Epigenetics & Chromatin最新文献

DNA methylation is a fundamental epigenetic modification that regulates gene expression and maintains genomic stability. Consequently, DNA methylation remains a key biomarker in cancer research, playing a vital role in diagnosis, prognosis, and tailored treatment strategies. Aberrant methylation patterns enable early cancer detection and therapeutic stratification; however, their complex patterns necessitates advanced analytical tools. Recent advances in artificial intelligence (AI) and machine learning (ML), including deep learning networks and graph-based models, have revolutionized cancer epigenomics by enabling rapid, high-resolution analysis of DNA methylation profiles. Moreover, these technologies are accelerating the development of Multi-Cancer Early Detection (MCED) tests, such as GRAIL's Galleri and CancerSEEK, which improve diagnostic accuracy across diverse cancer types. In this review, we explore the synergy between AI and DNA methylation profiling to advance precision oncology. We first examine the role of DNA methylation as a biomarker in cancer, followed by an overview of DNA profiling technologies. We then assess how AI-driven approaches transform clinical practice by enabling early detection and accurate classification. Despite their promise, challenges remain, including limited sensitivity for early-stage cancers, the black-box nature of many AI algorithms, and the need for validation across diverse populations to ensure equitable implementation. Future directions include integrating multi-omics data, developing explainable AI frameworks, and addressing ethical concerns, such as data privacy and algorithmic bias. By overcoming these gaps, AI-powered epigenetic diagnostics can enable earlier detection, more effective treatments, and improved patient outcomes, globally. In summary, this review synthesizes current advancements in the field and envisions a future where AI and epigenomics converge to redefine cancer diagnostics and therapy.

Oocyte maturation involves both nuclear and cytoplasmic processes that are critical for the acquisition of oocyte competence. Granulosa cells, surrounding the oocyte, play a pivotal role in the maturation process, with mechanisms such as cAMP signaling significantly influencing oocyte development. Epigenetic mechanisms - including DNA methylation and its oxidative derivatives, histone post-translational modifications and chromatin remodeling - interfere with the accessibility of transcription factors to regulatory regions of the genome, such as promoter regions of genes, hence generally regulating gene expression profiles; however, in oocytes, transcription is largely independent of DNA methylation patterns. Here we highlight epigenetic reprogramming events occurring during oocyte development and ageing, focusing on the establishment of gamete-specific epigenetic marks, including DNA modifications at imprinted regions, and age-related epigenetic changes. We focus on the mechanisms of DNA methylation and demethylation during mouse and human oocyte maturation, alongside an exploration of how ageing impacts the oocyte epigenome and its implications for reproductive success. By providing a comprehensive analysis of the role of epigenetics in oocyte development and maturation, this review addresses the importance of comprehending these processes to enhance in vitro fertilization treatments and improve reproductive outcomes.

Background: Cohesin is a major regulator of three-dimensional genome organization and gene expression. Cohesin associates with DNA and dynamically extrudes a DNA loop, often bringing two cis-regulatory elements physically close together. Extruding cohesin molecules can be stalled or stabilized when they encounter a CTCF insulator protein on DNA, thereby anchoring a DNA loop. However, many enhancer-promoter loops that are bound by cohesin lack CTCF and it is not clear how cohesin is stabilized at or recruited to these sites in the genome.

Results: Here, we investigated the localization of cohesin with common chromatin regulators and transcription factors on the mouse embryonic stem cell genome. The SP1 and NFYA transcription factors are ubiquitously expressed proteins known to regulate expression of genes associated with a variety of cellular processes, while WDR5 is a ubiquitous core component of multiple chromatin regulatory complexes. We found that cohesin co-bound promoters and enhancers with WDR5, with SP1, or with NFYA in mESCs. Cohesin physically interacted with and colocalized with WDR5, with SP1, or with NFYA on the same molecule of chromatin. Strikingly, depletion of WDR5, SP1, or NFYA caused a decrease in cohesin binding at shared binding sites, while depletion of cohesin did not alter binding of WDR5, SP1, or NFYA on the genome.

Conclusions: These results indicate that common transcription factors and chromatin regulators stabilize cohesin at specific sites in chromatin and may thereby serve as structural regulators of enhancer-promoter loops via the stabilization of cohesin.

Background: Mammalian cells have numerous DNA repair pathways to repair lesions generated by replication errors, metabolism, and exogenous agents. Cells can sense and respond to DNA damage within seconds, suggesting that there is a highly effective sensor of lesions although the mechanistic details are unclear. The DNA damage response in mammalian cells results in a localized transient de-condensation of chromatin, loss of linker histones and the recruitment of DNA repair proteins such as PARP1 and chromatin remodelers.

Results: Here we investigated the interactions between poly(ADP-ribose) polymerase-1 (PARP1), the linker histone H1.0 and linker histone chaperone Prothymosin α (PTMA). Using H1.0 tagged with a photoconvertible fluorescent protein, we observed a significant increase in the initial rate of exit of H1.0 from regions of chromatin containing microirradiation-induced DNA lesions. Surprisingly, this was also seen in Parp1^-/- cells but not in stable cell lines with homozygous null mutations in the PTMA gene (Ptma^-/-). The recruitment of PARP1 to damaged DNA was inhibited by overexpression of a mutant of H1.0 with a tighter chromatin-binding affinity or by reduced expression of PTMA. Relative to the wild type, Ptma^-/- cell lines displayed increased sensitivity to DNA-damaging agents.

Conclusion: We suggest that DNA damage alters the interaction of H1.0 with the nucleosome to allow the chaperone PTMA to bind and promote release of linker histones thereby initiating the local chromatin de-condensation necessary for the efficient recruitment of repair proteins such as PARP1. In this context linker histones may serve as in situ "sensors" of DNA damage.

Background: The evolutionarily conserved cohesin complex is a pleiotropic regulator of chromosome structure and function, participating in sister chromatid cohesion, transcriptional regulation of genes, DNA replication, and DNA repair. Cohesin uses ATP hydrolysis to dynamically extrude DNA loops that bring together cis-regulatory elements and thus regulate gene expression. Some DNA loops are anchored by the binding of CTCF insulator proteins which can stall extruding cohesin complexes, however many DNA loops that connect enhancers and promoters lack CTCF and it is unclear how cohesin is stabilized at these cis-regulatory sites. While cohesin has been found to co-purify with a number of proteins, some of which regulate cohesin function, our current knowledge of cohesin activity is incomplete. Identification of transient or less stable interactions between cohesin and chromatin-associated proteins is crucial for understanding regulation of gene expression and chromosome structure.

Results: Here we utilize a TurboID proximity labeling and mass spectrometry approach for identifying cohesin-interacting proteins. We identify > 400 cohesin-interacting proteins in NIH-3T3 cells, including previously known and potentially novel cohesin interactors. Among the cohesin interactors were chromatin remodeling complexes and histone-modifying complexes. Interactions between seven of these chromatin regulating complexes and cohesin were confirmed with co-immunoprecipitations performed in multiple cell lines. The SWI/SNF complex was found to co-purify with cohesin and SWI/SNF co-occupied enhancers and promoters with cohesin. To investigate the functional relevance of the cohesin-SWI/SNF interaction, we assessed whether the binding of cohesin to the genome is regulated by SWI/SNF or vice versa. Acute small molecule perturbations of SWI/SNF altered the amount of both SWI/SNF and cohesin on chromatin, particularly affecting cohesin binding to CTCF sites.

Conclusions: This work represents the most comprehensive investigation of cohesin-interacting proteins to date. These results identify a physical link between cohesin and a vast number of chromatin-associated proteins inside of cells, including chromatin remodeling complexes and histone-modifying complexes. Furthermore, these results indicate SWI/SNF activity stabilizes cohesin on chromatin particularly at insulator sites. These cohesin interactome data are a resource for future studies aimed at characterizing the functional interactions between cohesin and numerous chromatin-associated proteins in regulating chromosome structure and gene control.

Background: ATP-dependent nucleosome remodeling complexes of the imitation switch (ISWI) family slide and space nucleosomes. The ISWI ATPase subunit forms obligate complexes with accessory subunits whose mechanistic roles remain poorly understood. In baker's yeast, the Isw2 ATPase subunit associates with Itc1, the orthologue of human ACF1/BAZ1A. Prior data suggested that the genomic deletion of the 374 N-terminal amino acids from Itc1 (hereafter called itc1^ΔN) leads to a gain-of-toxic-function phenotype with severe growth defects in the BY4741 genetic background, possibly due to defective nucleosome spacing activity of the mutant complex.

Results: Here we show that the deletion encompasses a novel motif termed downWAC that forms a conserved structural module with the N-terminal WAC domain. The module is predicted to interact with DNA. However, it does not form a stable interaction interface with the remainder of the complex. Instead, it is connected through a long disordered polypeptide linker to the remainder of the complex. Curiously, the itc1^ΔN allele does not lead to measurable growth defects in haploid BY4741 and diploid BY4743 strains. It also does not alter genome-wide nucleosome organization in wild-type cells. To rule out that potentially redundant remodeling factors obscure itc1^ΔN-associated phenotypes, we repeated experiments in cells devoid of ISW1 and CHD1 remodelers with the same results. Only at known target genes of the ISW2 complex was the nucleosome organization perturbed in itc1^ΔN cells.

Conclusions: We conclude that the deletion of Itc1 N-terminus is indistinguishable from the full deletion of either ITC1 or ISW2. As such, itc1^ΔN should be considered a null allele of ISW2. We propose a model, in which the WAC-downWAC module, along with a flexible protein linker, helps ISW2 in searching for its target genes and positioning + 1-nucleosomes.

Background: Pheochromocytoma (Pheo) represents a potential metastatic neuroendocrine tumor. As a tumor suppressor gene, LRP1B is involved in the regulation of tumor progression. However, the precise regulatory mechanism of LRP1B in Pheo remains elusive.

Methods: RT-QPCR, western blot and immunohistochemistry (IHC) were used to identify the expression levels of DNMT3B and LRP1B. Biochemistry assays including luciferase and ChIP were utilized to detect the interaction between the methyltransferase DNMT3B and LRP1B promoter. LRP1B or DNMT3B were knock-down in Pheo cell line by shRNAs. Functional experiments including clonal formation, migration, and in vivo transplantation were performed to evaluate the regulation of LRP1B or DNMT3B on tumor growth.

Results: LRP1B was down-regulated, while DNMT3B was up-regulated in Pheo.Overexpression of LRP1B or inhibition of DNMT3B inhibited the progress of Pheo. DNMT3B was responsible for the hypermethylation of LRP1B promoter in Pheo. At the same time, overexpression of DNMT3B reversed the inhibitory effect of overexpression of LRP1B on Pheo progression.

Conclusion: DNMT3B mediated the hypermethylation of the tumor suppressive gene LRP1B and promotes Pheo progression.

Background: Thyroid-associated ophthalmopathy (TAO) is an autoimmune orbital disease influenced by multiple factors, including genetic and immune factors. The enlargement of orbital fat tissues are mainly due to abnormal activation of adipocyte differentiation. Epigenetic modifications provide mechanistic insight for regulating gene expression and cellular differentiation. Lysine specific demethylase 1 (LSD1) is reported in regulation of adipogenesis. Therefore, it is critical to investigate the relationship between epigenetic modifier LSD1 and histone modification level during TAO process.

Results: In this study, combined with the clinic study and highthrough sequencing approach, our results revealed that the volume of orbital fat tissue was lower in TAO patients compared to non-TAO patients, whereas the number of adipocytes was higher in TAO patients compared to non-TAO patients, the expression level of adipocyte differentiation markers were higher in TAO samples. Consistently, at the cellular system, the expression level of adipogenic markers were higher in the TAO derived cells compared with the non-TAO cells. And we found LSD1 was highly expressed in TAO-derived cells. However, knocking down LSD1 decreased the expression of adipocyte markers. Mechanistically, LSD1 promoted adipocyte gene activation by demethylating H3K9me2 at the promoter regions. Finally, treatment with pargyline, an LSD1 inhibitor, inhibited adipogenesis in a dose-dependent manner, and the same inhibition of adipogenesis results were obtained with treatment with teprotumumab alone or combined with pargyline.

Conclusions: Overall, our study indicates that epigenetic modifications were dysregulated in TAO process, and these data elucidated a novel mechanism of adipocyte differentiation during TAO progression and positioned LSD1 as a potential anti-adipogenesis target in TAO. Further understanding of the interaction betwen transcription factors and epigeneic modifiers or other histone modifications in TAO is essential for providing new perspectives in TAO mechanistic study and clinical intervention.

Background: The development of breast cancer is known to be greatly influenced by epigenetic changes. The impact of histone acetyltransferase KAT2B on AIM2 and AKT/Wnt/β-catenin signaling have not been studied yet.

Methods: In this study, clinical breast cancer tissue and para-cancer tissue samples were collected from 60 breast cancer patients, and correlations between AIM2 expression and pathological parameters were analyzed. Breast cancer cell lines were obtained for in vitro studies, and AIM2 overexpression or KAT2B knockdown models were constructed. The CCK8 and Edu assay were conducted to measure cell proliferation, and cell invasion was determined by Transwell analysis. For mRNA and protein expression measurement, RT-qPCR and western blotting were utilized, respectively. Co-immunoprecipitation was used to investigate the interaction between KAT2B and AIM2. Animal models were established using BALB/c-nu mice through subcutaneous injection with breast cancer cells transfected with AIM2 K90R mutant vectors. Expression of Ki-67, KAT2B and AIM2 AcK90 was measured using immunohistochemistry.

Results: The clinical samples showed that AIM2 was downregulated in breast cancer tissues and was linked to lymph node metastases and advanced clinical stage. Subsequently, the in vitro studies found that AIM2 exerted a suppressive impact on the growth, spread, and invasion of breast cancer cells. We further demonstrated that KAT2B mediates acetylation of AIM2 at the lysine 90 residue, which suppresses cancer cell growth, invasion, and migration through inhibiting the AKT/Wnt/β-catenin axis. In animal models, we further confirmed that acetylation of AIM2 inhibited the stimulation of the AKT/Wnt/β-catenin axis, thereby suppressing breast cancer growth in vivo. Finally, we proved that the KAT2B and acetylation of AIM2 correlated with the prognosis of clinical breast cancer.

Conclusion: Our study suggests that KAT2B-mediated acetylation of AIM2 can suppress the stimulation of the AKT/Wnt/β-catenin axis, consequently inhibiting breast carcinoma progression.

Background: Heterochromatin is a fundamental component of eukaryotic chromosome architecture, crucial for genome stability and cell type-specific gene regulation. In mammalian nuclei, heterochromatin forms condensed B compartments, distinct from the transcriptionally active euchromatic A compartments. Histone H3 lysine 9 and lysine 27 trimethylation (H3K9me3 and H3K27me3) are two major epigenetic modifications that enrich constitutive and facultative heterochromatin, respectively. Previously, we found that the redistribution of H3K27me3 following the loss of H3K9 methylation contributes to heterochromatin maintenance, while the simultaneous loss of both H3K27me3 and H3K9 methylation induces heterochromatin decondensation in mouse embryonic fibroblasts. However, the spatial positioning of B compartments largely persists, suggesting additional mechanisms are involved.

Results: In this study, we investigated the role of H2AK119 monoubiquitylation (uH2A), a repressive chromatin mark deposited by Polycomb Repressive Complex 1 (PRC1), in maintaining heterochromatin structure following the loss of H3K9 and H3K27 methylation. We observed that uH2A and H3K27me3 are independently enriched in B compartments after H3K9 methylation loss. Despite the absence of H3K9me3 and H3K27me3, uH2A remained localized and contributed to heterochromatin retention. These results suggest that PRC1-mediated uH2A functions independently and cooperatively with H3K27me3 to maintain heterochromatin organization originally created by H3K9 methylation.

Conclusion: Our findings highlight a compensatory role for uH2A in preserving heterochromatin structure after the loss of other repressive chromatin modifications. The PRC1-uH2A pathway plays a critical role in maintaining the integrity of B compartments and suggests that heterochromatin architecture is supported by a network of redundant epigenetic mechanisms in mammalian cells.