Epigenetics & Chromatin最新文献

Background: Mutations in tumour suppressor p53 are frequently implied in aggressive progression and metastasis in colorectal cancer. But the distinct phenotypes exhibited by site-specific mutations of p53 are not well elucidated. Here, we investigate the epigenetic and transcriptional impact of three major p53 hotspot mutations (R175H, R273H and R282W), through DNA methylation changes and single cell transcriptomics.

Results: We observed that the p53 R273H mutation is associated with a partial epithelial-mesenchymal transition (pEMT) and increased metastatic progression. Analysis of DNA methylation patterns revealed a distinct epigenetic landscape in R273H-mutant tumours, with hypomethylated regions correlating with enhanced transcriptional activation of YAP/TAZ target genes thus promoting pEMT and EMT-like phenotype in CRC tumours. In vitro ChIP-seq experiments in colorectal cancer cells expressing the R273H mutant p53 (HT29) showed enrichment of mutant p53 at the promoters of YAP/TAZ target genes suggesting EMT/pEMT like states with R273H mutation. Further, simulations from a gene regulatory network incorporating the interactions of p53R273H with EMT regulators explain how this mutation shapes the phenotypic landscape accessible to cancer cells. Our analysis of single-cell transcriptomes of colorectal tumours reveals R273H-linked enrichment of partial and mesenchymal EMT phenotypes across tumour subpopulations in CRC.

Conclusions: We identified a distinct epigenetic signature associated with the p53 R273H mutation, characterised by hypomethylation of YAP/TAZ signalling genes that drives partial EMT and aggressive tumour behaviour. These findings highlight the importance of mutation-specific epigenetic regulation in shaping colorectal cancer progression and the need for developing therapeutic strategies tailored to p53 mutation status.

Endothelial-mesenchymal transition (EndMT) is a biological process in which endothelial cells lose intercellular junctions and endothelial characteristics under specific pathophysiological stimuli and acquire mesenchymal traits. It plays a critical role in cardiac development, tissue fibrosis, tumor metastasis, atherosclerosis, and other diseases. In recent years, growing evidence has demonstrated that epigenetic modifications and post-translational modifications are central to the precise regulation of EndMT initiation and progression. This review systematically elaborates on how epigenetic mechanisms-such as DNA methylation, histone modifications, and non-coding RNAs-as well as post-translational modifications, including protein phosphorylation, acetylation, and ubiquitination, regulate EndMT by modulating key signaling pathways (e.g., TGF-β, Wnt, Notch) and transcription factors (e.g., Snail, Slug, Twist, ZEB1/2). A deeper understanding of these regulatory networks may provide novel diagnostic biomarkers and therapeutic strategies for diseases targeting EndMT.

Background: Steroid hormones drive the transcription of developmental genes by activating distinct sets of enhancers across tissues and developmental contexts, but the mechanisms that target specific enhancers remain incompletely understood, even in model organisms. It has been proposed that selective binding of nuclear receptors occurs at regulatory sites primed by other classes of DNA-binding transcription factors. However, direct studies of cooperation between nuclear receptors and different transcription factors remain limited. A previous study suggested that the GATA family factor SRP/dGATAb primes regulatory sites in S2 Schneider cells for activation by 20-hydroxyecdysone (20E), the principal steroid hormone in Drosophila development. Yet the genome-wide impact of SRP/dGATAb depletion on transcriptional responses to 20E has not been examined.

Results: We investigated the role of SRP/dGATAb in the response of S2 Schneider cells to 20E using SRP/dGATAb depletion via RNA interference. Combined RNA-Seq and ChIP-Seq analyses identified primary targets of SRP/dGATAb that (i) are transcriptionally induced by 20E and (ii) contain binding sites for both EcR and SRP/dGATAb. SRP/dGATAb depletion altered the transcription of different 20E-induced genes in opposite ways. For one subset of 20E-activated genes whose expression decreased upon depletion, SRP/dGATAb regulated active regulatory sites marked by H3K27Ac and enriched with SRP/dGATAb motifs. In these loci, SRP/dGATAb depletion reduced EcR binding at co-bound sites, demonstrating a priming role for this GATA family protein. In contrast, for a second subset of 20E-activated but SRP/dGATAb-suppressed genes (i.e., genes whose expression increased upon SRP/dGATAb depletion), SRP/dGATAb and EcR co-bound sites exhibited undisturbed EcR binding. Notably, the overall level of H3K27 acetylation at these loci increased upon SRP/dGATAb depletion.

Conclusions: Our data indicate that SRP/dGATAb positively regulates 20E-inducible transcription in S2 Schneider cells for some genes, functioning as a priming factor that facilitates EcR recruitment and chromatin acetylation. In contrast, for another subset of 20E-inducible genes, SRP/dGATAb exerts a negative regulatory effect, restraining activity of the regulatory sites.

DNA methylation is a most heritable epigenetic modification. Being a major vegetable crop, pepper (Capsicum spp.) possesses an over 3 Gb genome populated with TEs. This indicates a rich reservoir of epigenetic regulatory mechanisms. However, this large and complex genome renders the study of DNA methylation unaffordable and technically challenging. In this study, we analyzed DNA methylome in Capsicum spp., with a focus on C. annuum ST-8. We found that the genomes of Capsicum spp. are heavily methylated, particularly in the non-CG contexts. This is true when comparing to wheat, whose genome is over 16 Gb, containing over 80% TEs and repeats. Interestingly, we observed genic non-CG methylation and found that it is likely maintained by the CMTs, instead of RdDM. Overall, there is a negative relationship between gene expression and H3K9me2, and a positive relationship between genic non-CG methylation and H3K9me2, despite that genes without genic CHH methylation also possess some H3K9me2. Finally, we performed salt stress treatment with and without priming, and profiled active chromatin features as well as transcriptomes. We found that regardless of the environmental stimuli and developmental stages, the overall negative relationship between transcription and H3K9me2 is stably maintained. Altogether, our study revealed features of DNA methylation in ST-8 and we suggest that these features are likely common in Capsicum spp.

Chromatin remodeling in male germ cells and after fertilization plays a pivotal role in genetic transmission and early embryonic development. During spermatogenesis, histone-based chromatin undergoes progressive reorganization: canonical histones are gradually replaced by testis-specific variants, then by transition proteins, and ultimately by highly basic protamines (PRM1 and PRM2). This hierarchical replacement, modulated by histone post-translational modifications-including hyperacetylation, ubiquitination, and dynamic methylation-and supported by molecular chaperones and chromatin remodelers, ensures the efficient compaction of paternal DNA required for sperm function and genome stability. Upon fertilization, paternal chromatin undergoes rapid decondensation as protamine disulfide bonds are reduced, allowing maternal histone incorporation. In parallel, the paternal genome experiences extensive but regulated epigenetic reprogramming, including DNA demethylation and histone modification changes, which together establish a transcriptionally permissive state for zygotic genome activation and maternal-paternal chromatin integration. This review aims to provide an overview of chromatin remodeling from the male germline to post-fertilization stages in mammals, integrating recent findings on the molecular machinery involved in histone-to-protamine replacement and its reversal during early embryogenesis. It outlines the major processes involved in histone-to-protamine exchange, protamine removal, and chromatin reorganization after fertilization, defining the scope of the review for readers. Where available, comparative data from vertebrate and invertebrate models are discussed to provide an initial perspective on the possible evolutionary conservation of these mechanisms. Clarifying these processes offers valuable insight into male fertility, early embryonic regulation, and potential epigenetic inheritance, with implications for both fundamental and applied reproductive biology.

DNA methylation plays a critical regulatory role during insect development, yet the underlying mechanisms remain poorly understood. Here, we provide a comprehensive profile of DNA methylation dynamics across the developmental stages of the parasitoid wasp Nasonia vitripennis, a key insect model with functional methylation machinery. Using whole-genome bisulfite sequencing, we identify stage-specific methylation levels, including substantial genome-wide demethylation during the embryonic-to-larval transition and remethylation during subsequent metamorphic stages. Differential methylation analyses reveal significant enrichment of developmentally relevant Gene Ontology terms, highlighting roles in gastrulation, embryogenesis, larval development, regionalisation and morphogenesis. Analysis of protein binding motifs at differentially methylated sites further suggests DNA methylation may directly modulate transcription factor activity, a regulatory mechanism previously underappreciated in insects methylomics. RNA sequencing reveals coordinated expression of methylation-associated enzymes, including high embryonic expression of the demethylase tet and the methylation reader mbd, consistent with methylation dynamics. Although the regulatory relationship between DNA methylation and gene expression is complex, we observed that methylation may contribute to developmental transitions by influencing transcription factor accessibility and chromatin state. Our results suggest that DNA methylation levels are dynamic across Nasonia metamorphosis, and may modulate transcription factor binding across development. These findings refine current models of epigenetic regulation in holometabolous insects and establish a Nasonia vitripennis methylome across metamorphosis for the first time.

Background: Lysine demethylase 5 (KDM5) family proteins are transcriptional regulators best known for demethylating the promoter-proximal histone mark H3K4me3. KDM5-mediated regulation of gene expression is crucial in the brain, with pathogenic variants in human KDM5 genes leading to intellectual disability (ID) disorders. Although the demethylase activity of KDM5 proteins is vital for brain function, non-enzymatic functions also contribute. How KDM5 uses distinct features to regulate transcription in a context-dependent manner remains largely uncharacterized.

Results: Using Drosophila, we demonstrate that a demethylase-dead Kdm5^JmjC* strain expands the distribution of promoter-proximal H3K4me3 in the brain, whereas Kdm5^L854F, which models a pathogenic ID variant, has limited effects. Despite these divergent enzymatic effects, Kdm5^L854F and Kdm5^JmjC* exhibit similar transcriptional changes that do not correlate with changes to promoter recruitment of variant proteins, H3K4me3 levels, or chromatin accessibility. Instead, altered gene expression in both alleles correlates with preexisting chromatin signatures.

Conclusions: These findings suggest that KDM5 operates in conjunction with local chromatin contexts to employ demethylase-dependent and independent mechanisms of gene expression regulation in the brain. Disruption to this regulation affects pathways critical for neuronal function and is likely to contribute to the cognitive and behavioral features seen in patients.

Background: Interorgan communication, metabolite regulation and drug handling require fine-tuned small molecule transport across membranes. The Remote Sensing and Signaling (RSS) theory, which has found applicability in chronic kidney disease and uric acid disorders, emphasizes the central role of solute carrier (SLC) and ATP-binding cassette (ABC) transporters, enzymes and transcription factors in organ crosstalk. Based on prior network biology studies, ~ 1000 protein-coding genes are predicted to mediate RSS. This gene set largely overlaps with genes that are important for absorption, digestion, metabolism and excretion (ADME) of small molecules. However, it is not known how epigenetic regulation of these loci changes during the development of the liver and kidney, which control the small molecule composition of the blood, or the brain, whose physiology relies upon this process. Epigenetic regulation of these genes is also critical for understanding pharmacokinetics.

Results: We profiled chromatin state at 1034 RSS/ADME genes in the mouse kidney, liver and brain at the embryonic and adult stages. Using the high-resolution chromatin mapping method CUT&RUN, we examined the activating histone modifications H3K4me3, H3K27ac and H3K9ac, and the repressive modification H3K27me3. Activating modifications were most dynamic at the chromatin level in the liver and least dynamic in the brain. Acetylated histone modifications were more dynamic overall than methylation marks in all three tissues. Hierarchical clustering demonstrated that a subset of RSS/ADME genes undergoes a coordinated program of activation during kidney and liver development that correlates with changes in transcript abundance.

Conclusions: Defining the changes in chromatin that occur after birth within this gene set provides insight into tissue-specific regulation of RSS. Our findings carry implications for how the body acquires autonomous functionality through organ crosstalk mediated by transport of endogenous small molecules. Given their critical roles in ADME as well as handling of exogenous toxins, medications and metabolites derived from the gut microbiome, our analysis has ramifications for both precision pharmacology and diseases such as chronic kidney disease, metabolic syndrome and gout, in which dysregulation of RSS drives pathophysiology.

Background: The zinc finger-associated domain (ZAD), found in numerous Drosophila architectural proteins, such as Pita, enables homodimerization. Despite its prevalence in insects, only one human protein, ZFP276, possesses a ZAD-like domain. To date, the role of Pita has been studied in the formation of the boundaries of regulatory domains in the Bithorax complex, and the functional significance of its ZAD remains unclear.

Results: Using CRISPR/Cas9-mediated pita replacement with an attP site, we generated flies expressing modified Pita variants. Null pita mutants die in the late stages of embryogenesis. Flies expressing Pita lacking ZAD, Pita^ΔZ, exhibit reduced viability. Genome-wide chromatin immunoprecipitation revealed that Pita^ΔZ retains binding to housekeeping gene promoters and insulators, cooperating with other architectural C2H2 proteins and CP190. However, ZAD is essential for Pita binding to specific chromatin regions and its insulator function. Strikingly, the ZAD-like domain from human ZFP276 can functionally substitute for the ZAD in Pita.

Conclusions: ZAD is critical for the insulator activity of Pita and its ability to efficiently bind to specific genomic regions. The human ZFP276 ZAD-like domain may function similarly to the ZAD of Pita, raising the question of why ZADs spread in insects but not in mammals.

Background: The TET family of proteins-TET1, TET2, and TET3-are α-KG and Fe²⁺ dependent dioxygenases that play crucial roles in active DNA demethylation and the deposition of epigenetic marks such as 5-hydroxymethylcytosine, 5-formylcytosine, and 5-carboxycytosine. TET proteins can also oxidize thymine to 5-hydroxymethyluracil - a modification whose role is still poorly understood. TET proteins add a new layer of information in regulating gene expression, cellular development, and lineage specification. Dysregulation of TET activity is implicated in various cancers, especially in hematological malignancies, where TET2 loss-of-function mutations are prevalent. TET2's role in hematopoiesis is critical, as its knockdown skews progenitor differentiation toward the myeloid lineage and drives carcinogenesis. Therefore, restoring the lost activity of TET proteins is often proposed as an important component of cancer treatment. This study explores the distinct contributions of TET paralogs in generating active demethylation products in malignant cells. It examines whether vitamin C, a known cofactor of many dioxygenases, can compensate for the loss of specific TET paralogs. We applied a highly sensitive and specific methodology (2D-UPLC-MS/MS) to assess TET activity in the HAP1 cell line with single and double TET functional knockouts and in cells with the activity of all TET proteins impaired.

Results: Our findings reveal that TET2 is essential for all steps of iterative oxidation, and its loss has the most significant effect on 5-hydroxymethylcytosine and 5-formylcytosine levels. Vitamin C enhances TET activity and increases the levels of these oxidation products. However, its effect in TET2 knockout cells is limited. Vitamin C increased cytosine modification levels in TET2KO cells, but not to the extent observed in treated wild-type cells, indicating incomplete compensation for TET2 loss.

Conclusions: Our results demonstrated that each TET protein has a distinct, separate contribution to generating active demethylation products. The absence of individual TET paralog is linked with the specific pattern of active demethylation products in DNA, which is preserved after vitamin C treatment. Therefore, the deletion of one of the TET enzymes cannot be compensated for by the increased activity of the other TET family members, highlighting the unique roles of each TET paralog in epigenetic regulation.