Epigenetics & Chromatin最新文献

ING5, initially identified as a tumor-suppressor, serves as a chromatin regulator with a diverse and extensive range of biological functions. This review undertakes an in-depth exploration of the structural characteristics and domain organization of ING family proteins, with a specific emphasis on ING5. The functional characteristics of ING5 are highly intricate and multi-dimensional. In the context of chromatin regulation and gene expression control, ING5 engages in interactions with diverse protein complexes through its conserved domains. It actively participates in the fine-tuning of chromatin structure and gene expression within tumor cells. Moreover, ING5 plays a pivotal and indispensable role in the regulation of DNA replication, cell cycle, and apoptosis, thereby exerting a profound influence on the fundamental biological processes of cells. Additionally, the binding properties and genomic associations of ING5 contribute significantly to its wide-ranging functions. ING5 exerts multiple and intricate action mechanisms in the processes of tumorigenesis, tumor development, and cancer treatment. It has substantial impacts on the biological behaviors of tumor cells, including proliferation, migration, and invasion. Furthermore, ING5 has emerged as a highly promising target for cancer therapy, presenting novel opportunities for the development of tumor-specific treatment strategies. Beyond its well-established role in tumor suppression, ING5 exhibits a diverse array of physiological functions. In the context of stem cell differentiation, ING5 regulates gene expression patterns, which are of utmost importance for determining cell fate. During embryonic development, it ensures the normal expression of genes associated with cell proliferation and differentiation, thereby being essential for the proper morphogenesis of the embryo. ING5 is also involved in metabolic regulation, particularly lipid metabolism, by modulating relevant genes to influence lipid levels. Additionally, it participates in the maintenance of vascular function by regulating the activities of vascular endothelial cells and angiogenesis, which are crucial for vascular homeostasis. This review comprehensively summarizes the extensive functions of ING5 as an epigenetic regulator in maintaining physiological homeostasis. By delving into its roles beyond tumor suppression, we aspire to attain a more comprehensive and in-depth understanding of its significance and potential implications in various biological processes and medical applications.

Background: Protamines play a crucial role in nuclear condensation during spermiogenesis, a process associated with significant chromatin remodeling and replacement of histones. While much research has focused on the function of protamines in sperm development and fertility, their effects in non-sperm cells remain largely unexplored. Protamines are increasingly used in the clinical setting, and understanding better, the role of protamines in somatic cells remains a critical unmet need.

Results: In this study, we investigated the impact of overexpressing murine and human protamine 1 and 2 (PRM1 and PRM2) on nuclear architecture, histone eviction, DNA methylation, and transcription in HEK293T cells and mesenchymal stromal cells (MSCs). Overexpression of protamines resulted in nuclear condensation; particularly PRM1 showed notable enrichment in nucleoli, and cells exhibited cell cycle abnormalities. Immunofluorescence staining indicated a significant reduction in specific histone modifications (H3K9me3, H3K4me1, and H3K27Ac) in response to protamine expression, especially in MSCs. Interestingly, despite these changes in nuclear organization, the methylome remained largely stable. However, expression of protamines significantly diminished transcription, particularly of the ribosomal genes, upon PRM1 expression.

Conclusions: Our studies indicate that PRM1 and PRM2 may bind to and condense distinct genomic regions in somatic cells, resulting in widespread silencing of gene expression, while retaining a largely stable DNA methylome.

Background: Epigenetic modifications, nucleosome occupancy, and three-dimensional chromatin architecture collectively create a multi-layered, highly interactive regulatory system for controlling genomic functionality. Dysregulation of epigenetic processes leads to a plethora of abnormalities including disease states. Therapies focused on epigenetic modulation can alter gene expression to correct dysfunction, though the perpetuation of these states and the relationships among chromatin regulatory layers is not well understood.

Results: Here, we investigated global and local chromatin structural and functional responses after acute histone deacetylase inhibitor treatment (suberoylanilide hydroxamic acid) in lung cancer cells across time. Treatment substantially increased global histone acetylation resulting in a pervasive but not distinctive signature. The spread of acetylation did not significantly impact global chromatin accessibility, and nucleosome remodeling largely occurred at finer scales in functionally relevant genomic regions. Indeed, both H3K4 trimethylation, a mark of active transcription, and gene expression changes were altered in a controlled locus-specific manner, suggesting aberrant acetylation indirectly leads to balanced and bidirectional gene expression profiles from tighter regulation of other chromatin features. HDACi treatment induced (13%) genomic rearrangement in chromatin compartmentalization and moderate weakening of topologically associating domains.

Conclusions: Continuous wavelet analysis of these features demonstrates that scale-dependent, locus-specific factors influence the relationship between chromatin architecture and functional output, suggesting that regulation of transcription and nucleosome remodeling is not entirely (nor linearly) dependent upon large scale compartment exchange. Structural and functional responses are most pronounced early after treatment with partial persistence of differential local chromatin features and expression later in time; this highlights the plasticity of chromatin regulation, which may have implications for the efficacy of epigenetic treatments. These results demonstrate the effectiveness of multi-layered regulation of transcription: in resilient systems, disruption of one chromatin feature does not distort the regulation of other features in supporting a transcriptional program that allows for survival.

The transcription of satellite DNA is highly sensitive to environmental factors and represents a source of genomic instability. Therefore, tight regulation of (peri)centromeric transcription is essential for genome maintenance. Antibiotics are routinely used for in vitro studies and for medical treatment, however, their effect on pericentromeric satellite DNA transcription was not investigated. Here we show that antibiotics geneticin and hygromycin B, conveniently used in cell culture, as well as rifampicin (along with five other antibiotics), used to treat bacterial infections, increase transcription of a major human pericentromeric alpha satellite DNA in cell lines at standard concentrations. However, response differs among cell lines - maximal increase in A-1235 cells is obtained by rifampicin while in HeLa cells and fibroblasts by geneticin. There is also a positive correlation between antibiotic concentration and the level of alpha satellite transcription. The increase of transcription is accompanied with either H3K9me3 decrease or H3K18ac increase at tandemly arranged alpha satellite arrays while H3K4me2 remains unchanged. Our results suggest that induced alpha satellite DNA transcription upon antibiotic stress could be linked to epigenetic changes - histone modifications H3K9me3 and H3K18ac, which are associated with transcription of heterochromatin.

Epigenetic modifications, including the regulation of histone H3 lysine 4 methylation (H3K4me2/3), play critical roles in maintaining normal tissue homeostasis and influencing the progression of cancer, including growth, invasion, metastasis, and therapeutic resistance. The demethylation of H3K4me2/3 is orchestrated by the KDM5 demethylase family, comprising KDM5A, KDM5B, KDM5C, and KDM5D. Recent studies have highlighted the pivotal role of KDM5 demethylases in mediating resistance to cancer therapies, encompassing chemoresistance, radioresistance, immune evasion, and targeted therapy resistance. This review provides a comprehensive overview of the regulatory mechanisms by which KDM5 demethylases contribute to these resistance pathways, with a focus on their molecular targets and interactions within the tumor microenvironment. Furthermore, we discuss emerging therapeutic strategies aimed at overcoming treatment resistance by targeting KDM5 demethylases. These insights provide a foundation for the development of innovative therapeutic interventions to enhance the efficacy of existing cancer treatments, offering a transformative approach to improving long-term patient survival and quality of life.

Background: Proper control of gene expression is important for the development and functions of neurons in the brain. The three-dimensional organization of the genome facilitates gene expression by regulating interactions between gene promoters and their enhancers. Notably, the cohesin complex drives genome folding through loop extrusion, thereby increasing promoter-enhancer interactions. Although cohesin's roles have been well-characterized in proliferating cells and cultured developing neurons, its functions in nuclear organization and gene transcription in mature mammalian brain neurons in vivo remain incompletely understood.

Results: To investigate cohesin's functions in the brain, we induced the conditional knockout of the core cohesin subunit RAD21 specifically in cerebellar granule neurons during late development or in adulthood. We then performed RNA-seq and Hi-C approaches to determine the effects of RAD21 depletion on gene expression and 3D genome organization. We found that cohesin was required for the expression of genes that become active in mature granule neurons, and this was linked to its functions in increasing local genomic interactions that bring target gene promoters into spatial proximity with their enhancers. Moreover, for target genes with distal intergenic enhancers, cohesin also maintained those intergenic enhancers within the transcriptionally active A compartment.

Conclusions: Our results reveal the essential functions of cohesin in gene transcription by regulating genome folding across multiple length scales in cerebellar granule neurons. Its roles in orchestrating both local and compartment-level genomic interactions highlight the additional layers of regulation for genes selectively expressed in mature post-mitotic neurons in vivo.

DNA-methylation is a key epigenetic mark in chromatin that attenuates chromatin accessibility during transcription, implying a crucial role in gene regulation. Its symmetrical distribution and function is thought to be linked to the periodicity of the DNA helix and the positioning of DNA wrapped around the nucleosome. Epigenomic data suggest that DNA methyltransferases (DNMTs) can methylate DNA when wrapped around a histone octamer. Yet, how this is precisely linked to positioning and periodicity is yet to be elucidated. It has been hypothesized that the observed methylation patterns may be related to the changing accessibility of nucleosome-bound DNA to DNMTs. Here, incorporating NOMe-Seq data, which simultaneously measures nucleosome positioning and DNA methylation at CpG sites across the genome, the interaction of DNMT1 with nucleosomal DNA could be mechanistically modeled and compared to hypothesized dependencies. Furthermore, X-ray structures of DNMT1 were superimposed onto those of nucleosome core complexes at base resolution to determine which histone-bound DNA positions would be sterically accessible or inaccessible to DNMTs. Statistical comparison with experimental NOMe-Seq data revealed that structurally computed DNA accessibility scores can indeed explain DNA methylation patterns in actively transcribed regions with positioned high nucleosome density.

Mouse heterochromatin is characterized by A/T-rich, 234 bp DNA repeat arrays, called major satellite repeats (MSR). We investigated MSR expression in response to a variety of stress conditions by using small molecule compounds. We identified the isoflavone genistein to selectively stimulate MSR transcription, but not that of other DNA repeat elements. Genistein is a natural compound that is frequently used in dietary supplements and has been associated with reducing cancer risk. A 24 h exposure of mouse embryonic fibroblasts (MEF) to genistein results in a more than 100-fold induction of MSR transcripts. This up-regulation depends on the activity of RNA polymerase II and requires a cycling G1 cell population. Blocking the cell cycle at the G2/M stage significantly attenuates genistein-mediated stimulation of MSR transcription. Mechanistically, DNA topoisomerase poisons phenocopy the genistein-dependent up-regulation of MSR expression. Together, these data suggest that MSR transcriptional response is guided by an altered topology of the underlying A/T-rich MSR DNA repeat arrays and reveal a novel function for genistein that may contribute to the anticancer properties of this natural compound.

Background: DNA methylation is an epigenetic mechanism involved in gene regulation and cellular differentiation. Accurate and comprehensive assessment of DNA methylation patterns is thus essential for understanding their role in various biological processes and disease mechanisms. Bisulfite sequencing has long been the default method for analyzing methylation marks due to its single-base resolution, but the associated DNA degradation poses a concern. Although several methods have been proposed to circumvent this issue, there is no clear consensus on which method might be better suited for specific study designs.

Results: We conducted a comparative evaluation of four DNA methylation detection approaches: whole-genome bisulfite sequencing (WGBS), Illumina methylation microarray (EPIC), enzymatic methyl-sequencing (EM-seq) and third-generation sequencing by Oxford Nanopore Technologies (ONT). DNA methylation profiles were assessed across three human genome samples derived from tissue, cell line, and whole blood. We systematically compared these methods in terms of resolution, genomic coverage, methylation calling accuracy, cost, time, and practical implementation. EM-seq showed the highest concordance with WGBS, indicating strong reliability due to their similar sequencing chemistry. ONT sequencing, while showing lower agreement with WGBS and EM-seq, captured certain loci uniquely and enabled methylation detection in challenging genomic regions. Despite a substantial overlap in CpG detection among methods, each method identified unique CpG sites, emphasizing their complementary nature.

Conclusions: Our findings underscore the strengths and limitations of current DNA methylation detection methods. EM-seq and ONT emerge as robust alternatives to WGBS and EPIC, offering unique advantages: EM-seq delivers consistent and uniform coverage, while ONT excels in long-range methylation profiling and access to challenging genomic regions. These insights provide practical guidance for method selection based on specific experimental goals.

The memory of gene expression states, active or repressive, is a fundamental biological concept as it controls cell fate in development, immunity and abiotic stress responses. Such memory is maintained through cell division as a cornerstone of epigenetics. Cell division poses a threat to the stability of epigenetic memory as memory-encoding factors become diluted between daughter cells. Thus, long-term epigenetic memory must depend on the feedback loops to sustain it over cell generations.Despite a widespread presence and fundamental importance, maintenance mechanisms of epigenetic memory are far from being clear. Here, we summarize present knowledge about feedback loops that allow maintenance of epigenetic information. We describe conceptually distinct, cis- and trans-, feedback loops, which rely on local, read-write propagation mechanisms or regulatory loops of diffusible factors, respectively. Furthermore, we provide cases of their frequent coupling in epigenetic systems in cells and synthesize current challenges in understanding feedback mechanisms. Overall, we believe this review to benefit the scientific community in bringing a holistic perspective on such fundamental biological phenomenon.