Search Results (127)

Enhancer of zeste homologs inhibitory protein (EZHIP) is a eutherian-specific protein, with poorly defined developmental functions and physiological expression restricted to germ cells. Its aberrant re-expression characterizes posterior fossa ependymoma subtype A and a subset of diffuse midline gliomas with wild-type histone H3—aggressive pediatric brain tumors marked by global loss of the repressive H3 lysine 27 trimethylation (H3K27me3). Functionally analogous to the H3 lysine 27 to methionine (H3K27M) oncohistone, EZHIP inhibits Polycomb repressive complex 2 (PRC2), altering genome-wide H3K27me3 distribution and fate commitment. Unlike H3K27M, EZHIP is epigenetically silenced under physiological conditions yet inducible, suggesting context-dependent oncogenic roles. Its intrinsically disordered structure enables multifunctional interactions and biological versatility. Beyond brain tumors, EZHIP has emerged as an oncogenic driver in osteosarcoma, underscoring broader relevance across cancers. This review integrates current insights into EZHIP—from gene discovery and the mechanism of PRC2 inhibition to its emerging roles in metabolism, DNA repair, 3D chromatin regulation, and development. We outline EZHIP’s clinico-pathological significance in pediatric and adult malignancies, with an emphasis on EZHIP-driven hindbrain tumors. Finally, we discuss therapeutic opportunities, from the direct targeting of intrinsically disordered proteins to the indirect modulation of EZHIP-associated epigenetic and metabolic landscapes, highlighting implications for tumor evolution and precision oncology. Full article

The LAP2–emerin–MAN1-domain (LEM-D) proteins constitute a family of inner nuclear membrane proteins that play essential roles in the spatial regulation of intranuclear signaling. Defined by the conserved LEM domain, these proteins interact with chromatin, nuclear lamins, and barrier-to-autointegration factor (BAF), thereby linking nuclear architecture to signal-dependent transcriptional control. This review summarizes current knowledge on the structural features and molecular functions of representative LEM-D proteins, including LAP2, emerin, and MAN1, with a particular focus on their emerging roles as regulators of intranuclear signaling pathways. We discuss how these proteins modulate the activity of transcription factors involved in Hedgehog, Wnt/β-catenin, STAT3, Notch, and transforming growth factor-β (TGF-β) signaling by temporally retaining them at the inner nuclear membrane and controlling their access to chromatin. Furthermore, this review highlights the physiological and pathological relevance of LEM-D-mediated signaling regulation, especially in the context of muscle development, regeneration, and nuclear envelope-associated diseases such as muscular dystrophies. By integrating structural, signaling, and disease-related perspectives, this review proposes a conceptual framework in which LEM-D proteins function as critical intranuclear signaling hubs. Understanding these mechanisms provides new insights into nuclear signal transduction and suggests potential therapeutic targets for diseases associated with nuclear envelope dysfunction. Full article

Pork is one of the most widely consumed meats worldwide, with tenderness and intramuscular fat (IMF) content serving as key determinants of consumer acceptance. The rising demand for high-quality pork underscores the need to better understand the molecular mechanisms regulating IMF deposition and meat tenderness. In this study, we systematically examined the tenderness and IMF in the Longissimus dorsi (LD) muscle of 104 eight-month-old Songliao black pigs and Leixiang pigs raised under identical conditions. In addition, three pigs from each breed were randomly selected for multi-omics analyses, including Assay for Transposase-Accessible Chromatin sequencing (ATAC-seq), transcriptomics, and proteomics to elucidate the molecular networks underlying IMF deposition and tenderness. We identified a total of 2635 differentially accessible chromatin (DARs) regions associated with 2006 functional genes and 351 regulatory transcription factors, predominantly enriched in adipocyte differentiation and muscle metabolism pathways. Transcriptome analysis revealed 624 differentially expressed genes (DEGs) involved in lipid metabolism and tissue structure maintenance. While proteomic profiling detected 153 differentially expressed proteins (DEPs) enriched in fatty acid degradation/metabolism, PPAR signaling, energy metabolism, and thermogenesis pathways. Further, combined integrated multi-omics analysis identified nine candidate genes (MBP, DCLK1, COL3A1, ART3, COL14A1, PDK4, VCAN, LIPE, and GPX1) and transcription factor–target interaction networks predicted key regulatory factors including MEF2A/C/D, PR, GR, AR-HALLSITE, NF1-HALLSITE, AP4, TCF21, MYOG, ATOH1, TCF12, BHLHA15, MYF5, ASCL1, and SIX2, which were potentially involved in the regulation of meat tenderness and IMF deposition. These findings provide novel insights into the molecular determinants of IMF and tenderness, offering valuable targets for improving meat quality through genetic breeding strategies. Full article

The RCC1 gene is active in ensuring many cellular functions related to cell division in Drosophila melanogaster and Homo sapiens. A detailed comparison of the structure and functions of the RCC1 gene in Drosophila melanogaster and Homo sapiens was carried out using different analytical techniques (bioinformatics, immunofluorescence and confocal microscopy, FISH, and molecular genetic methods). The Drosophila RCC1 gene belongs to the family of housekeeping genes, since it resides in the interbands and gray bands of polytene chromosomes within aquamarine/lazurite chromatin in D. melanogaster. Furthermore, the databases demonstrate that RCC1 in D. melanogaster is expressed in all the tissues at all the developmental stages. According to The Human Protein Atlas, RCC1 in humans also exhibits low tissue specificity for 29 tissues. Immunostaining of polytene chromosomes with RCC1 antibodies revealed approximately 260 sites of RCC1 protein localization exclusively in black bands (sites of developmental genes) and in heterochromatin. The size of the coding gene portions is almost identical for D. melanogaster and H. sapiens, being ~2 kb. The group of Drosophila proteins related to condensed chromatin, RCC1 being a member of this group, has homologs forming similar interaction networks in humans. The conserved nature of the RCC1 gene has been confirmed by cell cycle studies in both species. It was found that expression of the RCC1 gene is upregulated in glioblastoma; the RCC1 protein predominantly resides on centrioles during metaphase. Full article

The RNAs present in spermatozoa play a crucial role in reproduction and embryonic development. They represent a promising diagnostic tool for assessing male infertility. However, their extraction is challenging due to their low concentration and highly condensed chromatin structure, as well as the presence of numerous cellular contaminants. These challenges vary across species and require the development of an optimized and reliable isolation method to obtain high-quality RNAs, which is essential for further molecular analyses regarding the roles played by these RNAs. This study evaluated two RNA extraction methods for spermatozoa in humans and other mammals (dogs, stallions, and bulls): a standard method using the NucleoSpin RNA^® II kit (Macherey-Nagel) and an optimized method that combined this kit with dithiothreitol and TRIzol™ pretreatment. In addition, the samples underwent pre-purification to eliminate somatic cells. The optimized method produced a significantly higher total RNA yield along with better purity, which was confirmed by the absence of the 18S and 28S ribosomal RNA peaks, indicating the absence of somatic cell contamination. Additionally, RT-PCR was performed to validate the presence of sperm-specific markers. The quality of the extracted RNAs was assessed by sequencing the mRNA encoding the human olfactory receptor OR1D2 and observing the resulting band on an agarose slab gel with a size corresponding to its entire open reading frame. By addressing long-standing challenges in sperm RNA isolation, our method provides an easy and standardized technique for research in reproductive biology and for advancing our understanding of paternal contributions to transgenerational inheritance. Full article

Cellular mechanical properties are critical indicators of cellular state and promising disease biomarkers. This study introduces a novel microhand system, featuring chopstick-like plate-shaped end-effectors, designed for stable and high-precision single-cell mechanical characterization. First, we automated the force sensor calibration to overcome the inefficiency and unreliability of conventional manual methods. To validate the system’s sensitivity, we precisely quantified the mechanical contributions of subcellular components, such as the actin cytoskeleton and chromatin, by measuring stiffness reductions after treatment with Cytochalasin D and Trichostatin A, respectively. Notably, when applied to a cellular model of Hutchinson–Gilford progeria syndrome, we successfully captured disease-induced mechanical alterations. A distinct population of high-stiffness cells was detected in progerin-overexpressing cells, a feature not observed in the control groups. Furthermore, by controlling the indentation speed and depth, the mechanical properties of the cytoplasm and nucleus could be distinctly evaluated. These results demonstrate that our microhand system is a highly sensitive and robust platform, capable of detecting subtle, disease-related changes and elucidating the contributions of specific subcellular structures to cell mechanics. Full article

The TIP60/NuA4 complex is a large, multifunctional histone acetyltransferase assembly of ~1.7 megadaltons, composed of 17–20 subunits, which plays a central role in epigenetic regulation. Through recognition of H3K4me3 by the ING3 reader, TIP60/NuA4 is recruited to sites of active transcription, where it remodels chromatin to regulate gene expression. Its activities include histone acetylation, histone variant exchange, transcriptional co-activation, and regulation of the cell cycle and apoptosis. In this review, we examine how altered subunit levels or mutations impact the chromatin structure and transcriptional activity, and how these changes influence differentiation across diverse cell types. We emphasize the molecular mechanisms by which TIP60/NuA4 shapes lineage specification, including histone H2A and H4 acetylation by the KAT5 catalytic subunit, H2A.Z incorporation by EP400, and interactions with transcription factors such as MyoD, PPARγ, and Myc. By integrating mechanistic and functional insights, we highlight how TIP60/NuA4 acts as a central epigenetic hub in differentiation and contributes to proper developmental transitions. Full article

Reversine is a small-molecule Aurora kinase inhibitor known for its pro-apoptotic effects and potential to remodel chromatin architecture. Although its impact on mitotic regulation is established, its effects on telomere dynamics and nuclear organization in chronic myeloid leukemia (CML) remain unclear. This study aimed to investigate the effects of reversine on telomere architecture, genomic instability, and apoptosis in CML cell lines (K-562 and MEG-01). Reversine was applied at increasing concentrations, and cytotoxicity was assessed using caspase-3/7 activation assays. Quantitative PCR was used to measure AURKA and AURKB mRNA expressions. Three-dimensional telomere architecture was analyzed with TeloView^® v1.03 software after Q-FISH labeling to quantify telomere number, signal intensity, aggregation, nuclear volume, and a/c ratio. Reversine induced a dose- and time-dependent apoptotic response in both cell lines and significantly downregulated AURKA and AURKB expressions. Three-dimensional telomere analysis revealed a marked reduction in telomere number and aggregates, signal intensity, and nuclear volume. While reduced signal intensity may indicate telomere shortening, the concurrent decrease in aggregation and altered spatial parameters suggests telomeric reorganization rather than progressive instability. These features reflect structural nuclear remodeling and early apoptotic commitment. Differences between K-562 and MEG-01 responses underscore potential heterogeneity in telomere maintenance mechanisms. Reversine modulates genomic stability in CML cells through dual mechanisms involving Aurora kinase inhibition and telomere architecture remodeling. The integration of 3D telomere profiling highlights reversine’s potential as a therapeutic agent targeting nuclear disorganization and mitotic dysregulation in leukemia. Full article

The 3D chromatin architecture establishes a complex network of genes and regulatory elements necessary for transcriptomic regulation in development and disease. This network can be modeled by cis-regulatory hubs (CRH), which underscore the local functional interactions between enhancers and promoter regions and differ from other higher-order chromatin structures such as topologically associated domains (TAD). The activity-by-contact (ABC) model of enhancer–promoter regulation has been recently used in the identification of these CRHs, but little is known about the role of transcription factor CCTC binding factor (CTCF) on ABC scores and their consequent impact on CRHs. Here, we show that the loss of CTCF leads to a reorganization of the ABC-derived rankings of putative enhancers in the mouse heart, a global reduction in the total number of CRHs and an increase in the size of CRHs. Furthermore, CTCF loss leads to a higher percentage of CRHs that cross TAD boundaries. These results provide additional evidence to support the importance of CTCF in forming the regulatory networks necessary for gene regulation. Full article

The mammalian genome is hierarchically packaged into distinct functional units, including chromatin loops, topologically associating domains, compartments and chromosome territories. This structural organization is fundamentally important because it orchestrates essential nuclear functions that underpin normal cellular identity and organismal development. In this review, we synthesize current understanding of the intricate relationship between genome architecture and its critical biological roles. We discuss how hierarchical structures are dynamically established and maintained by architectural proteins, transcription factors, epigenetic regulators and non-coding RNAs via distinct mechanisms. Importantly, we focus on the functional consequences of three-dimensional (3D) genome organization and discuss how it modulates fundamental biological processes such as transcription, gene co-expression, epigenetic modification, DNA replication and repair. We also examine the dynamics of 3D genome organization during cellular differentiation, early embryonic development and organogenesis, followed by discussing how structural disruptions are mechanistically linked to various human diseases. Understanding the biological function of 3D genome organization is thus not only essential for deciphering fundamental nuclear processes but also holds significant promise for elucidating disease etiologies and developing effective therapeutics. Full article

Background: While the fundamental principles of chromatin 3D organization and its interplay with transcriptional regulation are still not completely understood, increasing evidence suggests a considerable role of DNA repeats. Considering the influence of DNA repeats on local dinucleotide contents, the influence of dinucleotide contents on the structural properties of DNA, their influence on histone affinity, and the influence of histone occupancy on chromatin, an indirect influence of repeats on 3D organization, seems worth testing. Methods: In this study, we search for global correlations between annotations associated with transcription and 3D organization, dinucleotide contents, DNA properties, and repeats in human and mouse. In a second step, we search for local peaks in DNA properties around those annotations and derive the influences of the dinucleotide and repeat contents (including tandem repeats (TRs) and transposons). Results: We identify several strong and significant associations between annotations and DNA properties, which are influenced by a variety of different repeats. Consistent with former findings, the Roll property is found to be especially sensitive to the sequence context. Conclusions: Our results suggest a significant effect of repeats on DNA properties and thus an indirect effect on histone occupancy and 3D chromatin organization. Full article

Cancer remains a leading cause of mortality worldwide, arising from a complex interplay of genetic, epigenetic, and environmental factors. Although the role of micronutrients in cancer development has received limited attention, growing evidence suggests that vitamins, particularly vitamin D, may influence oncogenic pathways. This hypothesis manuscript explores the potential interaction between vitamin D and the oncogenic long non-coding RNA HOTAIR, providing a novel mechanistic explanation for the inverse correlation between vitamin D status and cancer risk. We support our hypothesis with in silico docking evidence, suggesting that vitamin D binds to bioactive domains within the structured regions of HOTAIR, potentially disrupting its interaction with chromatin regulators such as PRC2. This concept may offer a novel approach to cancer prevention and therapy. Full article

Breast cancer affects over 2 million women annually and results in 650,000 deaths. This study aimed to identify epigenetic mechanisms impacting breast cancer-related gene expression, discover potential biomarkers, and present a novel approach integrating feature selection, Natural Language Processing, and 3D chromatin structure analysis. We used The Cancer Genome Atlas database with over 800 samples and multi-omics datasets (mRNA, miRNA, DNA methylation) to select 2701 features statistically significant in cancer versus control samples, from an initial 417,486, using the Monte Carlo Feature Selection and Interdependency Discovery algorithm. Classification of cancer vs. control samples on the selected features returned very high accuracy, depending on feature-type and classifier. The cancer samples generally showed lower expression of differentially expressed genes (DEGs) and increased β-values of differentially methylated sites (DMSs). We identified mRNAs whose expression is explained by miRNA expression and β-values of DMSs. We recognized DMSs affecting NRF1 and MXI1 transcription factors binding, causing a disturbance in NKAPL and PITX1 expression, respectively. Our 3D models showed more loosely packed chromatin in cancer. This study highlights numerous possible regulatory dependencies, and the presented bioinformatic approach provides a robust framework for data dimensionality reduction, enabling the identification of key features for further experimental validation. Full article

The crustacean Daphnia magna produces genetically identical females and males by parthenogenesis. Males are produced in response to environmental cues including crowding and lack of food. For male development, the DM-domain containing transcription factor Doublesex1 (DSX1) is expressed spatiotemporally in male-specific traits and orchestrates male trait formation in both somatic and gonadal tissues. However, it remains unknown how the dsx1 gene is silenced in females to avoid male trait development. Heterochromatin Protein 1 (HP1) plays a crucial role in epigenetic gene silencing during developmental processes. Here we report the identification of four HP1 orthologs in D. magna. None of these orthologs exhibited sexually dimorphic expression, and among them, HP1-1 was most abundantly expressed during embryogenesis. The knock-down of HP1-1 in female embryos led to the derepression of dsx1 in the male-specific traits, resulting in the development of male characteristics, such as the elongation of the first antennae. These results suggest that HP1-1 silences dsx1 for female development while environmental cues unlock this silencing to induce male production. We infer the HP1-dependent formation of a sex-specific chromatin structure on the dsx1 locus is a key process in the environmental sex determination of D. magna. Full article

Background: Malaria remains a significant global health burden, particularly in sub-Saharan Africa, accounting for high rates of illness and death. The growing resistance to frontline antimalarial therapies underscores the urgent need for novel drug targets and therapeutics. Bromodomain-containing proteins, which regulate gene expression through chromatin remodeling, have gained attention as potential targets. Plasmodium falciparum bromodomain protein 1 (PfBDP1), a 55 kDa nuclear protein, plays a key role in recognizing acetylated lysine residues and facilitating transcription during parasite development. Methods: This study investigated ex vivo PfBDP1 gene mutations and identified potential small molecule inhibitors using computational approaches. Malaria-positive blood samples were collected. Genomic DNA was extracted, assessed for quality, and amplified using PfBDP1-specific primers. DNA sequencing and alignment were performed to determine single-nucleotide polymorphism (SNP). Structural modeling used the PfBDP1 crystal structure (PDB ID: 7M97), and active site identification was conducted using CASTp 3.0. Virtual screening and pharmacophore modeling were performed using Pharmit and AutoDock Vina, followed by ADME/toxicity evaluations with SwissADME, OSIRIS, and Discovery Studio. GROMACS was used for 100 ns molecular dynamics simulations. Results: The malaria prevalence rate stood at 12.24%, and the sample size was 165. Sequencing results revealed conserved PfBDP1 gene sequences compared to the 3D7 reference strain. Virtual screening identified nine lead compounds with binding affinities ranging from −9.8 to −10.7 kcal/mol. Of these, CHEMBL2216838 had a binding affinity of −9.9 kcal/mol, with post-screening predictions of favorable drug-likeness (8.60), a high drug score (0.78), superior pharmacokinetics, and a low toxicity profile compared to chloroquine. Molecular dynamics simulations confirmed its stable interaction within the PfBDP1 active site. Conclusions: Overall, this study makes a significant contribution to the ongoing search for novel antimalarial drug targets by providing both molecular and computational evidence for PfBDP1 as a promising therapeutic target. The prediction of CHEMBL2216838 as a lead compound with favorable binding affinity, drug-likeness, and safety profile, surpassing those of existing drugs like chloroquine, sets the stage for preclinical validation and further structure-based drug design efforts. These findings are supported by prior experimental evidence showing significant parasite inhibition and gene suppression capability of predicted hits. Full article