scholarly journals Coordinated regulation of heterochromatin inheritance by Dpb3–Dpb4 complex

2017 ◽  
Vol 114 (47) ◽  
pp. 12524-12529 ◽  
Author(s):  
Haijin He ◽  
Yang Li ◽  
Qianhua Dong ◽  
An-Yun Chang ◽  
Feng Gao ◽  
...  
Keyword(s):  
Dna Replication ◽  
Histone Deacetylases ◽  
Histone Deacetylation ◽  
H3k9 Methylation ◽  
Epigenetic Marks ◽  
Chromatin Remodelers ◽  
Dna Polymerase Epsilon ◽  
Histone Fold ◽  
Heterochromatin Silencing ◽  
Histone Hypoacetylation

During DNA replication, chromatin is disrupted ahead of the replication fork, and epigenetic information must be restored behind the fork. How epigenetic marks are inherited through DNA replication remains poorly understood. Histone H3 lysine 9 (H3K9) methylation and histone hypoacetylation are conserved hallmarks of heterochromatin. We previously showed that the inheritance of H3K9 methylation during DNA replication depends on the catalytic subunit of DNA polymerase epsilon, Cdc20. Here we show that the histone-fold subunit of Pol epsilon, Dpb4, interacts an uncharacterized small histone-fold protein, SPCC16C4.22, to form a heterodimer in fission yeast. We demonstrate that SPCC16C4.22 is nonessential for viability and corresponds to the true ortholog of Dpb3. We further show that the Dpb3–Dpb4 dimer associates with histone deacetylases, chromatin remodelers, and histones and plays a crucial role in the inheritance of histone hypoacetylation in heterochromatin. We solve the 1.9-Å crystal structure of Dpb3–Dpb4 and reveal that they form the H2A–H2B-like dimer. Disruption of Dpb3–Dpb4 dimerization results in loss of heterochromatin silencing. Our findings reveal a link between histone deacetylation and H3K9 methylation and suggest a mechanism for how two processes are coordinated during replication. We propose that the Dpb3–Dpb4 heterodimer together with Cdc20 serves as a platform for the recruitment of chromatin modifiers and remodelers that mediate heterochromatin assembly during DNA replication, and ensure the faithful inheritance of epigenetic marks in heterochromatin.

The histone chaperone FACT facilitates heterochromatin spreading through regulation of histone turnover and H3K9 methylation states

2021 ◽  
Author(s):  
Magdalena Murawska ◽  
R. A. Greenstein ◽  
Tamas Schauer ◽  
Karl C.F. Olsen ◽  
Henry Ng ◽  
...  
Keyword(s):  
Gene Expression ◽  
Histone Chaperone ◽  
Replication Cycle ◽  
H3k9 Methylation ◽  
Spreading Process ◽  
Epigenetic Marks ◽  
Heterochromatin Formation ◽  
Heterochromatin Silencing

Heterochromatin formation requires three distinct steps: nucleation, self-propagation (spreading) along the chromosome, and faithful maintenance after each replication cycle. Impeding any of those steps induces heterochromatin defects and improper gene expression. The essential histone chaperone FACT has been implicated in heterochromatin silencing, however, the mechanisms by which FACT engages in this process remain opaque. Here, we pin-pointed its function to the heterochromatin spreading process. FACT impairment reduces nucleation-distal H3K9me3 and HP1/Swi6 accumulation at subtelomeres and de-represses genes in the vicinity of heterochromatin boundaries. FACT promotes spreading by repressing heterochromatic histone turnover, which is crucial for the H3K9me2 to me3 transition that enables spreading. FACT mutant spreading defects are suppressed by removal of the H3K9 methylation antagonist Epe1 via nucleosome stabilization. Together, our study identifies FACT as a histone chaperone that specifically promotes heterochromatin spreading and lends support to the model that regulated histone turnover controls the propagation of epigenetic marks.

Dri1 mediates heterochromatin assembly via RNAi and histone deacetylation

Genetics ◽  
2021 ◽  
Author(s):  
Hyoju Ban ◽  
Wenqi Sun ◽  
Yu-hang Chen ◽  
Yong Chen ◽  
Fei Li
Keyword(s):  
Histone Deacetylases ◽  
Genome Stability ◽  
Rna Binding ◽  
Histone Deacetylation ◽  
Rnai Pathway ◽  
Chromatin Domain ◽  
Heterochromatin Protein 1 ◽  
Intrinsically Disordered ◽  
C Terminus ◽  
Heterochromatin Assembly

Abstract Heterochromatin, a transcriptionally silenced chromatin domain, is important for genome stability and gene expression. Histone 3 lysine 9 methylation (H3K9me) and histone hypoacetylation are conserved epigenetic hallmarks of heterochromatin. In fission yeast, RNA interference (RNAi) plays a key role in H3K9 methylation and heterochromatin silencing. However, how RNAi machinery and histone deacetylases (HDACs) are coordinated to ensure proper heterochromatin assembly is still unclear. Previously, we showed that Dpb4, a conserved DNA polymerase epsilon subunit, plays a key role in the recruitment of HDACs to heterochromatin during S phase. Here, we identified a novel RNA-binding protein Dri1 that interacts with Dpb4. GFP-tagged Dri1 forms distinct foci mostly in the nucleus, showing a high degree of colocalization with Swi6/Heterochromatin Protein 1. Deletion of dri1+ leads to defects in silencing, H3K9me, and heterochromatic siRNA generation. We also showed that Dri1 physically associates with heterochromatic transcripts, and is required for the recruitment of the RNA-induced transcriptional silencing (RITS) complex via interacting with the complex. Furthermore, loss of Dri1 decreases the association of the Sir2 HDAC with heterochromatin. We further demonstrated that the C-terminus of Dri1 that includes an intrinsically disordered (IDR) region and three zinc fingers is crucial for its role in silencing. Together, our evidences suggest that Dri1 facilitates heterochromatin assembly via the RNAi pathway and HDAC.

scholarly journals SUV39 SET domains mediate crosstalk of heterochromatic histone marks

eLife ◽  
2021 ◽  
Vol 10 ◽  
Author(s):  
Alessandro Stirpe ◽  
Nora Guidotti ◽  
Sarah J Northall ◽  
Sinan Kilic ◽  
Alexandre Hainard ◽  
...  
Keyword(s):  
Structure Function ◽  
Fission Yeast ◽  
Catalytic Domain ◽  
Constitutive Heterochromatin ◽  
Histone H3 ◽  
H3k9 Methylation ◽  
Set Domain ◽  
Heterochromatin Formation ◽  
Heterochromatin Silencing ◽  
Genomic Regions

The SUV39 class of methyltransferase enzymes deposits histone H3 lysine 9 di- and trimethylation (H3K9me2/3), the hallmark of constitutive heterochromatin. How these enzymes are regulated to mark specific genomic regions as heterochromatic is poorly understood. Clr4 is the sole H3K9me2/3 methyltransferase in the fission yeast Schizosaccharomyces pombe, and recent evidence suggests that ubiquitination of lysine 14 on histone H3 (H3K14ub) plays a key role in H3K9 methylation. However, the molecular mechanism of this regulation and its role in heterochromatin formation remain to be determined. Our structure-function approach shows that the H3K14ub substrate binds specifically and tightly to the catalytic domain of Clr4, and thereby stimulates the enzyme by over 250-fold. Mutations that disrupt this mechanism lead to a loss of H3K9me2/3 and abolish heterochromatin silencing similar to clr4 deletion. Comparison with mammalian SET domain proteins suggests that the Clr4 SET domain harbors a conserved sensor for H3K14ub, which mediates licensing of heterochromatin formation.

scholarly journals Food Bioactive HDAC Inhibitors in the Epigenetic Regulation of Heart Failure

Nutrients ◽  
2018 ◽  
Vol 10 (8) ◽  
pp. 1120 ◽  
Author(s):  
Levi Evans ◽  
Bradley Ferguson
Keyword(s):  
Gene Expression ◽  
Heart Failure ◽  
Signaling Pathways ◽  
Intracellular Signaling ◽  
Histone Deacetylases ◽  
Regulation Of Gene Expression ◽  
Hdac Inhibitors ◽  
Drug Efficacy ◽  
Histone Deacetylation ◽  
Epigenetic Modifiers

Approximately 5.7 million U.S. adults have been diagnosed with heart failure (HF). More concerning is that one in nine U.S. deaths included HF as a contributing cause. Current HF drugs (e.g., β-blockers, ACEi) target intracellular signaling cascades downstream of cell surface receptors to prevent cardiac pump dysfunction. However, these drugs fail to target other redundant intracellular signaling pathways and, therefore, limit drug efficacy. As such, it has been postulated that compounds designed to target shared downstream mediators of these signaling pathways would be more efficacious for the treatment of HF. Histone deacetylation has been linked as a key pathogenetic element for the development of HF. Lysine residues undergo diverse and reversible post-translational modifications that include acetylation and have historically been studied as epigenetic modifiers of histone tails within chromatin that provide an important mechanism for regulating gene expression. Of recent, bioactive compounds within our diet have been linked to the regulation of gene expression, in part, through regulation of the epi-genome. It has been reported that food bioactives regulate histone acetylation via direct regulation of writer (histone acetyl transferases, HATs) and eraser (histone deacetylases, HDACs) proteins. Therefore, bioactive food compounds offer unique therapeutic strategies as epigenetic modifiers of heart failure. This review will highlight food bio-actives as modifiers of histone deacetylase activity in the heart.

scholarly journals Histone Deacetylation Inhibitors as Therapy Concept in Sepsis

2019 ◽  
Vol 20 (2) ◽  
pp. 346 ◽  
Author(s):  
Andreas von Knethen ◽  
Bernhard Brüne
Keyword(s):  
Organ Failure ◽  
Expression Profile ◽  
Histone Deacetylases ◽  
Hdac Inhibitors ◽  
Histone Deacetylation ◽  
Histone Acetyltransferases ◽  
Open Chromatin ◽  
Nucleosome Structure ◽  
Active Transcription ◽  
Anti Inflammatory

Sepsis is characterized by dysregulated gene expression, provoking a hyper-inflammatory response occurring in parallel to a hypo-inflammatory reaction. This is often associated with multi-organ failure, leading to the patient’s death. Therefore, reprogramming of these pro- and anti-inflammatory, as well as immune-response genes which are involved in acute systemic inflammation, is a therapy approach to prevent organ failure and to improve sepsis outcomes. Considering epigenetic, i.e., reversible, modifications of chromatin, not altering the DNA sequence as one tool to adapt the expression profile, inhibition of factors mediating these changes is important. Acetylation of histones by histone acetyltransferases (HATs) and initiating an open-chromatin structure leading to its active transcription is counteracted by histone deacetylases (HDACs). Histone deacetylation triggers a compact nucleosome structure preventing active transcription. Hence, inhibiting the activity of HDACs by specific inhibitors can be used to restore the expression profile of the cells. It can be assumed that HDAC inhibitors will reduce the expression of pro-, as well as anti-inflammatory mediators, which blocks sepsis progression. However, decreased cytokine expression might also be unfavorable, because it can be associated with decreased bacterial clearance.

scholarly journals H3K9 Promotes Under-Replication of Pericentromeric Heterochromatin in Drosophila Salivary Gland Polytene Chromosomes

Genes ◽  
2019 ◽  
Vol 10 (2) ◽  
pp. 93 ◽  
Author(s):  
Robin Armstrong ◽  
Taylor Penke ◽  
Samuel Chao ◽  
Gabrielle Gentile ◽  
Brian Strahl ◽  
...  
Keyword(s):  
Salivary Gland ◽  
Dna Replication ◽  
Polytene Chromosomes ◽  
Cell Types ◽  
Gene Replacement ◽  
Pericentric Heterochromatin ◽  
Replication Initiation ◽  
H3k9 Methylation ◽  
Diploid Cells ◽  
And Function

Chromatin structure and its organization contributes to the proper regulation and timing of DNA replication. Yet, the precise mechanism by which chromatin contributes to DNA replication remains incompletely understood. This is particularly true for cell types that rely on polyploidization as a developmental strategy for growth and high biosynthetic capacity. During Drosophila larval development, cells of the salivary gland undergo endoreplication, repetitive rounds of DNA synthesis without intervening cell division, resulting in ploidy values of ~1350C. S phase of these endocycles displays a reproducible pattern of early and late replicating regions of the genome resulting from the activity of the same replication initiation factors that are used in diploid cells. However, unlike diploid cells, the latest replicating regions of polyploid salivary gland genomes, composed primarily of pericentric heterochromatic enriched in H3K9 methylation, are not replicated each endocycle, resulting in under-replicated domains with reduced ploidy. Here, we employ a histone gene replacement strategy in Drosophila to demonstrate that mutation of a histone residue important for heterochromatin organization and function (H3K9) but not mutation of a histone residue important for euchromatin function (H4K16), disrupts proper endoreplication in Drosophila salivary gland polyploid genomes thereby leading to DNA copy gain in pericentric heterochromatin. These findings reveal that H3K9 is necessary for normal levels of under-replication of pericentric heterochromatin and suggest that under-replication at pericentric heterochromatin is mediated through H3K9 methylation.

Epigenetics in the Biology and Treatment of Multiple Myeloma

2016 ◽  
Vol 12 (02) ◽  
pp. 96
Author(s):  
Andrew Spencer ◽  
Sridurga Mithraprabhu ◽  
◽  
Keyword(s):  
Multiple Myeloma ◽  
Histone Deacetylases ◽  
Locally Advanced ◽  
Hdac Inhibitors ◽  
Histone Deacetylation ◽  
Tumour Suppressor Genes ◽  
Cellular Functions ◽  
Global Methylation ◽  
Cytoplasmic Proteins ◽  
Class 1

There is a critical need for more effective therapies in multiple myeloma (MM) since all patients eventually relapse following front-line treatment. A variety of both genetic and epigenetic abnormalities may be present in MM, the latter including DNA and histone methylation and histone deacetylation, and are thought to contribute to the pathogenesis of the disease. For example, global methylation analysis in MM has identified inactivated tumour suppressor genes that are prognostically important. Through their ability to acetylate histones and cytoplasmic proteins, histone deacetylases (HDAC) influence a wide variety of cellular functions, such as proliferation, differentiation and apoptosis. Increased class 1 HDAC expression has been linked in solid tumours with more locally advanced, de-differentiated and proliferative tumours, and with poor prognosis in MM. HDAC inhibitors, panobinostat and ricolinostat, have been demonstrated to be effective in combination with bortezomib and dexamethasone in newly diagnosed patients with MM and in heavily pre-treated patients with advanced MM. HDAC inhibitor–monoclonal antibody combinations are also being explored. The potential of HDAC inhibitors to improve outcome for patients with MM is evident but a greater understanding of their anti-tumour effects is needed.

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