Epigenetics & Chromatin最新文献

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.

Background: Bmi1, a key component of the Polycomb repressive complex 1, plays a critical role in regulating gene expression by modulating chromatin structure. Its depletion is known to cause hair cell loss in the neonatal mouse cochlea. This study aimed to investigate the epigenetic mechanisms and transcriptional consequences of Bmi1 depletion in the neonatal auditory sensory epithelium.

Results: Analysis of neonatal Bmi1 knockout mice using H3K27me3 chromatin immunoprecipitation sequencing, assay for transposase-accessible chromatin sequencing, and RNA sequencing revealed significant transcriptional alterations, particularly in genes governing cell proliferation, senescence, and death. Bmi1 depletion resulted in widespread gene upregulation and increased chromatin accessibility, which correlated with reduced H3K27me3 enrichment. Notably, expression of Cdkn2c, a key cell cycle regulator, was significantly upregulated. Inhibition of Cdkn2c rescued the proliferative capacity of inner ear epithelial cells in Bmi1 knockout mice.

Conclusions: These findings demonstrate that Bmi1 maintains transcriptional repression and chromatin state in the developing cochlea, primarily through H3K27me3 deposition. Depletion disrupts this control, leading to Cdkn2c overexpression and impaired cell proliferation. This identifies Cdkn2c and its regulatory pathway as potential therapeutic targets for hearing loss associated with hair cell depletion.

Background: Nucleosome ubiquitination at lysine 119 of histone H2A (H2AK119ub) and lysine 120 of histone H2B (H2BK120ub) are prominent post-translational modifications with opposing roles in chromatin regulation. Although H2AK119ub is associated with transcriptional repression and H2BK120ub with activation, the molecular basis for these contrasting effects has remained unclear.

Results: Here, we use microsecond all-atom and millisecond coarse-grained molecular dynamics simulations to reveal how the position of ubiquitin reshapes nucleosome structure and assembly. H2AK119ub rigidifies the histone core by indirectly reinforcing the L1-L1 interface between H2A histones, strengthening both tetramer-dimer and dimer-dimer interactions, and slowing complete nucleosome assembly. In contrast, H2BK120ub disrupts these interfaces, weakens the histone core, and favors partially assembled hexasome and tetrasome states. Both modifications cause dramatic slowdowns in nucleosome folding, with H2BK120ub producing an order-of-magnitude greater effect. These simulations establish clear molecular mechanisms by which site-specific ubiquitination alters nucleosome stability and assembly kinetics.

Conclusion: Our findings quantitatively explain how H2A and H2B ubiquitination exert opposing effects on chromatin regulation. This mechanism is directly relevant to the opposing roles of these marks in transcriptional activation and repression, and may represent one way that combinations of histone modifications modulate chromatin function in vivo.

5-hydroxymethylcytosine (5hmC), an epigenetic modification derived from the oxidation of 5-methylcytosine (5mC) by the ten-eleven translocation (TET) family of dioxygenases, plays a pivotal role in the regulation of gene expression, cellular differentiation, and developmental plasticity. Once considered an intermediate in DNA demethylation, 5hmC is now recognized as a stable and functionally significant epigenetic mark with distinct genomic distributions and significant regulatory implications. This review provides a comprehensive analysis of the biological functions of 5hmC in normal cellular processes, including its role in maintaining tissue-specific gene expression, lineage commitment, and genomic integrity. We also describe its role in cancer, the mechanistic underpinnings of its loss or redistribution in tumor cells, and how these changes contribute to oncogenic signaling pathways, epithelial-mesenchymal transition, and tumor heterogeneity. Furthermore, we explore the utility of 5hmC as a biomarker in cancer diagnostics and prognostics, supported by recent advances in sequencing technologies and cell-free DNA profiling. We also examine the intersection of 5hmC and chemotherapy, highlighting how aberrant 5hmC levels can influence drug resistance and sensitivity, and assess the therapeutic potential of targeting TET enzymes and associated pathways. By integrating insights from basic epigenetics, cancer biology, and therapeutic research, this review underscores the multifaceted role of 5hmC in human malignancies and outlines the translational opportunities for exploiting 5hmC-related mechanisms in precision oncology.

Background: Flatfish metamorphosis involves dramatic tissue remodeling, including the migration of one eye to the opposite side of the body, enabling the transition from pelagic to benthic life. While this process requires precise transcriptional regulation, the role of epigenetic mechanisms remains poorly understood. Here, we investigate DNA methylation dynamics during turbot metamorphosis using reduced-representation bisulfite sequencing (RRBS) across three key stages: pre-metamorphosis, climax, and post-metamorphosis.

Results: We identified stage-specific methylation patterns, with more than 31% of hypermethylated regions emerging during the climax phase-coinciding with upregulated dnmt3a (de novo methyltransferase) and altered expression of photoreceptor adaptation genes. Critically, the migrating and non-migrating eyes exhibited divergent methylation and expression of retinal ganglion cell (RGC) regulators (eomesa, tbr1b), linking epigenetic changes to asymmetric ocular development.

Conclusion: Our results suggest that DNA methylation may play a role in visual system remodeling, particularly in processes associated with RGC-mediated eye migration and light-sensing adaptation, providing new understanding of the epigenetic regulation of vertebrate metamorphosis.