Epigenetics & Chromatin最新文献

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.

Background: Topologically associating domains (TADs) are believed to play a role in the regulation of gene expression by constraining or guiding interactions between the regulatory elements. While the impact of TAD perturbations is typically studied in developmental genes with highly cell-type-specific expression patterns, this study examines genes with broad expression profiles separated by a strong insulator boundary. We focused on the mouse Slc29a3/Unc5b locus, which encompasses two distinct TADs containing ubiquitously expressed and essential for viability genes. We disrupted the CTCF-boundary between these TADs and analyzed the resulting changes in gene expression.

Results: Deletion of four CTCF binding sites at the TAD boundary altered local chromatin architecture, abolishing pre‑existing loops and creating novel long‑range interactions that spanned the original TAD boundary. Using UMI-assisted targeted RNA-seq we evaluated transcriptional changes of Unc5b, Slc29a3, Psap, Vsir, Cdh23, and Sgpl1 across various organs. We found that TAD boundary disruption led to variable transcriptional responses, where not only the magnitude but also the direction of gene expression changes were tissue-specific. Current hypotheses on genome architecture function, such as enhancer competition and hijacking, as well as genomic deep learning models, only partially explain these transcriptional changes, highlighting the need for further investigation into the mechanisms underlying TAD function and gene regulation.

Conclusions: Disrupting the insulator element between broadly expressed genes resulted in moderate, tissue-dependent transcriptional alterations, rather than uniformly activating or silencing the target genes. These findings show that TAD boundaries contribute to context‑specific regulation even at housekeeping loci and underscore the need for refined models to predict the effects of non‑coding structural variants.

Introduction: Skeletal muscle stem cells (MuSCs) have strong regenerative abilities, but as we age, their ability to regenerate decreases, leading to a decline in muscle function. Although the methylation reprogramming of super-enhancers (SEs) plays a pivotal role in regulating gene expression associated with the aging process, our understanding of the molecular diversity of stem cells during aging remains limited. This study aimed to identify the methylation profile of SEs in MuSCs and explore potential therapeutic molecular targets associated with aging.

Methods: The ROSE software was employed to identify super enhancers from the ChIP-seq data obtained from the ENCODE database. Additionally, the ALLCools and Methylpy packages were applied to analyze the methylation profile of SEs and to identify differentially methylated regions (DMRs) between aged and control samples using single-cell bisulfite sequencing (scBS-seq) data from the Gene Expression Omnibus (GEO) database. Overlap analysis was used to assess the regions of SEs and DMRs. The target genes and motifs were analyzed using KEGG, GO, and HOMER to identify key biological pathways and functions, followed by validation through snATAC-seq and immunofluorescence techniques.

Results: In conclusion, we conducted a multi-omics and cross-species analysis of MuSCs, creating a detailed methylation profile of SEs during aging. We identified key motifs and genes affected by SE methylation reprogramming, revealing important molecular pathways involved in aging. Notably, further analysis of the key gene PLXND1 revealed a decreasing expression trend in aged MuSCs, which appears to be linked to the hypermethylation of SE Rank 869. This epigenetic alteration is likely to contribute to the dysregulation of the SEMA3 signaling pathway, with profound implications for muscle regeneration in MuSCs during aging.

Conclusion: These findings suggest that epigenetic alterations in the methylation reprogramming of SEs are closely linked to the disruption of transcriptional networks during MuSCs aging. Moreover, our results offer valuable insights into the mechanisms driving SE methylation reprogramming, shedding light on how these epigenetic changes contribute to the molecular processes underlying aging.

Background: Ten-Eleven Translocation (TET1-3) dioxygenases oxidize 5-methylcytosine (5mC) in DNA to generate 5-hydroxymethylcytosine (5hmC), 5-formylcytosine (5fC), and 5-carboxylcytosine (5caC), initiating DNA demethylation. Since their discovery in 2009, there have been contradictory reports regarding the roles of TET proteins in cancer. TET genes have been characterized as tumor suppressors because their expression levels are reduced in many human cancers including lymphoma, prostate, and pancreas, and TET2 gene mutations are common in hematological cancers. In contrast, TET1 was recently reported to be overexpressed in triple negative breast cancer and to act as a protooncogene in lung cancer.

Results: In the present study, we employed genetic approaches to directly address the function of TET1 protein in lung adenocarcinoma. We found that overexpression (OE) of TET1 in human lung adenocarcinoma (H441, H1975) cells decreased their proliferation and inhibited colony formation, cell migration, and 3D spheroid tumorigenesis. In contrast, TET1 knockout (KO) accelerated lung adenocarcinoma cell growth and promoted colony formation, cell migration, and 3D spheroid tumorigenesis. Transcriptomics and proteomics analyses revealed that TET1 overexpression was associated with increased prevalence of immune markers, primarily via activation of the TNF and NF-kB signaling pathways. Conversely, TET1 knockout in lung adenocarcinoma cells induced the expression of genes involved in cellular metabolism and cell growth.

Conclusions: Our results are consistent with tumor suppressor role of TET1 gene in lung adenocarcinoma cells (H441, H1975) and reveal its possible role in activating antitumor immunity.

Morphogenesis and development of hair follicle fundamentally depend on the interaction between the epidermis and dermis, with dermal papilla cells (DPCs) playing a critical role in these processes. H3K4me3, one of the key histone modifications, is essential for coordinating gene expression. However, the epigenetic modification profile of H3K4me3 in cashmere goat DPCs and its mechanism of action in hair follicle development remain unexplored. In this study, the apparent regulation map of H3K4me3 was drawn by CUT&Tag technology. DPCs were exogenously treated with the H3K4me3 inhibitor BCL-121 and the agonist PBIT. Functional experiment results showed that increasing H3K4me3 levels significantly enhanced the proliferation capacity of DPCs and promoted the expression of Wnt signaling pathway-related genes. Subsequently, the regulatory mechanism of H3K4me3 was explored, and the differentially expressed gene RSPO3 in the embryonic stage regulated by H3K4me3 was screened through CUT&Tag and RNA-seq correlation analysis. Functional studies demonstrated that RSPO3 could promote DPCs proliferation, inhibit apoptosis, and increase the expression of genes related to the Wnt signaling pathway. In summary, our findings indicated that H3K4me3 regulates the transcription of RSPO3 in DPCs, which would lay the foundation for the molecular mechanism of hair follicle development.