DNA methylation, histone H3 methylation, and histone H4 acetylation in the genome of a crustacean

In this work, we used antibodies against histone H3 trimethylated at lysine 9 (H3K9m3); against histone H4 acetylated at lysines 5, 8, 12, and 16 (H4ac); and against DNA methylated at 5C cytosine (m5C) to study the presence and distribution of these markers in the genome of the isopod crustacean Asellus aquaticus. The use of these 3 antibodies to immunolabel spermatogonial metaphases yields reproducible patterns on the chromosomes of this crustacean. The X and Y chromosomes present an identical banding pattern with each of the antibodies. The heterochromatic telo meric regions and the centromeric regions are rich in H3K9m3, but depleted in m5C and H4ac. Thus, m5C does not seem to be required to stabilize the silence of these regions in this organism.Key words: DNA methylation, H3 methylation, H4 acetylation, crustacean, Asellus aquaticus.

Download Full-text

DNMT1 reads heterochromatic H4K20me3 to reinforce LINE-1 DNA methylation

Nature Communications ◽

10.1038/s41467-021-22665-4 ◽

2021 ◽

Vol 12 (1) ◽

Author(s):

Wendan Ren ◽

Huitao Fan ◽

Sara A. Grimm ◽

Jae Jin Kim ◽

Linhui Li ◽

...

Keyword(s):

Dna Methylation ◽

Dna Methyltransferase ◽

Histone H3 ◽

Genomic Stability ◽

Mammalian Genome ◽

Dna Methyltransferase 1 ◽

Chromatin Modifications ◽

Direct Link ◽

Histone H4 ◽

Radiation Induced

AbstractDNA methylation and trimethylated histone H4 Lysine 20 (H4K20me3) constitute two important heterochromatin-enriched marks that frequently cooperate in silencing repetitive elements of the mammalian genome. However, it remains elusive how these two chromatin modifications crosstalk. Here, we report that DNA methyltransferase 1 (DNMT1) specifically ‘recognizes’ H4K20me3 via its first bromo-adjacent-homology domain (DNMT1BAH1). Engagement of DNMT1BAH1-H4K20me3 ensures heterochromatin targeting of DNMT1 and DNA methylation at LINE-1 retrotransposons, and cooperates with the previously reported readout of histone H3 tail modifications (i.e., H3K9me3 and H3 ubiquitylation) by the RFTS domain to allosterically regulate DNMT1’s activity. Interplay between RFTS and BAH1 domains of DNMT1 profoundly impacts DNA methylation at both global and focal levels and genomic resistance to radiation-induced damage. Together, our study establishes a direct link between H4K20me3 and DNA methylation, providing a mechanism in which multivalent recognition of repressive histone modifications by DNMT1 ensures appropriate DNA methylation patterning and genomic stability.

Download Full-text

Sites of Acetylation on Newly Synthesized Histone H4 Are Required for Chromatin Assembly and DNA Damage Response Signaling

Molecular and Cellular Biology ◽

10.1128/mcb.00460-13 ◽

2013 ◽

Vol 33 (16) ◽

pp. 3286-3298 ◽

Cited By ~ 19

Author(s):

Zhongqi Ge ◽

Devi Nair ◽

Xiaoyan Guan ◽

Neha Rastogi ◽

Michael A. Freitas ◽

...

Keyword(s):

Dna Damage ◽

Dna Damage Response ◽

Histone H3 ◽

Model Organism ◽

Strand Break ◽

Chromatin Assembly ◽

Histone H4 ◽

Histone H4 Acetylation ◽

Damage Response ◽

A Site

The best-characterized acetylation of newly synthesized histone H4 is the diacetylation of the NH2-terminal tail on lysines 5 and 12. Despite its evolutionary conservation, this pattern of modification has not been shown to be essential for either viability or chromatin assembly in any model organism. We demonstrate that mutations in histone H4 lysines 5 and 12 in yeast confer hypersensitivity to replication stress and DNA-damaging agents when combined with mutations in histone H4 lysine 91, which has also been found to be a site of acetylation on soluble histone H4. In addition, these mutations confer a dramatic decrease in cell viability when combined with mutations in histone H3 lysine 56. We also show that mutation of the sites of acetylation on newly synthesized histone H4 results in defects in the reassembly of chromatin structure that accompanies the repair of HO-mediated double-strand breaks. This defect is not due to a decrease in the level of histone H3 lysine 56 acetylation. Intriguingly, mutations that alter the sites of newly synthesized histone H4 acetylation display a marked decrease in levels of phosphorylated H2A (γ-H2AX) in chromatin surrounding the double-strand break. These results indicate that the sites of acetylation on newly synthesized histones H3 and H4 can function in nonoverlapping ways that are required for chromatin assembly, viability, and DNA damage response signaling.

Download Full-text

Dynamics of DNA methylation and Histone H4 acetylation during floral bud differentiation in azalea

BMC Plant Biology ◽

10.1186/1471-2229-10-10 ◽

2010 ◽

Vol 10 (1) ◽

pp. 10 ◽

Cited By ~ 27

Author(s):

Mónica Meijón ◽

Isabel Feito ◽

Luis Valledor ◽

Roberto Rodríguez ◽

María Cañal

Keyword(s):

Dna Methylation ◽

Histone H4 ◽

Histone H4 Acetylation ◽

Floral Bud

Download Full-text

Vitrification of pig oocytes induces changes in histone H4 acetylation and histone H3 lysine 9 methylation (H3K9)

Veterinary Research Communications ◽

10.1007/s11259-012-9527-9 ◽

2012 ◽

Vol 36 (3) ◽

pp. 165-171 ◽

Cited By ~ 19

Author(s):

M. Spinaci ◽

C. Vallorani ◽

D. Bucci ◽

C. Tamanini ◽

E. Porcu ◽

...

Keyword(s):

Histone H3 ◽

Histone H4 ◽

Histone H4 Acetylation

Download Full-text

The Involvement of Histone H3 Acetylation in Bovine Herpesvirus 1 Replication in MDBK Cells

Viruses ◽

10.3390/v10100525 ◽

2018 ◽

Vol 10 (10) ◽

pp. 525 ◽

Cited By ~ 3

Author(s):

Liqian Zhu ◽

Xinyi Jiang ◽

Xiaotian Fu ◽

Yanhua Qi ◽

Guoqiang Zhu

Keyword(s):

Histone H3 ◽

Bovine Herpesvirus ◽

Productive Infection ◽

Histone H4 ◽

Bovine Herpesvirus 1 ◽

Amino Acid Synthesis ◽

Histone H4 Acetylation ◽

Histone H3 Acetylation ◽

Herpesvirus 1 ◽

H3 Acetylation

During bovine herpesvirus 1 (BoHV-1) productive infection in cell cultures, partial of intranuclear viral DNA is present in nucleosomes, and viral protein VP22 associates with histones and decreases histone H4 acetylation, indicating the involvement of histone H4 acetylation in virus replication. In this study, we demonstrated that BoHV-1 infection at the late stage (at 24 h after infection) dramatically decreased histone H3 acetylation [at residues K9 (H3K9ac) and K18 (H3K18ac)], which was supported by the pronounced depletion of histone acetyltransferases (HATs) including CBP/P300 (CREB binding protein and p300), GCN5L2 (general control of amino acid synthesis yeast homolog like 2) and PCAF (P300/CBP-associated factor). The depletion of GCN5L2 promoted by virus infection was partially mediated by ubiquitin-proteasome pathway. Interestingly, the viral replication was enhanced by HAT (histone acetyltransferase) activator CTPB [N-(4-Chloro-3-trifluoromethylphenyl)-2-ethoxy-6-pentadecylbenzamide], and vice versa, inhibited by HAT inhibitor Anacardic acid (AA), suggesting that BoHV-1 may take advantage of histone acetylation for efficient replication. Taken together, we proposed that the HAT-dependent histone H3 acetylation plays an important role in BoHV-1 replication in MDBK (Madin-Darby bovine kidney) cells.

Download Full-text

Posttranslational modifications in histones underlie heat acclimation-mediated cytoprotective memory

Journal of Applied Physiology ◽

10.1152/japplphysiol.00469.2010 ◽

2010 ◽

Vol 109 (5) ◽

pp. 1552-1561 ◽

Cited By ~ 34

Author(s):

Anna Tetievsky ◽

Michal Horowitz

Keyword(s):

Heat Shock ◽

Posttranslational Modifications ◽

Histone Acetyltransferase ◽

Histone H3 ◽

Heat Acclimation ◽

Heat Shock Factor 1 ◽

Histone H4 ◽

Heat Shock Element ◽

H3 Phosphorylation ◽

Histone H4 Acetylation

We have demonstrated that heat acclimation (AC) causes selective, long-lasting, transcriptional changes in cytoprotective and chromatin remodeling-associated genes, which maintain their AC transcriptome profile, despite the loss of the AC phenotype (Tetievsky et al. Physiol Genomics 34: 78–87, 2008). We postulated that AC memory involves upstream epigenetic information, which predisposes to rapid reacclimation (ReAC) and cytoprotective memory. Here we tested the hypothesis that posttranslational histone modifications are linked to this process. Rats subjected to AC (34°C for 2 or 30 days), deacclimation (DeAC; 24°C, 30 days), and ReAC (34°C, 2 days), and untreated controls were used. Histone H4 lysine acetylation and histone H3 acetylation and phosphorylation in the heat shock element (HSE) of the promoters of heat shock protein-70 ( hsp70) and -90 ( hsp90) genes were examined. Histone acetyltransferase recruitment of TIP60 (60-kDa histone acetyltransferase-interactive protein), the catalytic subunit of NuH4, was used to validate acetylation. Heat shock factor-1 (HSF-1)-HSE binding to the hsp70 and hsp90 genes was measured to confirm HSF-1 binding to euchromatin. Our results indicate that, while histone H3Ser10 phosphorylation occurred during the AC 2-day phase, AC constitutively elevated histone H4 acetylation in the HSE of hsp70 and hsp90 promoters. HSF-1-HSE binding was detected in the hsp70 gen e throughout AC-DeAC-ReAC. The hsp90 gene lacked HSF-1 binding during DeAC, but resumed a high binding level upon ReAC. HSP-90 is a critical cytoprotective protein, and the HSF-1- hsp90 binding profile matched levels of this protein. We conclude that, while early histone H3 phosphorylation is probably required for subsequent histone H4 acetylation, the constitutively acetylated histone H4 and the preserved euchromatin state throughout AC-DeAC-ReAC predispose to rapid cytoprotective acclimatory memory.

Download Full-text

Epigenetic chromatin modifications in Brassica genomes

Genome ◽

10.1139/g09-088 ◽

2010 ◽

Vol 53 (3) ◽

pp. 203-210 ◽

Cited By ~ 19

Author(s):

Agnieszka Braszewska-Zalewska ◽

Tytus Bernas ◽

Jolanta Maluszynska

Keyword(s):

Dna Methylation ◽

Ploidy Level ◽

Genome Structure ◽

Histone H3 ◽

Diploid Species ◽

Brassica Species ◽

Epigenetic Modifications ◽

Chromatin Modifications ◽

Histone H3 Methylation ◽

Allotetraploid Species

Epigenetic modifications such as histone and DNA methylation are highly conserved among eukaryotes, although the nuclear patterns of these modifications vary between different species. Brassica species represent a very attractive model for analysis of epigenetic changes because of their differences in genome size, ploidy level, and the organization of heterochromatin blocks. Brassica rapa and B. oleracea are diploid species, and B. napus is an allotetraploid species that arose from the hybridization of these two diploids. We found that patterns of DNA and histone H3 methylation differ between Brassica species. The most prominent differences concern the two diploids. DNA methylation was present exclusively in the heterochromatin only in B. rapa. In B. oleracea and B. napus this modification was detected in both euchromatin and heterochromatin. A similar pattern was observed for dimethylation of lysine 9. Dimethylation of lysine 4 is a typical marker of euchromatin in Brassica species, like it is in other plant species. We conclude that the diploid species differ in patterns of analyzed epigenetic modifications and the allotetraploid B. napus has combined patterns from both diploids. Differences in patterns of DNA and histone H3 methylation between Brassica species can be attributed mainly to the genome structure and heterochromatin localization rather than ploidy level.

Download Full-text

Epigenetic characterization of the vegetative and floral stages of azalea buds: Dynamics of DNA methylation and histone H4 acetylation

Journal of Plant Physiology ◽

10.1016/j.jplph.2009.04.014 ◽

2009 ◽

Vol 166 (15) ◽

pp. 1624-1636 ◽

Cited By ~ 26

Author(s):

Mónica Meijón ◽

Luis Valledor ◽

Estrella Santamaría ◽

Pilar S. Testillano ◽

Ma Carmen Risueño ◽

...

Keyword(s):

Dna Methylation ◽

Histone H4 ◽

Histone H4 Acetylation

Download Full-text

Transcription-Coupled Methylation of Histone H3 at Lysine 36 Regulates Dosage Compensation by Enhancing Recruitment of the MSL Complex in Drosophila melanogaster

Molecular and Cellular Biology ◽

10.1128/mcb.00006-08 ◽

2008 ◽

Vol 28 (10) ◽

pp. 3401-3409 ◽

Cited By ~ 38

Author(s):

Oliver Bell ◽

Thomas Conrad ◽

Jop Kind ◽

Christiane Wirbelauer ◽

Asifa Akhtar ◽

...

Keyword(s):

Drosophila Melanogaster ◽

X Chromosome ◽

Dosage Compensation ◽

Histone H3 ◽

The Body ◽

Histone H4 ◽

Histone H3 Methylation ◽

Msl Complex ◽

Male Specific ◽

Active Genes

ABSTRACT In Drosophila melanogaster, dosage compensation relies on the targeting of the male-specific lethal (MSL) complex to hundreds of sites along the male X chromosome. Transcription-coupled methylation of histone H3 lysine 36 is enriched toward the 3′ end of active genes, similar to the MSL proteins. Here, we have studied the link between histone H3 methylation and MSL complex targeting using RNA interference and chromatin immunoprecipitation. We show that trimethylation of histone H3 at lysine 36 (H3K36me3) relies on the histone methyltransferase Hypb and is localized promoter distal at dosage-compensated genes, similar to active genes on autosomes. However, H3K36me3 has an X-specific function, as reduction specifically decreases acetylation of histone H4 lysine 16 on the male X chromosome. This hypoacetylation is caused by compromised MSL binding and results in a failure to increase expression twofold. Thus, H3K36me3 marks the body of all active genes yet is utilized in a chromosome-specific manner to enhance histone acetylation at sites of dosage compensation.

Download Full-text