Epigenetics & Chromatin最新文献

Background: Repeat-induced epigenetic changes are observed in many repeat expansion disorders (REDs). These changes result in transcriptional deficits and/or silencing of the associated gene. MSH2, a mismatch repair protein that is required for repeat expansion in the REDs, has been implicated in the maintenance of DNA methylation seen in the region upstream of the expanded CTG repeats at the DMPK locus in myotonic dystrophy type 1 (DM1). Here, we investigated the role of MSH2 in aberrant DNA methylation in two additional REDs, fragile X syndrome (FXS) that is caused by a CGG repeat expansion in the 5' untranslated region (UTR) of the Fragile X Messenger Ribonucleoprotein 1 (FMR1) gene, and Friedreich's ataxia (FRDA) that is caused by a GAA repeat expansion in intron 1 of the frataxin (FXN) gene.

Results: In contrast to what is seen at the DMPK locus in DM1, loss of MSH2 did not decrease DNA methylation at the FMR1 promoter in FXS embryonic stem cells (ESCs) or increase FMR1 transcription. This difference was not due to the differences in the CpG density of the two loci as a decrease in DNA methylation was also not observed in a less CpG dense region upstream of the expanded GAA repeats in the FXN gene in MSH2 null induced pluripotent stem cells (iPSCs) derived from FRDA patient fibroblasts. Surprisingly, given previous reports, we found that FMR1 reactivation was associated with a high frequency of MSH2-independent CGG-repeat contractions that resulted a permanent loss of DNA methylation. MSH2-independent GAA-repeat contractions were also seen in FRDA cells.

Conclusions: Our results suggest that there are mechanistic differences in the way that DNA methylation is maintained in the region upstream of expanded repeats among different REDs even though they share a similar mechanism of repeat expansion. The high frequency of transcription-induced MSH2-dependent and MSH2-independent contractions we have observed may contribute to the mosaicism that is frequently seen in carriers of FMR1 alleles with expanded CGG-repeat tracts. These contractions may reflect the underlying problems associated with transcription through the repeat. Given the recent interest in the therapeutic use of transcription-driven repeat contractions, our data may have interesting mechanistic, prognostic, and therapeutic implications.

Background: Respiratory syncytial virus (RSV) poses significant morbidity and mortality risks in childhood, particularly for previously healthy infants admitted to hospitals lacking predisposing risk factors for severe disease. This study aimed to investigate the role of the host epigenome in RSV infection severity using non-invasive buccal swabs from sixteen hospitalized infants admitted to the hospital for RSV infection. Eight patients had severe symptoms, and eight had mild to moderate symptoms. For DNA methylation analyses, the Illumina EPIC BeadChip was used with DNA isolated from saliva samples. To evaluate the basal DNA methylation level of the identified biomarkers a cohort of healthy control children was used. Furthermore, DNA methylation levels of candidate genes were confirmed by pyrosequencing in both the discovery and validation cohorts of patients with mild to moderate symptoms.

Results: A panel of differentially methylated positions (DMPs) distinguishing severe from mild to moderate symptoms in infants was identified. DMPs were determined using a threshold of an adjusted P-value (false discovery rate, FDR) < 0.01 and an absolute difference in DNA methylation (delta beta) > 0.10. Differentially methylated regions (DMRs) were identified in the ZBTB38 (implicated in asthma and pulmonary disease) and the TRIM6-TRM34 gene region (associated with viral infections). The differential DNA methylation of these genes was validated in an independent replication cohort. A weighted correlation network analysis emphasized the pivotal role of a module with RAB11FIP5 as the hub gene, known for its critical function in regulating viral infections.

Conclusions: Oral mucosa methylation may play a role in determining the severity of RSV disease in infants.

Background: Heterozygous histone H3.3K27M mutation is a primary oncogenic driver of Diffuse Midline Glioma (DMG). H3.3K27M inhibits the Polycomb Repressive Complex 2 (PRC2) methyltransferase activity, leading to global reduction and redistribution of the repressive H3 lysine 27 tri-methylation (H3K27me3). This epigenomic rewiring is thought to promote gliomagenesis, but the precise role of K27M in gene regulation and tumorigenesis remains incompletely understood.

Results: We established isogenic DMG patient-derived cell lines using CRISPR-Cas9 editing to create H3.3 wild-type (WT), H3.3K27M, and combinations with EZH2 and EZH1 co-deletion, thereby eliminating PRC2 function and H3K27me3. RNA-seq and ATAC-seq analysis revealed that K27M exerts a novel epigenetic effect independent of PRC2 inhibition. While PRC2 loss led to widespread gene induction including HOX gene clusters, and activation of biological pathways, K27M induced a balanced gene deregulation with an overall repressive effect on pathway activity. Genes uniquely affected by K27M, independent of PRC2 loss, showed concordant changes in chromatin accessibility, with upregulated genes becoming more accessible. Importantly, xenografts of H3.3K27M/EZH1/2 WT cells formed tumors, whereas /EZH1/2 knockout cells did not, demonstrating a PRC2-independent role of K27M in tumorigenesis.

Conclusion: Our findings reveal that the H3.3K27M mutation alters chromatin accessibility and uniquely deregulates gene expression independent of H3K27 methylation loss. These PRC2-independent functions of K27M contribute to changes in biological pathway activity and are necessary for tumor development, highlighting novel mechanisms of K27M-driven gliomagenesis.

The SWI/SNF complex was first identified in yeast and named after studies of mutants critical for the mating-type switch (SWI) and sucrose non-fermenting (SNF) pathways.The SWI/SNF complex plays a pivotal role in regulating gene expression by altering chromatin structure to promote or suppress the expression of specific genes, maintain stem cell pluripotency, and participate in various biological processes. Mutations in the SWI/SNF complex are highly prevalent in various human cancers, significantly impacting tumor suppressive or oncogenic functions and influencing tumor initiation and progression. This review focuses on the mechanisms by which ARID1A/ARID1B, PBRM1, SMARCB1, and SMARCA2/SMARCA4 contribute to cancer, the immunoregulatory roles of the SWI/SNF complex, its involvement in DNA repair pathways, synthetic lethality, and applications in precision oncology.

HIV-1 can establish a lifelong infection by incorporating its proviral DNA into the host genome. Once integrated, the virus can either remain dormant or start active transcription, a process governed by the HIV Tat protein, host transcription factors and the chromatin landscape at the integration site. Histone-modifying enzymes and chromatin-remodeling enzymes play crucial roles in regulating this chromatin environment. Chromatin remodelers, a group of ATP-dependent proteins, collaborate with host proteins and histone-modifying enzymes to restructure nucleosomes, facilitating DNA repair, replication, and transcription. Recent studies have highlighted the importance of chromatin remodelers in HIV-1 latency, spurring research focused on developing small molecule modulators that can either reactivate the virus for eradication approaches or induce long-term latency to prevent future reactivation. Research efforts have primarily centered on the SWI/SNF family, though much remains to be uncovered regarding other chromatin remodeling families. This review delves into the general functions and roles of each chromatin remodeling family in the context of HIV and discusses recent advances in small molecule development targeting chromatin remodelers and the HIV Tat protein, aiming to improve therapeutic approaches against HIV.

Background: In Drosophila, architectural proteins are frequently found in promoters, including those of genes with extremely high expression levels, such as ribosomal protein genes (RPGs). The involvement of several of these proteins in gene regulation in Drosophila has been shown, but the exact mechanisms of their possible cooperative action have not been fully elucidated.

Results: In this study we dissected the contribution of the architectural proteins Opbp and M1BP, which are co-localized at several RPG promoters near the transcription start site, to promoter functioning. We found that Opbp has two domains that directly interact with CP190, Putzig (Pzg), and Chromator (Chro) proteins, the cofactors which are required for the activation of housekeeping (hk) gene promoters. These domains have redundant functions in vivo and can tether the cofactors forming open chromatin regions when are artificially recruited to the "closed" chromatin. Additionally, we observed interactions between M1BP and the same cofactors. In the transgene assay, the transcription driven by the 192-bp part of Rpl27A RPG promoter is fully dependent on the presence of at least one Opbp or M1BP binding site and it is sufficient for the very high activity of this promoter integrated into the hk gene cluster and moderate expression outside the cluster, while presence of both sites even more facilitates transcription.

Conclusions: This study demonstrates that different architectural proteins can work independently and in cooperation and fulfill partially redundant functions in the activation of RPG promoters.

Background: Epigenetic modifications provide mechanisms for influencing gene expression, regulating cell differentiation and maintaining long-term memory of cellular identity and function. As oocytes transmit epigenetic information to offspring, correct establishment of the oocyte epigenome is important for normal offspring development. Oocyte epigenetic programming is highly complex, involving a range of epigenetic modifiers which interact to establish a specific distribution of DNA methylation and histone modifications. Disruptions to oocyte epigenetic programming can alter epigenetic memory and prevent normal developmental outcomes in the next generation. Therefore, it is critical that we further our understanding of the interdependent relationships between various epigenetic modifiers and modifications during oogenesis.

Results: In this study we investigated the spatial and temporal distribution of a range of epigenetic modifiers and modifications in growing oocytes of primordial to antral follicles. We provide comprehensive immunofluorescent profiles of SETD2, H3K36me3, KDM6A, RBBP7, H3K27me3, DNMT3A and DNMT3L and compare these profiles to our previously published profiles of the Polycomb Repressive Complex 2 components EED, EZH2 and SUZ12 in growing oocytes of wildtype mice. In addition, we examined the nuclear levels and spatial distribution of these epigenetic modifiers and modifications in oocytes that lacked the essential Polycomb Repressive Complex 2 subunit, EED. Notably, histone remodelling in primary-secondary follicle oocytes preceded upregulation of DNMT3A and DNMT3L in secondary-antral follicle oocytes. Moreover, loss of EED and H3K27me3 led to significantly increased levels of the H3K36me3 methyltransferase SETD2 during early-mid oocyte growth, although the average levels of H3K36me3 were unchanged.

Conclusions: Overall, these data demonstrate that oocyte epigenetic programming is a highly ordered process, with histone remodelling in early growing oocytes preceding de novo DNA methylation in secondary-antral follicle oocytes. These results indicate that tight temporal and spatial regulation of histone modifiers and modifications is essential to ensure correct establishment of the unique epigenome present in fully grown oocytes. Further understanding of the temporal and spatial relationships between different epigenetic modifications and how they interact is essential for understanding how germline epigenetic programming affects inheritance and offspring development in mammals, including humans.

TIP60 is a crucial lysine acetyltransferase protein that catalyzes the acetylation of histone and non-histone proteins. This enzyme plays a crucial role in maintaining genomic integrity, by participating in DNA damage repair, ensuring accurate chromosomal segregation, and regulating a myriad of cellular processes such as apoptosis, autophagy, and wound-induced cell migration. One of the primary mechanisms through which TIP60 executes these diverse cellular functions is via post-translational modifications (PTMs). Over the years, extensive studies have demonstrated the importance of PTMs in controlling protein functions. This review aims to summarize the findings on PTMs occurring on the TIP60 protein and their functional implications. We also discuss previously uncharacterized PTM sites identified on TIP60 and examine their relationship with cancer-associated mutations, with a particular focus on residues potentially modified by various PTMs, to understand the cause of deregulation of TIP60 in various cancers.

Background: DNA methylation plays a crucial role in gene regulation and epigenetic inheritance across diverse organisms. Daphnia magna, a model organism in ecological and evolutionary research, has been widely used to study environmental responses, pharmaceutical toxicity, and developmental plasticity. However, its DNA methylation landscape and age-related epigenetic changes remain incompletely understood.

Results: In this study, we characterized DNA methyltransferases (DNMTs) and mapped DNA methylation across the D. magna genome using whole-genome bisulfite sequencing. Our analysis identified three DNMTs: a highly expressed but nonfunctional de novo methyltransferase (DNMT3.1), alongside lowly expressed yet functional de novo methyltransferase (DNMT3.2) and maintenance methyltransferase (DNMT1). D. magna exhibits overall low DNA methylation, targeting primarily CpG dinucleotides. Methylation is sparse at promoters but elevated in the first exons downstream of transcription start sites, with these exons showing hypermethylation relative to adjacent introns. To examine age-associated DNA methylation changes, we analyzed D. magna individuals across multiple life stages. Our results showed no significant global differences in DNA methylation levels between young, mature, and old individuals, nor any age-related clustering in dimensionality reduction analyses. Attempts to construct an epigenetic clock using machine learning models did not yield accurate age predictions, likely due to the overall low DNA methylation levels and lack of robust age-associated methylation changes.

Conclusions: This study provides a comprehensive characterization of D. magna's DNA methylation landscape and DNMT enzymes, highlighting a distinct pattern of exon-biased CpG methylation. Contrary to prior studies, we found no strong evidence supporting age-associated epigenetic changes, suggesting that DNA methylation may have a limited role in aging in D. magna. These findings enhance our understanding of invertebrate epigenetics and emphasize the need for further research into the interplay between DNA methylation, environmental factors, and gene regulation in D. magna.

Macrophage polarization is a dynamic process driven by a complex interplay of cytokine signaling, metabolism, and epigenetic modifications mediated by pathogens. Upon encountering specific environmental cues, monocytes differentiate into macrophages, adopting either a pro-inflammatory (M1) or anti-inflammatory (M2) phenotype, depending on the cytokines present. M1 macrophages are induced by interferon-gamma (IFN-γ) and are characterized by their reliance on glycolysis and their role in host defense. In contrast, M2 macrophages, stimulated by interleukin-4 (IL-4) and interleukin-13 (IL-13), favor oxidative phosphorylation and participate in tissue repair and anti-inflammatory responses. Metabolism is tightly linked to epigenetic regulation, because key metabolic intermediates such as acetyl-coenzyme A (CoA), α-ketoglutarate (α-KG), S-adenosylmethionine (SAM), and nicotinamide adenine dinucleotide (NAD⁺) serve as cofactors for chromatin-modifying enzymes, which in turn, directly influences histone acetylation, methylation, RNA/DNA methylation, and protein arginine methylation. These epigenetic modifications control gene expression by regulating chromatin accessibility, thereby modulating macrophage function and polarization. Histone acetylation generally promotes a more open chromatin structure conducive to gene activation, while histone methylation can either activate or repress gene expression depending on the specific residue and its methylation state. Crosstalk between histone modifications, such as acetylation and methylation, further fine-tunes macrophage phenotypes by regulating transcriptional networks in response to metabolic cues. While arginine methylation primarily functions in epigenetics by regulating gene expression through protein modifications, the degradation of methylated proteins releases arginine derivatives like asymmetric dimethylarginine (ADMA), which contribute directly to arginine metabolism-a key factor in macrophage polarization. This review explores the intricate relationships between metabolism and epigenetic regulation during macrophage polarization. A better understanding of this crosstalk will likely generate novel therapeutic insights for manipulating macrophage phenotypes during infections like tuberculosis and inflammatory diseases such as diabetes.