHRF1 has five functional domains, UBL, Tandem Tudor (TTD), pland homeo domain (PHD), SET and RING-associated doain (SRA) and RING finger. To maintain DNA methylation pattern, UHRF1 recognizes hemi-methylated DNA generated during DNA replication through interactions with its SRA domain, and recruit maintenance of DNA methyltransferase Dnmt1 to the site [1], [2]. UHRF1 also recognizes histone H3 containing tri-methylated Lys9 (H3K9me3) via its TTD-PHD moiety. [3]. To obtain the structural basis for recognition of epigenetic marks by UHRF1, we determined the crystal structure of the SRA domain in complex with hemi-methylated DNA. The structure showed that the DNA binding caused a loop and an N-terminal tail of the SRA domain. Interestingly, the methyl-cytosine base at the hemi-methylation site was flipped out from the DNA helix, which has not observed in other DNA binding proteins. These results suggest that the Base flip out mechanism is important event for maintenance of DNA methylation. We also determined the crystal structure of TTD-PHD region of UHRF1 in complex with H3K9me3 peptide. To our surprise, the linker region between the reader modules, which is predicted as an intrinsically disorder, was formed a stable structure with binding to the groove of TTD and plays an essential role in the formation of histone H3 binding hole between the reader modules. The structure revealed how multiple histone modifications were simultaneously decoded by the linked histone reader modules of UHRF1.

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