Networks are widely applied to investigate relationships among individual components of complex biological systems. Recent application of biological networks, such as gene co-expression networks and gene regulatory networks, has been instrumental to define principles of transcriptional modulation in development and disease. However, computational methods that can embed the activity of cis-regulatory elements (CRE) into a network are still limited. Capturing temporal CRE activity within a network could help reveal regulatory programs involved in cell fate commitment and disease development. To address this, we present T-ChroNet (Time-aware Chromatin Network), a network-based method that models CRE as nodes and their temporal co-accessibility as edges. Through the detection of CRE sharing similar accessibility patterns over time, T-ChroNet allows the inference of putative upstream regulators and downstream biological pathways. We applied T-ChroNet to temporally-resolved CRE datasets, from both human and mouse, including chromatin accessibility (ATAC-seq) and histone post-translational modifications (H3K27ac ChIP-seq). T-ChroNet successfully recovered known regulators and enriched pathways for both modalities and species, while also uncovering novel putative factors and mechanisms regulating cell identity, organ development and disease progression.

The development and progression of glioblastoma, the most aggressive malignant intracranial tumor with a poor prognosis, are influenced by mutations, oncogene overexpression, and epigenetic factors, particularly those relating to DNA methylation status and histone post-translational modifications. Valproic acid (VPA), a well-known histone deacetylase (HDAC) inhibitor, has shown promise both alone and in combination with other agents against various solid tumors, including gliomas. Given VPA's reported effects on chromatin supramolecular organization and expression activity across different cell types, we studied textural features indicative of chromatin structural changes in U-251MG glioblastoma cells cultured in the presence of VPA, utilizing image cytometry and immunofluorescence techniques. For comparison, cells treated with 5-aza-CdR served as a positive control for DNA demethylation. Chromatin remodeling was observed in VPA-treated cells, which exhibited decreased HDAC activity and increased histone H3 acetylation, whereas no such changes were detected in 5-aza-CdR-treated cells. These findings suggest that, despite alterations in DNA methylation within glioblastoma cells and a possible effect of VPA on DNA demethylation, the chromatin remodeling phenomenon observed through image cytometry in VPA-treated U-251MG cells is more closely associated with induced changes involving histone modifications rather than with DNA demethylation. Although these findings are based on in vitro conditions, present findings of basic character may acquire pre-clinical perspective implications if corroborated by further results obtained from various glioblastoma cell cultures and animal models treated with drugs that may influence epigenetic markers, while bypassing the question of blood-to-brain drug flux.

Nitric oxide generates a coordinated histone modification signature consistent with chromatin compaction, linked to methyl-modifying enzyme dysregulation and tumor-permissive gene silencing.

The host defense against emerging respiratory pathogens begins with the induction of cell-intrinsic, interferon-mediated antiviral responses. The interferon response induces innate effector and adaptive cellular responses crucial for viral clearance and the establishment of long-lasting immune memory. Although these antiviral processes are primarily characterized at the transcriptional level, the epigenetic mechanisms that orchestrate the cellular transcriptional output during infection remain understudied. Technological advances in systems immunology and virology have revealed dynamic changes in the cellular epigenetic landscape following infection, and their contextual roles in the fine-tuning of antiviral defense. This minireview covers our current understanding of how DNA methylation, post-translational modifications of histones, and chromatin remodelers are dynamically reprogrammed during respiratory virus infections, and the distinct strategies that respiratory viruses employ to subvert epigenetic control. We place further emphasis on cell-type-specific programs and the biological factors that alter the epigenetic landscape and regulate the balance between protective or pathogenic immune responses to infection.

Post-translational modifications (PTMs) of histones play a pivotal role in chromatin condensation, with increasingly more evidence pointing to the involvement of liquid-liquid phase separation (LLPS). Here, we report the significant impact of the acetylation site of the N-terminal histone H3 peptide on LLPS with nucleosomal-linker DNA. In our model system, wherein the synthesized H3 peptide and DNA undergo LLPS, acetylation of the H3 peptide significantly inhibits LLPS, with the effects varying markedly depending on the acetylation site; acetylation near the H3 peptide end more strongly inhibits LLPS than acetylation near the H3 peptide center. Through experiments and molecular dynamics (MD) simulations, we show that this phenomenon arises from multiple contributing factors, including differences in the thermal stability of DNA, hydrophobic effects, and charge distribution within the H3 peptide/DNA complexes, which together promote the formation of intercomplex networks. Our findings not only provide fundamental insights that link LLPS-mediated chromatin condensation to biological phenomena depending on the acetylation sites but also suggest novel avenues for site-specific chemical modulation to regulate LLPS, which may, in turn, inspire new strategies in biotechnological applications and materials design.

De-novo discovery of posttranslational histone modifications in Schistosoma mansoni stages.

Genetic and epigenetic predictors of antidepressant response.

Cells and organisms are often exposed to various metabolic environments that require adaptive responses for survival. One common way cells adapt to fluctuating nutrient environments is through regulated transcription of metabolic genes. Intermediary metabolites, such as acetyl-CoA, produced by metabolic pathways, serve as cofactors for histone post-translational modifications, which in turn regulate gene expression. However, increasing evidence shows that non-acetyl acyl-CoAs, such as propionyl-CoA, participate in gene regulation during metabolic stress. In this report, we find that histone propionylation functions as a global response to glucose starvation. Furthermore, we find that Acetyl-CoA Synthetase 1 (Acs1) binds chromatin and is the primary enzyme responsible for generating propionyl-CoA in the nucleus. Together, our findings reveal that Acs1-mediated histone propionylation constitutes a novel pathway for metabolic adaptation, linking nutrient availability to chromatin modification.

Chromatin function emerges from combinatorial patterns of histone post-translational modifications (PTMs) that are read, written, and erased by dedicated enzymes. Over the past 30years, increasing evidence suggests that specific histone PTMs or combinations of PTMs influence one another, constituting epigenetic cross-talk that shapes chromatin structure, protein-protein interactions, and catalytic efficiency of nucleosome-targeting enzymes. Here, we summarize mechanistic and methodological advances that enable rigorous interrogation of histone PTM interplay. We highlight selected nucleosome engineering strategies that build precisely modified substrates to test in vitro, proteomic pipelines that preserve combinatorial information, and omics technology that can globally profile integrated chromatin regulatory events in cells and tissues. Furthermore, we survey multivalent reader modules and engineered biosensors that report combinatorial marks in nucleosomes and living cells. Representative case studies illustrate how defined PTMs modulate catalytic parameters of writer and eraser complexes, including lysine methyltransferases, demethylases, acetyltransferases, and deacetylases, focusing on cross-talk with histone H3 N-terminal tail marks. These include the role of H3K9me2/3 and K14ac in directing propagation of H3K9me3, the role of H3K4me1/2 and K14ac in slowing H3K4 demethylation, the role of H3K4me2/3 in directing H3K9 acetylation, and the role of H3K36 methylation in directing deacetylation of H3 and H4. The substrates for these case studies include both mononucleosomes and nucleosome arrays. These examples illustrate the principle of epigenetic cross-talk, namely, that specific combinatorial PTMs can affect enzymes and alter local biochemistry.

At fertilization, two highly specialized gametic genomes must rapidly reprogram into a single totipotent nucleus. In mammals, this transformation is marked by a dramatic protamine-to-histone exchange and pronounced asymmetry between the parental pronuclei. Zebrafish offer a contrasting vertebrate model in which sperm chromatin is already organized in nucleosomes and carries both active and repressive histone modifications, eliminating the need for protamine replacement. This histone-based configuration provides a unique opportunity to examine how parental chromatin transitions are initiated and coordinated directly in vivo. Although zebrafish is a well-established model organism in developmental biology, the detailed cellular and molecular steps of its fertilization process, particularly the timing and coordination of parental chromatin remodelling, remain largely unknown. Using immunofluorescence coupled with spinning-disk confocal microscopy, we mapped histone variants and post-translational modifications with temporal sampling at minute-level intervals across 3,549 zebrafish embryos from fertilization to the first cleavage. This analysis resolved the main steps of fertilization, from sperm entry and chromatin decondensation to the formation, expansion, and apposition of the parental pronuclei. Throughout these stages, maternal and paternal genomes were remodelled almost synchronously. Activation-associated marks (H3K4me1/2/3, H3K9ac, H4K12ac) appeared shortly after fertilization, spread to both pronuclei by apposition, and disappeared before mitosis. The histone modification H3K9me3, commonly associated with compact or heterochromatin-like chromatin states, was present from the earliest time point examined and became more prominent during pronuclear maturation, whereas H3K27me3 was not detectable at any stage. H2A.Z showed strong paternal enrichment after sperm entry and was later detected in both pronuclei during apposition with weaker maternal signal. Polar bodies did not show evidence of undergoing the extensive chromatin remodelling observed in the zygotic pronuclei. In gametes, sperm contained core histones and methylation marks but lacked acetylation, indicating a compact, semi-active chromatin state, while unfertilized eggs displayed H3K9me3 and H3S10ph but no activating marks, consistent with meiotic arrest. Zebrafish fertilization involves direct, histone-based chromatin remodelling that occurs without protamine replacement and proceeds almost simultaneously in both parental pronuclei. The sperm genome enters fertilization already in a semi-active, histone-bound state, enabling rapid and coordinated remodelling of both parental chromatin. This process results in a transient change in chromatin configuration that is more symmetrical between the parental genomes than that reported in mammalian systems.

Comprehensive mass spectrometry screening-derived atlas of HDAC inhibitors reveals histone-specific acetylation changes.

Nonenzymatic covalent modification (NECM) of lysine residues can be physiologically consequential. A NECM is formed by the oxidized abasic site (C4-AP), which is produced by DNA-damaging agents. C4-AP reacts with the ε-amine of histone lysines in nucleosome core particles (NCPs) to form an electrophilic 5-methylene pyrrolone NECM (KMP). KMP is also produced on histones in bleomycin-treated human cells. Here, we describe a molecule (1a) that yields KMP by reacting directly with histones in NCPs. KMP forms on lysines of all four core histones in the order H3 > H2A/H2B > H4. Biotinylated KMP-containing NCPs prepared using 1a were incubated with HeLa nuclear lysates in the presence of glutathione. NCP-protein cross-links were observed by native PAGE. Protein-protein cross-links (PPCs) were enriched through intact NCP pull-down and identified via tryptic digests by LC-MS/MS. Model reactions demonstrate KMP is more electrophilic than N-acyllysine post-translational modifications (PTMs) but does not form PPCs indiscriminately within NCPs. Enriched proteins are functionally biased, with overrepresentation of DNA binding, histone binding, histone PTMs, and transcription regulation. Proteins enriched by KMP-containing NCPs produced by generating C4-AP on DNA were analyzed in parallel. Similar overrepresented functions were observed when C4-AP was introduced near the H3/H4 N-tails, whereas a distinct group of proteins was enriched when C4-AP was introduced near the H2A acidic patch. PPC formation by KMP is modulated by the NCP environment. Combined with the known intracellular formation of KMP, this study inspires investigating whether PPC formation by this NECM impacts cell function and viability.

Epigenetic regulation of chromatin structure is strongly influenced by histone variants and post-translational modifications. The conserved histone variant H2A.Z has been functionally linked to the pioneer factors Sox2 and Oct4, which open chromatin and activate cell fate-specific transcriptional programs. However, the molecular basis of this interaction is not well understood. Here, we combine biochemistry, NMR spectroscopy, and molecular dynamics (MD) simulations to investigate how H2A.Z nucleosome dynamics influence pioneer factor binding. We find that H2A.Z enhances Sox2 and Oct4 association at distinct positions within 601 nucleosomes, correlating with increased DNA accessibility and altered H3 N-terminal tail dynamics. We show that the H3 tail competes with Sox2 for DNA binding and is more efficiently displaced with H2A.Z, while also allowing for unique Sox2-H3 tail interactions. MD simulations reveal that H2A.Z promotes DNA unwrapping, increases inter-gyre spacing, and enhances H3 tail flexibility, while simultaneously reducing contacts with DNA and with the H2A.Z C-terminal tail. This destabilizing effect is DNA-sequence dependent and prominent in the less stable Lin28B nucleosome, which Sox2 appears to substantially reshape. Together, our results suggest that H2A.Z promotes pioneer factor binding by increasing DNA accessibility and reducing histone tail competition, with broad implications for epigenetic regulation and chromatin recognition.

Methyltransferase PRC2 (Polycomb Repressive Complex 2) deposits histone H3K27 trimethylation to establish and maintain epigenetic gene silencing. PRC2 is precisely regulated by accessory proteins, histone post-translational modifications, and, particularly, RNA. Research on PRC2-associated RNA has mostly focused on the tight-binding G-quadruplex (G4) RNAs, which inhibit PRC2 enzymatic activity in vitro and in cells, a mechanism explained by our recent cryo-EM structure showing G4 RNA-mediated PRC2 dimerization. However, PRC2 binds a wide variety of RNA sequences, and it remained unclear how diverse RNAs beyond G4 associate with and regulate PRC2. Here, we show that variations in RNA sequence elicit disparate effects on PRC2 function. A G-rich RNA lacking consecutive G's and an atypical G4 structure called a pUG-fold mediate PRC2 dimerization nearly identical to that induced by G4 RNA. In contrast, pyrimidine-rich RNAs, including a motif identified by CLIP-seq in cells, do not induce PRC2 dimerization and instead bind PRC2 monomers with retention of methyltransferase activity. Only RNAs that dimerize PRC2 compete with nucleosome binding and inhibit PRC2 methyltransferase activity. Thus, PRC2 binds many different RNAs with similar affinity; however, the functional effect on enzymatic activity depends entirely on the sequence of the bound RNA, a conclusion potentially applicable to any RNA-binding protein with a large transcriptome.

Certain regulatory DNA regions remain accessible even under conditions of widespread chromatin compaction. These regions are often marked by specific protein factors and histone modifications that help maintain their accessibility. Here, we examine the genomic landscape of acetyl-methyllysine (Kacme), a recently discovered histone post-translational modification. Across multiple systems, Kacme is highly enriched at sites of accessible chromatin, including active promoters, enhancers, silencers, and CTCF-binding sites. We find that Kacme is selectively retained at loci that resist condensation during mitosis, marks XIST and escapee regions on the inactive X chromosome in female cells and demarcates the boundaries of broad heterochromatin domains. Kacme-marked insulator elements block heterochromatin spreading and protect adjacent genes from transcriptional repression, even when H3K27me3 levels are pharmacologically elevated through KDM6A/6B inhibition. Taken together, our findings establish the chromatin features associated with Kacme and support a model in which Kacme helps safeguard chromatin accessibility at loci that resist compaction.

Hypertension is a leading global cause of cardiovascular, renal, and cerebrovascular morbidity. Beyond classical genetic and environmental determinants, accumulating evidence highlights epigenetic regulation as a key contributor to blood pressure control and vascular pathology. Epigenetic mechanisms including DNA methylation, histone post-translational modifications, and non-coding RNAs govern gene expression without altering the underlying DNA sequence, thereby linking environmental and physiological stimuli to stable transcriptional changes. Aberrant epigenetic signatures have been identified in vascular, renal, and endocrine tissues integral to blood pressure regulation, influencing pathways that mediate vascular tone, sodium handling, oxidative stress, and inflammation. Among these, differential methylation and histone modification of renin angiotensin aldosterone system (RAAS) genes, including AGT, REN, ACE, and AT1R, have been shown to promote sustained activation of vasoconstrictive and sodium-retentive signaling cascades. Chronic exposure to a high-salt diet (HSD) represents a potent environmental modifier of this epigenetic landscape. Excess dietary sodium can alter CpG methylation patterns, histone acetylation states, and microRNA profiles across multiple tissues, leading to enhanced RAAS activity and vascular dysfunction. These HSD-induced alterations often persist despite subsequent sodium normalization, reflecting an enduring "epigenetic memory" of dietary stress that contributes to salt-sensitive hypertension. Understanding how HSD and other environmental factors reprogram RAAS-related gene networks through epigenetic mechanisms provides critical insight into the molecular basis of hypertension. Moreover, these findings open new avenues for therapeutic intervention utilizing DNA methyltransferase and histone deacetylase inhibitors, as well as RNA-based precision therapies aimed at reversing the maladaptive epigenetic imprint underlying chronic blood pressure elevation.

Chromatin architecture is a central determinant of genomic stability. Effective DNA repair requires dynamic chromatin remodeling to grant repair factors timely access to lesions and to orchestrate repair pathway choice. Disruption of chromatin-regulatory mechanisms or DNA damage response pathways undermines repair fidelity and contributes to a wide spectrum of human disorders, including developmental syndromes, premature aging, and multiple cancers. Here, we review how chromatin state and remodeling complexes shape detection, signaling, and resolution of DNA double-strand breaks, and we examine how their misregulation drives disease and presents opportunities for therapeutic intervention. Specifically, we discuss how post-translational modifications and ATP-dependent chromatin remodeling complexes contribute to DNA damage repair with a particular focus on DNA double-strand breaks, one of the most deleterious DNA lesions. We summarize how chromatin remodeling and histone post-translational modifications regulate DNA repair pathway choice, and how these processes are essential for safeguarding genomic integrity and preventing human disease. Finally, we discuss emerging concepts and major unanswered questions in the context of chromatin function and DNA double-strand break repair, with a focus on exploring the emerging literature on the role of chromatin compartments and topological associated domains for orchestrating DNA repair within chromatin and safeguarding genomic stability.

Multiple myeloma (MM) is a plasma cell malignancy that originates in the bone marrow (BM) and is characterized by the clonal expansion of Bcell-derived plasma cells producing abnormal monoclonal immunoglobulins. Despite significant therapeutic advances that have improved patient outcomes, drug resistance remains a major obstacle to effective disease management. Genetic and epigenetic heterogeneity are key features of MM that drive disease onset, progression, and therapeutic resistance. Both early and advanced stages of MM exhibit global and locus specific DNA methylation abnormalities that silence tumor suppressor genes and disrupt key regulatory pathways, including Wnt/β-catenin, JAK/STAT, and apoptotic signaling. Altered activity of histone modifiers, including methyltransferases (e.g., EZH2, MMSET) and deacetylases (e.g., HDAC4, HDAC6), promotes chromatin remodeling and myeloma cell survival, representing promising therapeutic targets. Dysregulated long non-coding RNAs (lncRNAs), such as MALAT1 and MIAT1, further contribute to genomic instability and drug resistance. Emerging epigenetic therapies targeting DNA methyltransferases, HDACs, and bromodomains show promise in overcoming therapeutic resistance and improving patient outcomes. In this article, we summarize current insights into the central role of epigenetic alterations including DNA methylation changes, histone post-translational modifications, and lncRNA dysregulation in MM pathogenesis, discuss their mechanistic and clinical implications, and highlight therapeutic opportunities emerging from these discoveries.

Erythropoiesis is tightly regulated by lineage-specific transcription factors that govern erythroid commitment, proliferation, and differentiation. A core erythroid transcriptional network, together with non-DNA-binding cofactors, occupies regulatory regions of genes essential for erythroid development. This process is further shaped by epigenetic mechanisms, including histone post-translational modifications and long-range chromatin interactions. CCCTC-binding factor (CTCF) is a multifunctional regulator with a central role in three-dimensional chromatin organization. Although CTCF has been implicated in hematopoietic differentiation and leukemogenesis, its specific function in erythropoiesis remains poorly defined. Here, we investigated the role of CTCF during erythroid differentiation using two complementary models: pluripotent K562 leukemia cells and primary human CD34+ hematopoietic stem/progenitor cells, each induced toward the erythroid lineage by distinct stimuli. In both systems, CTCF silencing impaired erythroid differentiation by repression of key erythroid transcription factor genes, including LMO2, KLF1, MYB, and ETS1. This repression was associated with enrichment of repressive histone marks at CTCF-binding sites within their regulatory regions. Moreover, CTCF cooperated with cohesin to establish and stabilize long-range chromatin interactions at these loci. These results provide new insight into how CTCF-dependent chromatin regulation contributes to normal erythroid development and suggest that perturbation of this regulatory axis may have implications for hematopoietic disorders and malignancies.

Skeletal muscle is highly plastic and capable of remodeling its contractile and metabolic properties depending on physical demands. Such remodeling requires modification of chromatin structure to support transcriptional activation and repression of gene programs. Chromatin dynamics depend, in part, on the acetylation and methylation of histone 3 lysine 27 (H3K27), which is controlled by several enzymes that add and remove these histone marks. Several histone post-translational modifications in muscle have been shown to be modulated by exercise. Here, we sought to examine whether major H3K27 regulators themselves are altered by endurance training. Male and female C57BL/6J mice were provided with voluntary running wheels for 6 weeks and compared to sex-matched sedentary controls with locked running wheels. We found that exercise altered gene expression of epigenetic machinery responsible for regulating acetylation and methylation enrichment in both a muscle- and sex-specific manner, including major H3K27 acetyltransferases and core components of the polycomb repressive complex-2. Our findings add to a growing body of evidence implicating H3K27 post-translational modifications, and thereby chromatin dynamics, as a mechanistic component of exercise-induced muscle remodeling.