The language of covalent histone modifications

Current research status on the structure, physicochemical properties, bioactivities, and mechanism of soybean-derived bioactive peptide lunasin

Since the 21st century, chronic diseases have become a worldwide health problem due to their high morbidity and mortality. Soybean bioactive substances, especially soybean peptides, are considered to have health benefits beyond nutritional effects. As the most studied peptide in soybean, lunasin has been proven to exert beneficial effects on various chronic disorders. This review summarizes the content of lunasin in soybeans, soy derived foods, and other crops, as well as its structural characteristics and bioavailability. Moreover, we focused on the relationship between the physicochemical characteristics and structural composition of lunasin, and its significance for the bioactivities of lunasin. Ultimately, the therapeutic effects of lunasin on cancer, oxidative stress, inflammation, immune response, and hyperlipidemia were described, as well as the molecular mechanisms involved in these impacts. In conclusion, lunasin is a promising multifunctional bioactive peptide, yet further research is required to optimize and expedite its application in the food industry.

Histone modifications in development

In eukaryotic cells, the genetic material is organized into chromatin, which consists mainly of DNA, histones and chromatin-associated proteins. An important regulator of chromatin structure and function are histone post-translational modifications, which can shape gene expression patterns and control the epigenetic landscape. Here, we summarize the role of some key histone modifications in animal development, with a focus on the two best-studied types of histone modifications: lysine methylation and acylations, specifically, acetylation.

Epigenetics and diabetic wound healing: Wilms tumor 1-associated protein as a therapeutic target

In this editorial, we highlight the study by Xiao et al. Despite progress in the management of diabetic foot ulcers (DFUs), impaired wound healing remains a significant clinical challenge. Recent studies have highlighted the critical role of epigenetic modifications in diabetic wound healing, with particular emphasis on DNA and RNA methylation pathways. This editorial discusses the findings of Xiao et al, who identified the Wilms tumor 1-associated protein (WTAP) - DNA methyltransferase 1 (DNMT1) axis as a pivotal regulator of endothelial dysfunction in DFUs. WTAP, a regulatory subunit of N6-methyladenosine (m6A) methyltransferase, is upregulated under high-glucose conditions and drives the excessive expression of DNMT1 via m6A modification. This contributes to impaired angiogenesis, reduced cell viability, and delayed wound closure. WTAP knockdown restored endothelial function and significantly improved wound healing in a diabetic mouse model. Furthermore, DNMT1 overexpression abrogated the benefits of WTAP suppression, confirming its downstream effector role. Thus, targeting the WTAP-DNMT1 axis provides a new avenue for DFU management. Moreover, epigenetic interventions that modulate both the m6A and RNA methylation pathways could restore endothelial function and enhance tissue repair in patients with diabetes.

Advances in molecular pathology and therapy of non-small cell lung cancer

Over the past two decades, non-small cell lung cancer (NSCLC) has witnessed encouraging advancements in basic and clinical research. However, substantial unmet needs remain for patients worldwide, as drug resistance persists as an inevitable reality. Meanwhile, the journey towards amplifying the breadth and depth of the therapeutic effect requires comprehending and integrating diverse and profound progress. In this review, therefore, we aim to comprehensively present such progress that spans the various aspects of molecular pathology, encompassing elucidations of metastatic mechanisms, identification of therapeutic targets, and dissection of spatial omics. Additionally, we also highlight the numerous small molecule and antibody drugs, encompassing their application alone or in combination, across later-line, frontline, neoadjuvant or adjuvant settings. Then, we elaborate on drug resistance mechanisms, mainly involving targeted therapies and immunotherapies, revealed by our proposed theoretical models to clarify interactions between cancer cells and a variety of non-malignant cells, as well as almost all the biological regulatory pathways. Finally, we outline mechanistic perspectives to pursue innovative treatments of NSCLC, through leveraging artificial intelligence to incorporate the latest insights into the design of finely-tuned, biomarker-driven combination strategies. This review not only provides an overview of the various strategies of how to reshape available armamentarium, but also illustrates an example of clinical translation of how to develop novel targeted drugs, to revolutionize therapeutic landscape for NSCLC.

High-Throughput Epigenetic Profiling Immunoassays for Accelerated Disease Research and Clinical Development

Epigenetics, which examines the regulation of genes without modification of the DNA sequence, plays a crucial role in various biological processes and disease mechanisms. Among the different forms of epigenetic modifications, histone post-translational modifications (PTMs) are important for modulating chromatin structure and gene expression. Aberrant levels of histone PTMs are implicated in a wide range of diseases, including cancer, making them promising targets for biomarker discovery and therapeutic intervention. In this context, blood, tissues, or cells serve as valuable resources for epigenetic research and analysis. Traditional methods such as mass spectrometry and western blotting are widely used to study histone PTMs, providing qualitative and (semi)quantitative information. However, these techniques often face limitations that could include throughput and scalability, particularly when applied to clinical samples. To overcome these challenges, we developed and validated 13 Nu.Q® immunoassays to detect and quantify specific histone PTM-nucleosomes from K2EDTA plasma samples. Then, we tested these assays on other types of samples, including chromatin extracts from frozen tissues, as well as cell lines and white blood cells Our findings demonstrate that the Nu.Q® assays offer high specificity, sensitivity, precision and linearity, making them effective tools for epigenetic profiling. A comparative analysis of HeLa cells using mass spectrometry, Western blot, and Nu.Q® immunoassays revealed a consistent histone PTMs signature, further validating the effectiveness of these assays. Additionally, we successfully applied Nu.Q® assays across various biological samples, including human tissues from different organs and specific white blood cell subtypes, highlighting their versatility and applicability in diverse biological contexts.

Unlocking the Mysteries of Breast Cancer: The Role of Epigenetics in Diagnosis, Treatment, and Beyond

OBJECTIVES

Breast cancer is an intricate and varied disease exhibiting a range of molecular subgroups and clinical consequences. Epigenetic alterations have become essential players in the pathophysiology of breast cancer because they control gene expression without changing the DNA sequence. This review provides a comprehensive overview of epigenetics' diagnostic, prognostic, and therapeutic implications in breast cancer. This review aims to present a comprehensive study of the function of epigenetics in breast cancer, emphasizing current developments and potential avenues for future research.

METHODS

A narrative review methodology involved an extensive literature search and selection to gather relevant studies and trial data. PubMed, Embase, and Web of Science databases were searched using relevant keywords such as "epigenetics," "breast cancer," "DNA methylation," "histone modification," "noncoding RNA," and "linical trials." Relevant studies and clinical trial data were selected and synthesized to summarize the topic comprehensively.

RESULTS

The review synthesizes critical findings from current research, underscoring the pivotal role of epigenetic mechanisms in breast cancer initiation, progression, and therapeutic response. It highlights the potential of epigenetic biomarkers for diagnosis and prognosis and the promise of epigenetic-targeted therapies in breast cancer management. Furthermore, the review outlines future directions for research, emphasizing the importance of elucidating the dynamic interplay between epigenetic alterations and tumor microenvironments in shaping breast cancer phenotypes.

CONCLUSIONS

Epigenetic modifications influence breast cancer progression, diagnosis, and therapy. Emerging biomarkers and targeted treatments hold promise, but further research is essential to refine their clinical application and improve personalized cancer management strategies.

Histone variants: expanding the epigenetic potential of neurons one amino acid at a time

Replication-independent histone variants play an essential role in postmitotic neurons. Here, we review how the subtle sequence differences of histone variants compared to their canonical counterparts underly neuronal function. We focus on variants H3.3, H2A.Z, H2A.X, macroH2A, and H2BE; all of which contain divergent sequences that coordinate a diverse set of outcomes. In particular, we highlight their role in neuronal development, plasticity, and memory, with an emphasis on how single amino acid changes can mediate these complex functions. Lastly, we comment on an emerging field of study evaluating the link between histone variants and neurological disorders. Future studies of histone variants will be important to furthering our understanding of neuronal function.

The Epigenetic Landscape: From Molecular Mechanisms to Biological Aging

Epigenetics, the study of heritable changes in gene expression that do not involve alterations to the deoxyribonucleic acid (DNA) sequence, plays a pivotal role in cellular function, development, and aging. This review explores key epigenetic mechanisms, including DNA methylation (DNAm), histone modifications, chromatin remodeling, RNA-based regulation, and long-distance chromosomal interactions. These modifications contribute to cellular differentiation and function, mediating the dynamic interplay between the genome and environmental factors. Epigenetic clocks, biomarkers based on DNAm patterns, have emerged as powerful tools to measure biological age and predict health span. This article highlights the evolution of epigenetic clocks, from first-generation models such as Horvath's multi-tissue clock to advanced second- and third-generation clocks such as DNAGrimAge and DunedinPACE, which incorporate biological parameters and clinical biomarkers for precise age estimation. Moreover, the role of epigenetics in aging and age-related diseases is discussed, emphasizing its impact on genomic stability, transcriptional regulation, and cellular senescence. Epigenetic dysregulation is implicated in cancer, genetic disorders, and neurodegenerative diseases, making it a promising target for therapeutic interventions. The reversibility of epigenetic modifications offers hope for mitigating age acceleration and enhancing health span through lifestyle changes and pharmacological approaches.

Targeting epigenetic regulators to overcome drug resistance in the emerging human fungal pathogen Candida auris

The rise of drug-resistant fungal species, such as Candida auris, poses a serious threat to global health, with mortality rates exceeding 40% and resistance rates surpassing 90%. The limited arsenal of effective antifungal agents underscores the urgent need for novel strategies. Here, we systematically evaluate the role of histone H3 post-translational modifications in C. auris drug resistance, focusing on acetylation mediated by Gcn5 and Rtt109, and methylation mediated by Set1, Set2, and Dot1. Mutants deficient in these enzymes exhibit varying degrees of antifungal drug sensitivity. Notably, we discover that GCN5 depletion and the subsequent loss of histone H3 acetylation downregulates key genes involved in ergosterol biosynthesis and drug efflux, resulting in increased susceptibility to azoles and polyenes. Additionally, Gcn5 regulates cell wall integrity and echinocandin resistance through the calcineurin signaling pathway and transcription factor Cas5. In infection models using Galleria mellonella and immunocompromised mice, GCN5 deletion significantly reduces the virulence of C. auris. Furthermore, the Gcn5 inhibitor CPTH2 synergizes with caspofungin in vitro and in vivo without notable toxicity. These findings highlight the critical role of Gcn5 in the resistance and pathogenicity of C. auris, positioning it as a promising therapeutic target for combating invasive fungal infections.

Lead Optimization and Target Identification of Carboline Antifungal Agents

Cryptococcal meningitis is a severe invasive fungal infection that poses a significant global health burden due to the lack of effective treatment options. To address this, there is an urgent need to develop novel antifungal drugs and identify new antifungal targets to provide more effective therapeutic strategies. On the basis of our previously identified anticryptococcal lead compound JYJ-19, herein, four series of new derivatives were designed by scaffold hopping. Notably, hexahydroazepino[3,4-b]indole derivative D2 exhibited favorable oral bioavailability (F = 47.13%) and potent antifungal activity both in vitro and in vivo, making it a promising oral antifungal candidate for the treatment of cryptococcal meningitis. Furthermore, we employed affinity-based protein profiling to identify the potential targets of the carboline derivatives. Proteomic analysis of a photoaffinity probe revealed that the SET domain-containing protein was the potential target. Taken together, this study provides a promising lead compound and potential drug target for future antifungal drug development.

Negative Cooperativity in the UHRF1 TTD-PHD Dual Domain Masks the Contributions of Cation-π Interactions between Trimethyllysine and the TTD Aromatic Cage

UHRF1 is a promising epigenetic target in oncology, but inhibitor development has proven challenging due to the interplay between its tandem Tudor domain (TTD) and plant homeodomain (PHD). The TTD binds trimethyllysine (Kme3) at position 9 while the PHD binds Arg at position 2 on histone 3. Herein, we report how the PHD influences TTD recognition of the histone 3 tail containing Kme3 (H3K9me3) versus its neutral isostere, tert-butyl norleucine (tBuNle). Our findings show that the dual domain binds both peptides equally, supporting tBuNle's potential for inhibitor development. However, unexpectedly, the binding mechanism of H3K9me3 differs between the single and dual domains. In the TTD alone, Kme3 is bound in the aromatic cage via electrostatically tunable cation-π interactions, but in the dual domain, Kme3 binding is independent of electrostatics in the aromatic cage-an unprecedented observation. Computational studies suggest cation-π interactions should contribute in both cases. The contrasting experimental and computational results point to an unusual example of negative chelate cooperativity: interactions between the histone and PHD mask the mechanism of TTD recognition of K9me3. This work underscores the complexity of histone post-translational modification (PTM) readout in multi-domain proteins and demonstrates the first example of a masked cation-π interaction.

Heat stress induces specific methylation, transcriptomic and metabolic pattern in dairy cows and their female progeny

A heat stress (HS) cattle research design was implemented to study HS effects on the three different "omics features" methylations, gene expressions and metabolic pattern from a direct perspective in pregnant cows and from an indirect time-lagged intergenerational perspective in offspring (the respective F1 and as F1 offspring before calving). In this regard, a total number of 88 German Holstein dairy cows and their 93 female calves were blood sampled for DNA and RNA extraction and for metabolic phenotyping, and allocated to HS and respective control groups (the cows (dams) as well as their calves) according to a temperature-humidity threshold of 60. Separate principal component analyses for all "omics-tiers" revealed clear separations of HS from respective control groups, as well as dam-offspring separations according to gene expressions and metabolic pattern. The GO enrichment analyses based on the differentially expressed genes contributed to the detection of 10 significantly overrepresented biological processes in heat stressed dams, and of 95 overrepresented biological processes due to indirect maternal heat stress in calves. With regard to direct HS in dams and the first PCs of the different "omics" features, the correlation coefficient was 0.45 between methylation and gene expression data, 0.62 between expression and metabolites, and 0.38 between methylation and metabolite data. The separation of HS from the control group was very obvious when using the average and weighted average of the first and second components from the three multi-omics datasets. The present study provides extended insights into the complex genetic and physiological mechanisms of HS response in dam and calf groups from different generations, contributing to a deeper understanding of the interplay of prompt and time lagged HS effects between different omics-tiers.

Nucleosomes represent a crucial target for the intra-S phase checkpoint in response to replication stress

The intra-S phase checkpoint is essential for stability of stalled DNA replication forks. However, the mechanisms underlying checkpoint regulation remain poorly understood. This study identifies a critical checkpoint target-the ubiquitin E3 ligase Brl2, revealing a new dimension of checkpoint regulation. Upon replication fork stalling, Brl2 undergoes phosphorylation at five serine residues by Cds1Chk2 kinase, resulting in the loss of its ligase activity and a marked reduction in H2BK119ub1 levels. In the brl2-5D (the five serine residues are replaced with aspartic acid) and htb-K119R mutants, chromatin becomes highly compacted. Furthermore, the rates of stalled replication fork collapse, and dsDNA breaks are significantly reduced in brl2-5D cds1Chk2∆ cells compared to cds1Chk2∆ cells. Thus, this study demonstrates that nucleosomes are targeted by the intra-S phase checkpoint and highlights the checkpoint's critical role in configuring compact chromatin structures at replication fork stalling sites. These findings may explain why ATR and Chk1 are essential for cell proliferation and embryonic development, while ATM is not.

KMT2D: A key emerging epigenetic regulator in head and neck diseases and tumors

Histone modifications are critical determinants of chromatin accessibility and gene expression, both of which are intrinsically linked to human development and disease. Lysine methyltransferase 2D (KMT2D), a prominent member of the H3K4 methyltransferase family, is ubiquitously expressed across human tissues. Recent studies have found that it can regulate gene expression and signal pathway opening and closing in more than one way, playing an important role in cell proliferation and cell cycle homeostasis. Although previous studies have identified KMT2D as a potentially pivotal factor in the development and pathology of head and neck tissues, the regulatory networks associated with KMT2D in various complex head and neck diseases remain incompletely elucidated. This review seeks to consolidate recent findings on KMT2D's involvement in head and neck diseases, thereby laying the groundwork for future research into its mechanistic role in disease progression. A deeper understanding of KMT2D's functions and regulatory mechanisms is essential for advancing our comprehension of histone modifications and for the development of diagnostic tools and targeted therapeutic strategies for head and neck diseases.

A Brief Overview of the Epigenetic Regulatory Mechanisms in Plants

Plants continuously adapt to their environments by responding to various intrinsic and extrinsic signals. They face numerous biotic and abiotic stresses such as extreme temperatures, drought, or pathogens, requiring complex regulatory mechanisms to control gene activity and adapt their proteome for survival. Epigenetic regulation plays a crucial role in these adaptations, potentially leading to both heritable and non-heritable changes across generations. This process enables plants to adjust their gene expression profiles and acclimate effectively. It is also vital for plant development and productivity, affecting growth, yield, and seed quality, and enabling plants to "remember" environmental stimuli and adapt accordingly. Key epigenetic mechanisms that play significant roles include DNA methylation, histone modification, and ubiquitin ligase complex activity. These processes, which have been extensively studied in the last two decades, have led to a better understanding of the underlying mechanisms and expanded the potential for improving agriculturally and economically important plant traits. DNA methylation is a fundamental process that regulates gene expression by altering chromatin structure. The addition of methyl groups to cytosines by DNA methylases leads to gene suppression, whereas DNA demethylases reverse this effect. Histone modifications, on the other hand, collectively referred to as the "histone code", influence chromatin structure and gene activity by promoting either gene transcription or gene silencing. These modifications are either recognized, added, or removed by a variety of enzymes that act practically as an environmental memory, having a significant impact on plant development and the responses of plants to environmental stimuli. Finally, ubiquitin ligase complexes, which tag specific histones or regulatory proteins with ubiquitin, are also crucial in plant epigenetic regulation. These complexes are involved in protein degradation and play important roles in regulating various cellular activities. The intricate interplay between DNA methylation, histone modifications, and ubiquitin ligases adds complexity to our understanding of epigenetic regulation. These mechanisms collectively control gene expression, generating a complex and branching network of interdependent regulatory pathways. A deeper understanding of this complex network that helps plants adapt to environmental changes and stressful conditions will provide valuable insights into the regulatory mechanisms involved. This knowledge could pave the way for new biotechnological approaches and plant breeding strategies aimed at enhancing crop resilience, productivity, and sustainable agriculture.

Unveiling the Conformational Dynamics of the Histone Tails Using Markov State Modeling

Biomolecules predominantly exert their function by altering conformational dynamics. The nucleosome core particle (NCP) is the fundamental unit of chromatin. DNA with ∼146 base pairs wraps around the histone octamer to form a nucleosome. The histone octamer is composed of two copies of each histone protein (H3, H4, H2A, and H2B) with a globular core and disordered N-terminal tails. Epigenetic modifications of the histone N-terminal tails play a critical role in regulating the chromatin structure and biological processes such as transcription and DNA repair. Here, we report all-atom molecular dynamics (MD) simulations of the nucleosome at microsecond time scales to construct Markov state models (MSMs) to elucidate distinct conformations of the histone tails. We employ time-lagged independent component analysis (tICA) to capture their essential slow dynamics, with k-means clustering used to discretize the conformational space. MSMs unveil distinct states and transition probabilities to characterize the dynamics and kinetics of the tails. Next, we focus on the H2B tail, which is one of the least studied tails. We show that acetylation increases secondary structure formation with increased transition rates. These findings will aid in understanding the functional implications of tail conformations for nucleosome stability and gene regulation.

Ubiquitin proteasome system (UPS): a crucial determinant of the epigenetic landscape in cancer

The ubiquitin proteasome system (UPS), comprising of ubiquitinases, deubiquitinases and 26S proteasome plays a significant role in directly or indirectly regulating epigenetic players. DNA-templated processes like replication, repair and transcription require chromatin decondensation to allow access to specific DNA sequence. A thorough survey of literary articles in PubMed database revealed that the UPS functions as a key regulator, determining the precise state of open and closed chromatin by influencing histones and histone modifiers through proteolytic or non-proteolytic means. However, a comprehensive understanding of how specific UPS components affect particular epigenetic pathways in response to environmental cues remains underexplored. This axis holds substantial potential for deciphering mechanisms of tumorigenesis. Although our current knowledge is limited, it can still guide the development of novel therapeutic strategies that can potentially bridge the gap between cancer chemotherapeutics in bench and bedside.

Chromatin and epigenetics in aging biology

This book chapter will focus on modifications to chromatin itself, how chromatin modifications are regulated, and how these modifications are deciphered by the cell to impact aging. In this chapter, we will review how chromatin modifications change with age, examine how chromatin-modifying enzymes have been shown to regulate aging and healthspan, discuss how some of these epigenetic changes are triggered and how they can regulate the lifespan of the individual and its naïve descendants, and speculate on future directions for the field.

Structure of an Unfavorable de Novo DNA Methylation Complex of Plant Methyltransferase ZMET2

DNA methylation is an important epigenetic mechanism that controls the assembly of heterochromatin and gene expression. In plants, DNA methylation occurs in both CG and non-CG contexts, with non-CG methylation showing notable substrate sequence dependence. The plant DNA methyltransferase CMT3 mediates maintenance of CHG (H = A, C, or T) DNA methylation, with a strong substrate preference for the hemimethylated CWG (W = A, T) motif. Yet, the underlying mechanism remains elusive. Here we present a crystal structure of ZMET2, the CMT3 ortholog from Zea mays (maize), in complex with a DNA substrate containing an unmethylated CTG motif and a histone peptide carrying a mimic of the histone H3K9me2 modification. Structural comparison of the ZMET2-CTG complex with the previously reported structure of ZMET2 bound to hemimethylated CAG DNA reveals similar but distinct protein-DNA interactions centered on the CWG motif, providing insight into the methylation state- and substrate sequence-specific ZMET2/CMT3-substrate interaction. Furthermore, our combined structural and biochemical analysis reveals a role for the +3-flanking base of the target cytosine in fine-tuning ZMET2-mediated DNA methylation and its functional interplay with the +1- and +2-flanking sites. Together, these results provide deep mechanistic insights into the substrate specificity of CMT3 DNA methyltransferases in plants.

Epigenetic mechanisms involved in hepatocellular carcinoma development and progression

Hepatocellular carcinoma (HCC) typically develops in the context of chronic liver disease, where prolonged hepatocyte exposure to inflammation drives the synergistic accumulation of genetic and epigenetic alterations. Epigenetic regulation encompasses multiple mechanisms that govern the transcription machinery accessibility to DNA. This process is regulated by the addition and removal of covalent marks on chromatin, which can either affect DNA-histone interactions or serve as scaffolds for other proteins, among other mechanisms. Recent research has revealed that epigenetic alterations can disrupt chromatin homeostasis, redirecting transcriptional regulation to favour cancer-promoting states. Consequently, these alterations play a pivotal role in the acquisition of cancer hallmarks and provide insights into several biological processes involved in hepatocarcinogenesis. This review highlights the key epigenetic mechanisms underlying the development, progression and dissemination of HCC, with a particular focus on DNA methylation and histone post-translational modifications. This knowledge is relevant for guiding the development of innovative therapeutic approaches based on epigenetic modulators.

Histone modifications and metabolic reprogramming in tumor-associated macrophages: a potential target of tumor immunotherapy

Histone modifications, including methylation, acetylation, lactylation, phosphorylation, ubiquitination, SUMOylation, ADP-ribosylation, and crotonylation, critically regulate tumor-associated macrophages (TAMs) polarization by modulating gene expression and functional states. Reprogramming TAMs from M2 to M1 phenotypes through epigenetic targeting has emerged as a promising strategy to enhance anti-tumor immunity and improve the efficacy of cancer immunotherapy. This review explores the role of histone modifications in TAM biology, their interplay with metabolic reprogramming, and the opportunities and challenges in developing epigenetic-based therapies to advance cancer immunotherapy.

Emerging Techniques in Spatial Multiomics: Fundamental Principles and Applications to Dermatology

Molecular pathology, such as high-throughput genomic and proteomic profiling, identifies precise disease targets from biopsies but require tissue dissociation, losing valuable histologic and spatial context. Emerging spatial multi-omic technologies now enable multiplexed visualization of genomic, proteomic, and epigenomic targets within a single tissue slice, eliminating the need for labeling multiple adjacent slices. Although early work focused on RNA (spatial transcriptomics), spatial technologies can now concurrently capture DNA, genome accessibility, histone modifications, and proteins with spatially-resolved single-cell resolution. This review outlines the principles, advantages, limitations, and potential for spatial technologies to advance dermatologic research. By jointly profiling multiple molecular channels, spatial multiomics enables novel studies of copy number variations, clonal heterogeneity, and enhancer dysregulation, replete with spatial context, illuminating the skin's complex heterogeneity.

G9a an Epigenetic Therapeutic Strategy for Neurodegenerative Conditions: From Target Discovery to Clinical Trials

This review provides a comprehensive overview of the role of G9a/EHMT2, focusing on its structure and exploring the impact of its pharmacological and/or gene inhibition in various neurological diseases. In addition, we delve into the advancements in the design and synthesis of G9a/EHMT2 inhibitors, which hold promise not only as a treatment for neurodegeneration diseases but also for other conditions, such as cancer and malaria. Besides, we presented the discovery of dual therapeutic approaches based on G9a inhibition and different epigenetic enzymes like histone deacetylases, DNA methyltransferases, and other lysine methyltransferases. Hence, findings offer valuable insights into developing novel and promising therapeutic strategies targeting G9a/EHMT2 for managing these neurological conditions.

IDH1 regulates human erythropoiesis by eliciting chromatin state reprogramming

Isocitrate dehydrogenase 1 (IDH1) is the key enzyme that can modulate cellular metabolism, epigenetic modification, and redox homeostasis. Gain-of-function mutations and decreased expression of IDH1 have been demonstrated to be associated with pathogenesis of various myeloid malignancies characterized by ineffective erythropoiesis, such as acute myeloid leukemia (AML) and myelodysplastic syndrome (MDS). However, the function and mechanism of IDH1 in human erythropoiesis still remains unclear. Here, utilizing the human erythropoiesis system, we present an evidence of IDH1-mediated chromatin state reprogramming besides its well-characterized metabolism effects. We found that knockdown IDH1 induced chromatin reorganization and subsequently led to abnormalities biological events in erythroid precursors, which could not be rescued by addition of reactive oxygen species (ROS) scavengers or supplementation of α-ketoglutarate (α-KG).We further revealed that knockdown IDH1 induces genome-wide changes in distribution and intensity of multiple histone marks, among which H3K79me3 was identified as a critical factor in chromatin state reprogramming. Integrated analysis of ChIP-seq, ATAC-seq, and RNA-seq recognized that SIRT1 was the key gene affected by IDH1 deficiency. Thus, our current work provided novel insights for further clarifying fundamental biological function of IDH1 which has substantial implications for an in-depth understanding of pathogenesis of diseases with IDH1 dysfunction and accordingly development of therapeutic strategies.

Designer Catalyst-Enabled Regiodivergent Histone Acetylation

The "histone code," defined by the combinatorial patterns of post-translational modifications (PTMs) on histones, plays a pivotal role in chromatin structure and gene expression. Tools for the regioselective introduction of histone PTMs in living cells are critical for dissecting the functions of these epigenetic marks. Here, we report the design and development of three regioselective catalysts that acetylate distinct lysine residues (K43, K108, and K120) on histone H2B. Using a combination of molecular dynamics simulations of catalyst-nucleosome complexes and systematic experimental optimization of catalyst structures, we identified key design principles for achieving regioselectivity. Specifically, excluding highly reactive off-target lysine residues from the catalyst effective region (CER) while maintaining proximity to a target lysine residue proved crucial. Biochemical and cellular analyses of the catalytic histone acetylation revealed that each lysine acetylation elicited unique effects on the binding affinity and activity of nucleosome-interacting molecules, as well as on transcriptional programs and cellular phenotypes. These findings establish a framework for designing regioselective histone acetylation catalysts and advance our understanding of the regulatory mechanisms underlying histone PTMs.

Quantitative Top-Down Proteomics Reveals Significant Differences in Histone Proteoforms Between Metastatic and Nonmetastatic Colorectal Cancer Cells

Colorectal cancer (CRC) development is closely associated with the accumulation of both genetic and epigenetic alterations. Many efforts have been made to investigate the role of epigenetic modifications in CRC metastasis. In this work, we present the quantitative top-down proteomics study focusing on histone proteoforms between metastatic (SW620) and nonmetastatic (SW480) CRC cells to reveal potentially critical histone proteoforms in CRC metastasis. We isolated histone proteins from CRC cells, fractionated them by sodium dodecyl-sulfate (SDS)-polyacrylamide gel electrophoresis (PAGE), and analyzed them by capillary zone electrophoresis (CZE)-tandem mass spectrometry (MS/MS). A total of 230 histone proteoforms were quantified in SW480 and SW620 cell lines, among which 34 proteoforms were significantly altered in abundance in the metastatic cells, indicating a significant transformation of histone proteoforms during metastasis. We observed a significant increase in abundance of all nine differentially expressed histone H4 proteoforms in metastatic SW620 cells compared to SW480 cells, while differentially expressed proteoforms of other histone proteins display diversified expression patterns. Additionally, two histone H2A proteoforms with a combination of N-terminal acetylation and phosphorylation were upregulated in the metastatic CRC cells. These differentially expressed histone proteoforms could be novel proteoform biomarkers of CRC metastasis.

Histone Deacetylase Inhibitors Promote the Anticancer Activity of Cisplatin: Mechanisms and Potential

Cisplatin is a widely used DNA-targeting anticancer drug. Histone deacetylase inhibitors (HDACi) cause histone hyperacetylation, changing chromatin structure and accessibility of genomic DNA by the genotoxic drug. As a consequence, HDACi could promote cisplatin cytotoxicity. Hence, the underlying mechanisms by which HDACi alter the action pathways of cisplatin to promote its anticancer activity have attracted increasing attention during the past decades. It has been commonly accepted that HDACi elevate the acetylation level of histones to release genomic DNA to cisplatin attack, increasing the level of cisplatin-induced DNA lesions to promote cisplatin cytotoxicity. However, how the HDACi-enhanced cisplatin lesion on DNA impacts the downstream biological processes, and whether the promotion of HDACi to cisplatin activity is attributed to their inherent anticancer activity or to their induced elevation of histone acetylation, have been in debate. Several studies showed that HDACi-enhanced DNA lesion could promote cisplatin-induced apoptosis, cell cycle arrest, and reactive oxygen species (ROS) generation, subsequently promoting cisplatin efficiency. In contrast, HDACi-induced elimination of ROS and inhibition of ferroptosis were thought to be the main ways by which HDACi protect kidneys from acute injury caused by cisplatin. Based on our recent research, we herein review and discuss the advances in research on the mechanisms of HDACi-induced enhancement in cisplatin cytotoxicity. Given that histone acetyltransferase (HAT) inhibitors also show an effect enhancing cisplatin cytotoxicity, we will discuss the diverse roles of histone acetylation in cancer therapy in addition to the synergistic anticancer effect and potential of HDACi with genotoxic drugs and radiotherapy.

Epigenetic reader chromodomain as a potential therapeutic target

Epigenetic mechanisms involve cooperative actions of enzymes that produce or remove post-translational modifications in histones and 'readers', the protein domains that bind these modifications. Methylation of lysine residues represents one of the most common modifications and is recognized by a family of chromodomains. Chromodomain containing proteins are implicated in transcriptional regulation and chromatin remodeling, and aberrant functions of these proteins are linked to human diseases, such as cancer, neurodegenerative disorders and developmental abnormalities. In this work, we review biological and pathological activities of chromodomains, highlighting their potential as prognostic biomarkers and their attractiveness as therapeutic targets. In the past few years, significant progress has been made in the development of chromodomain inhibitors, however sequence similarity within this family of readers presents challenges in designing selective probes. We describe recent advances and new strategies that are employed to overcome these challenges, including structure-based drug design, high-throughput screening, the use of peptide and DNA encoded libraries, and summarize research underscoring the benefit of targeting chromodomains to combat diseases.

Systematic genetic perturbation reveals principles underpinning robustness of the epigenetic regulatory network

The molecular control of epigenetic information relies on hundreds of proteins of diverse function, which cooperate in defining chromatin structure and DNA methylation landscapes. While many individual pathways have been characterized, how different classes of epigenetic regulators interact to build a resilient epigenetic regulatory network (ERN) remains poorly understood. Here, we show that most individual regulators are dispensable for somatic cell fitness, and that robustness emerges from multiple layers of functional cooperation and degeneracy among network components. By disrupting 200 epigenetic regulator genes, individually or in combination, we generated network-wide maps of functional interactions for representative regulators. We found that paralogues represent only a first layer of functional compensation within the ERN, with intra- or inter-class interactions buffering the effects of perturbation in a gene-specific manner: while CREBBP cooperates with multiple acetyltransferases to form a subnetwork that ensures robust chromatin acetylation, ARID1A interacts with regulators from across all functional classes. When combined with oncogene activation, the accumulated epigenetic disorder exposes a synthetic fragility and broadly sensitizes ARID1A-deficient cells to further perturbation. Our findings reveal homeostatic mechanisms through which the ERN sustains somatic cell fitness and uncover how the network remodels as the epigenome is progressively deregulated in disease.

A two-step regulatory mechanism dynamically controls histone H3 acetylation by SAGA complex at growth-related promoters

Acetylation of histone H3 at residue K9 (H3K9ac) is a dynamically regulated mark associated with transcriptionally active promoters in eukaryotes. However, our understanding of the relationship between H3K9ac and gene expression remains mostly correlative. In this study, we identify a large suite of growth-related (GR) genes in yeast that undergo a particularly strong down-regulation of both transcription and promoter-associated H3K9ac upon stress, and delineate the roles of transcriptional activators (TAs), repressors, SAGA (Spt-Ada-Gcn5 acetyltransferase) histone acetyltransferase, and RNA-polymerase II in this response. We demonstrate that H3K9 acetylation states are orchestrated by a two-step mechanism driven by the dynamic binding of transcriptional repressors (TRs) and activators, that is independent of transcription. In response to stress, promoter release of TAs at GR genes is a prerequisite for rapid reduction of H3K9ac, whereas binding of TRs is required to establish a hypo-acetylated, strongly repressed state.

Advances in the chemical synthesis of human proteoforms

Access to structurally-defined human proteoforms is essential to the biochemical studies on human health and medicine. Chemical protein synthesis provides a bottom-up and atomic-resolution approach for the preparation of homogeneous proteoforms bearing any number of post-translational modifications of any structure, at any position, and in any combination. In this review, we summarize the development of chemical protein synthesis, focusing on the recent advances in synthetic methods, product characterizations, and biomedical applications. By analyzing the chemical protein synthesis studies on human proteoforms reported to date, this review demonstrates the significant methodological improvements that have taken place in the field of human proteoform synthesis, especially in the last decade. Our analysis shows that although further method development is needed, all the human proteoforms could be within reach in a cost-effective manner through a divide-and-conquer chemical protein synthesis strategy. The synthetic proteoforms have been increasingly used to support biomedical research, including spatial-temporal studies and interaction network analysis, activity quantification and mechanism elucidation, and the development and evaluation of diagnostics and therapeutics.

Exploring epigenetic modifications as potential biomarkers and therapeutic targets in amyotrophic lateral sclerosis

Amyotrophic lateral sclerosis (ALS) is a neurodegenerative disorder and the most common motor neuron disease. Whole-genome sequencing has identified many novel ALS-associated genes, but genetics alone cannot fully explain the onset of ALS and an effective treatment is still lacking. Moreover, we need more biomarkers for accurate diagnosis and assessment of disease prognosis. Epigenetics, which includes DNA methylation and hydroxymethylation, histone modifications, chromatin remodeling, and non-coding RNAs, influences gene transcription and expression by affecting chromatin accessibility and transcription factor binding without altering genetic information. These processes play a role in the onset and progression of ALS. Epigenetic targets can serve as potential biomarkers and more importantly, the reversibility of epigenetic changes supports their potential role as versatile therapeutic targets in ALS. This review summarized the alterations in different epigenetic modulations in ALS. Additionally, given the close association between aberrant metabolic profiles characterized by hypoxia and high glycolytic metabolism in ALS and epigenetic changes, we also integrate epigenetics with metabolomics. Finally, we discuss the application of therapies based on epigenetic mechanisms in ALS. Our data integration helps to identify potential diagnostic and prognostic biomarkers and support the development of new effective therapies.

Therapeutic potentials of natural products for post-traumatic stress disorder: A focus on epigenetics

Post-traumatic stress disorder (PTSD) is a relatively common but complex mental illness with a range of diverse risk factors. Typical symptoms include the re-experience or avoidance of traumatic events, cognitive impairment, and hypervigilance. While the exact pathogenesis of PTSD is unclear, many studies indicate that epigenetic regulation plays a key role in its development. Specifically, numerous studies have indicated that the levels of histone acetylation and methylation, DNA methylation, and noncoding RNA are altered in PTSD patients. Further to this, natural products have been found to achieve epigenetic regulation of PTSD by regulating the expression of epigenetic enzymes, long noncoding RNA (lncRNA), and miRNA, thereby playing a role in improving PTSD symptoms. To date, however, no epigenetic regulation related drugs have been used in the treatment of PTSD. Furthermore, while natural products that can epigenetically regulate PTSD have received increasing levels of attention, there have not yet been any systematic reports on the topic. Here, we summarized the roles and mechanisms of natural products in the epigenetic regulation of PTSD, providing a novel and unique perspective that will help to guide the development and application of new PTSD treatments.

'Nomadic' Hematopoietic Stem Cells Navigate the Embryonic Landscape

Hematopoietic stem cells are a unique population of tissue-resident multipotent cells with an extensive ability to self-renew and regenerate the entire lineage of differentiated blood cells. Stem cells reside in a highly specialized microenvironment with surrounding supporting cells, forming a complex and dynamic network to preserve and maintain their function. The survival, activation, and quiescence of stem cells are largely influenced by niche-derived signals, with aging niche contributing to a decline in stem cell function. Although the role of niche in regulating hematopoiesis has long been established by transplantation studies, limited methods in observing the process in vivo have eluded a detailed understanding of the various niche components. Danio rerio (zebrafish) has emerged as a solution in the past few decades, enabling discovery of cellular interactions, in addition to chemical and genetic factors regulating HSCs. This review reiterates zebrafish as a suitable model for studies on vertebrate embryonic and adult hematopoiesis, delving into this temporally and spatially dissected multi-step process. The critical role played by epigenetic regulators are discussed, along with contributions of the various physiological processes in sustaining the stem cell population. Stem cell niche transcends mere knowledge acquisition, assuring scope in cell therapy, organoid cultures, aging research, and clinical applications including bone marrow transplantation and cancer. A better understanding of the various niche components could also leverage therapeutic efforts to drive differentiation of HSCs from pluripotent progenitors, sustain stemness in laboratory cultures, and improve stem cell transplantation outcomes.

Temporal and spatial distribution of histone acetylation in mouse molar development

Histone acetylation is one of the most widely studied histone modification, regulating a variety of biological activities like organ development and tumorigenesis. However, the role of histone acetylation in tooth development is poorly understood. Using the mouse molar as a model, we mapped the distribution patterns of histone H3 and H4, as well as their corresponding acetylation sites during tooth formation in order to unveil the connection between histone acetylation modification and tooth development. Moreover, key histone acetyltransferases and histone deacetylases were detected in both epithelial and mesenchymal cells during tooth development by scRNA-seq and immunohistochemistry. These results suggest that histone acetylation modification functions as an important mechanism in tooth development at different stages.

The Frequency of a Magnetic Field Reduces the Viability and Proliferation of Numerous Tumor Cell Lines

The frequency of a magnetic field has led to the development of physicochemical interaction models and to the consideration of the role of frequency as a fundamental parameter in the change of cell behavior. The main objective of this article is to find a frequency window to decrease the viability and proliferation of different tumor cell lines to compare the frequency response of each. For this purpose, tumor cell lines PC12 (rat), B16F10 (mouse), SKBR3 (human), MDA-MB-231 (human), and the non-tumor cell line 3T3 (mouse) are exposed to a magnetic field of 100 µT for 24, 48, and 72 hours in frequency windows contained in the range [20-100] Hz, and their viability and proliferation behavior is evaluated. The results show a frequency-, exposure-time-, and cell-line-dependent behavior, with the most pronounced changes for most cell lines at frequencies of 45, 50, and 55 Hz. It is concluded that each cell type could respond to specific frequency codes that allow the modification of its behavior in vital cellular processes related to tumor development. Knowledge of these codes would allow for the therapeutic application of magnetic fields in oncological pathologies.

CHD7 binds to insulators during neuronal differentiation

Spiral ganglion neurons (SGNs) are crucial for hearing, and the loss of SGNs causes hearing loss. Stem cell-based therapies offer a promising approach for SGN regeneration and require understanding the mechanisms governing SGN differentiation. We investigated the chromatin remodeler CHD7 in neuronal differentiation using immortalized multipotent otic progenitor (iMOP) cells. We demonstrated that CHD7 knockdown impaired neuronal differentiation. Genome-wide analysis revealed CHD7 binding at diverse cis-regulatory elements, with notable enrichment at sites marked by the insulator-binding protein CTCF between topologically associating domains (TADs). Insulators marked by the enrichment of CHD7 and CTCF resided near genes critical for neuronal differentiation, including Mir9-2. Targeting these regulatory regions in iMOPs with CRISPR interference (CRISPRi) and activation (CRISPRa) increased miR-9 transcription, irrespective of the method. Blocking the CHD7 and CTCF marked sites suggested that the elements function as insulators to regulate gene expression. The study highlights CHD7 activity at insulators and underscores an unreported mechanism for promoting neuronal differentiation.

Understanding How Chromatin Folding and Enzyme Competition Affect Rugged Epigenetic Landscapes

Epigenetics plays a key role in cellular differentiation and maintaining cell identity, enabling cells to regulate their genetic activity without altering the DNA sequence. Epigenetic regulation occurs within the context of hierarchically folded chromatin, yet the interplay between the dynamics of epigenetic modifications and chromatin architecture remains poorly understood. In addition, it remains unclear what mechanisms drive the formation of rugged epigenetic patterns, characterised by alternating genomic regions enriched in activating and repressive marks. In this study, we focus on post-translational modifications of histone H3 tails, particularly H3K27me3, H3K4me3, and H3K27ac. We introduce a mesoscopic stochastic model that incorporates chromatin architecture and competition of histone-modifying enzymes into the dynamics of epigenetic modifications in small genomic loci comprising several nucleosomes. Our approach enables us to investigate the mechanisms by which epigenetic patterns form on larger scales of chromatin organisation, such as loops and domains. Through bifurcation analysis and stochastic simulations, we demonstrate that the model can reproduce uniform chromatin states (open, closed, and bivalent) and generate previously unexplored rugged profiles. Our results suggest that enzyme competition and chromatin conformations with high-frequency interactions between distant genomic loci can drive the emergence of rugged epigenetic landscapes. Additionally, we hypothesise that bivalent chromatin can act as an intermediate state, facilitating transitions between uniform and rugged landscapes. This work offers a powerful mathematical framework for understanding the dynamic interactions between chromatin architecture and epigenetic regulation, providing new insights into the formation of complex epigenetic patterns.

Role and mechanisms of histone methylation in osteogenic/odontogenic differentiation of dental mesenchymal stem cells

Dental mesenchymal stem cells (DMSCs) are pivotal for tooth development and periodontal tissue health and play an important role in tissue engineering and regenerative medicine because of their multidirectional differentiation potential and self-renewal ability. The cellular microenvironment regulates the fate of stem cells and can be modified using various optimization techniques. These methods can influence the cellular microenvironment, activate disparate signaling pathways, and induce different biological effects. "Epigenetic regulation" refers to the process of influencing gene expression and regulating cell fate without altering DNA sequences, such as histone methylation. Histone methylation modifications regulate pivotal transcription factors governing DMSCs differentiation into osteo-/odontogenic lineages. The most important sites of histone methylation in tooth organization were found to be H3K4, H3K9, and H3K27. Histone methylation affects gene expression and regulates stem cell differentiation by maintaining a delicate balance between major trimethylation sites, generating distinct chromatin structures associated with specific downstream transcriptional states. Several crucial signaling pathways associated with osteogenic differentiation are susceptible to modulation via histone methylation modifications. A deeper understanding of the regulatory mechanisms governing histone methylation modifications in osteo-/odontogenic differentiation and immune-inflammatory responses of DMSCs will facilitate further investigation of the epigenetic regulation of histone methylation in DMSC-mediated tissue regeneration and inflammation. Here is a concise overview of the pivotal functions of epigenetic histone methylation at H3K4, H3K9, and H3K27 in the regulation of osteo-/odontogenic differentiation and renewal of DMSCs in both non-inflammatory and inflammatory microenvironments. This review summarizes the current research on these processes in the context of tissue regeneration and therapeutic interventions.

Elucidating neuroepigenetic mechanisms to inform targeted therapeutics for brain disorders

The evolving field of neuroepigenetics provides important insights into the molecular foundations of brain function. Novel sequencing technologies have identified patient-specific mutations and gene expression profiles involved in shaping the epigenetic landscape during neurodevelopment and in disease. Traditional methods to investigate the consequences of chromatin-related mutations provide valuable phenotypic insights but often lack information on the biochemical mechanisms underlying these processes. Recent studies, however, are beginning to elucidate how structural and/or functional aspects of histone, DNA, and RNA post-translational modifications affect transcriptional landscapes and neurological phenotypes. Here, we review the identification of epigenetic regulators from genomic studies of brain disease, as well as mechanistic findings that reveal the intricacies of neuronal chromatin regulation. We then discuss how these mechanistic studies serve as a guideline for future neuroepigenetics investigations. We end by proposing a roadmap to future therapies that exploit these findings by coupling them to recent advances in targeted therapeutics.

Harnessing microbial co-culture to increase the production of known secondary metabolites

Covering: 2019 to 2024Secondary metabolites (SMs) are naturally occurring defense or signaling molecules that are also utilized as human and animal drugs, crop protection agents, and fine chemicals. Currently, SMs are primarily produced in monoculture settings, devoid of the intricate microbial interactions found in natural environments. Monoculture may lead to the silencing of gene clusters, requiring various genetic or bioprocess strategies to activate the biosynthesis of the corresponding metabolites. Less considered is the effect of monoculture on the efficiency of the production of important, known SMs during microbial fermentations. Co-culturing aims to mimic the complexity of natural microbial habitats, thus may increase the titer, the rate and/or the yield of fermentations. This review summarizes the progress in utilizing co-culture to promote the synthesis of known SMs by describing the types of various microbial co-cultures, listing the mechanisms for enhancing the biosynthesis of SMs, and navigating the challenges and strategies for applying such an approach in the biotechnology industries.

Connected Chromatin Amplifies Acetylation-Modulated Nucleosome Interactions

Histone acetylation is a key regulatory post-translational modification closely associated with gene transcription. In particular, H4K16 acetylation (H4K16ac) is a crucial gene activation marker that induces an open chromatin configuration. While previous studies have explored the effects of H4K16ac on nucleosome interactions, how this local modification affects higher-order chromatin organization remains unclear. To bridge the chemical modifications of these histone tail lysine residues to global chromatin structure, we utilized a residue-resolution coarse-grained chromatin model and enhanced sampling techniques to simulate charge-neutralization effects of histone acetylation on nucleosome stability, internucleosome interactions, and higher-order chromatin structure. Our simulations reveal that H4K16ac stabilizes a single nucleosome due to the reduced entropic contribution of histone tails during DNA unwrapping. In addition, acetylation modestly weakens internucleosome interactions by diminishing contacts between histone tails, DNA, and nucleosome acidic patches. These weakened interactions are amplified when nucleosomes are connected by linker DNA, where increases in linker DNA entry-exit angles lead to significant chromatin destacking and decompaction, exposing nucleosomes to transcriptional activity. Our findings suggest that the geometric constraint imposed by chromatin DNA plays a critical role in driving chromatin structural reorganization upon post-translational modifications.

The Role of HDAC3 in Pulmonary Diseases

Histone deacetylases (HDACs), a class of enzymes involved in epigenetic modifications, play a pivotal role in modulating chromatin structure and gene expression. Among these, histone deacetylase 3 (HDAC3) has emerged as a key regulator in diverse cellular pathophysiological processes. The remarkable therapeutic potential of HDAC inhibitors in lung cancer has intensified research into the role of HDAC3 in pulmonary diseases. Through deacetylating histones and non-histone proteins, HDAC3 has been increasingly recognized for its critical involvement in regulating inflammatory responses, fibrotic processes, and oncogenic signaling pathways, positioning it as a compelling therapeutic target. This review systematically examines the structural and functional features of HDAC3 and discusses its multifaceted contributions to pulmonary pathologies, including lung injury, pulmonary fibrosis, and lung cancer. Additionally, we critically evaluate advances in HDAC inhibitor-based therapies for lung cancer, with emphasis on the development of HDAC3-targeted therapies. As a promising therapeutic target for pulmonary diseases, HDAC3 needs to be further investigated to elucidate its regulatory mechanisms and facilitate the development of selective inhibitors for clinical translation.

Macromolecular and cytological changes in fission yeast G0 nuclei

When starved of nitrogen, cells of the fission yeast Schizosaccharomyces pombe enter a quiescent 'G0' state with smaller nuclei and transcriptional repression. The genomics of S. pombe G0 cells has been well studied, but much of its nuclear cell biology remains unknown. Here, we use confocal microscopy, immunoblots and electron cryotomography to investigate the cytological, biochemical and ultrastructural differences between S. pombe proliferating, G1-arrested and G0 cell nuclei, with an emphasis on the histone acetylation, RNA polymerase II fates and macromolecular complex packing. Compared to proliferating cells, G0 cells have lower levels of histone acetylation, nuclear RNA polymerase II and active transcription. The G0 nucleus has similar macromolecular crowding yet fewer chromatin-associated multi-megadalton globular complexes. Induced histone hyperacetylation during nitrogen starvation results in cells that have larger nuclei and therefore chromatin that is less compact. However, these histone-hyperacetylated cells remain transcriptionally repressed with similar nuclear crowding. Canonical nucleosomes - those that resemble the crystal structure - are rare in proliferating, G1-arrested and G0 cells. Our study therefore shows that extreme changes in nucleus physiology are possible without extreme reorganization at the macromolecular level.

Chromatin Structure Around Long Non-Coding RNA (lncRNA) Genes in Schistosoma mansoni Gonads

In this study, we employed a total of eight distinct modifications of histone proteins (H3K23ac, H3K27me3, H3K36me3, H3K4me3, H3K9ac, H3K9me3, H4K12ac, and H4K20me1) to discern the various chromatin colors encompassing lncRNA genes in both mature and immature gonads of the human parasite Schistosoma mansoni. Our investigation revealed that these chromatin colors exhibit a tendency to aggregate based on the similarities in their metagene shapes, leading to the formation of less than six distinct clusters. Moreover, these clusters can be further grouped according to their resemblances by shape, which are co-linear with specific regions of the genes, and potentially associated with transcriptional stages.

Incorporating multiscale methylation effects into nucleosome-resolution chromatin models for simulating mesoscale fibers

Histone modifications play a crucial role in regulating chromatin architecture and gene expression. Here we develop a multiscale model for incorporating methylation in our nucleosome-resolution physics-based chromatin model to investigate the mechanisms by which H3K9 and H3K27 trimethylation (H3K9me3 and H3K27me3) influence chromatin structure and gene regulation. We apply three types of energy terms for this purpose: short-range potentials are derived from all-atom molecular dynamics simulations of wildtype and methylated chromatosomes, which revealed subtle local changes; medium-range potentials are derived by incorporating contacts between HP1 and nucleosomes modified by H3K9me3, to incorporate experimental results of enhanced contacts for short chromatin fibers (12 nucleosomes); for long-range interactions we identify H3K9me3- and H3K27me3-associated contacts based on Hi-C maps with a machine learning approach. These combined multiscale effects can model methylation as a first approximation in our mesoscale chromatin model, and applications to gene systems offer new insights into the epigenetic regulation of genomes mediated by H3K9me3 and H3K27me3.

Anti-Tumor Effects of Cecropin A and Drosocin Incorporated into Macrophage-like Cells Against Hematopoietic Tumors in Drosophila mxc Mutants

Five major antimicrobial peptides (AMPs) in Drosophila are induced in multiple sex combs (mxc) mutant larvae harboring lymph gland (LG) tumors, and they exhibit anti-tumor effects. The effects of other well-known AMPs, Cecropin A and Drosocin, remain unexplored. We investigated the tumor-elimination mechanism of these AMPs. A half-dose reduction in either the Toll or Imd gene reduced the induction of these AMPs and enhanced tumor growth in mxcmbn1 mutant larvae, indicating that their anti-tumor effects depend on the innate immune pathway. Overexpression of these AMPs in the fat body suppressed tumor growth without affecting cell proliferation. Apoptosis was promoted in the mutant but not in normal LGs. Conversely, knockdown of them inhibited apoptosis and enhanced tumor growth; therefore, they inhibit LG tumor growth by inducing apoptosis. The AMPs from the fat body were incorporated into the hemocytes of mutant but not normal larvae. Another AMP, Drosomycin, was taken up via phagocytosis factors. Enhanced phosphatidylserine signals were observed on the tumor surface. Inhibition of the signals exposed on the cell surface enhanced tumor growth. AMPs may target phosphatidylserine in tumors to induce apoptosis and execute their tumor-specific effects. AMPs could be beneficial anti-cancer drugs with minimal side effects for clinical development.

The main sources of molecular organization in the cell. Atlas of self-organized and self-regulated dynamic biostructures

One of the most important goals of contemporary biology is to understand the principles of the molecular order underlying the complex dynamic architecture of cells. Here, we present an overview of the main driving forces involved in the cellular molecular complexity and in the emergent functional dynamic structures, spanning from the most basic molecular organization levels to the complex emergent integrative systemic behaviors. First, we address the molecular information processing which is essential in many complex fundamental mechanisms such as the epigenetic memory, alternative splicing, regulation of transcriptional system, and the adequate self-regulatory adaptation to the extracellular environment. Next, we approach the biochemical self-organization, which is central to understand the emergency of metabolic rhythms, circadian oscillations, and spatial traveling waves. Such a complex behavior is also fundamental to understand the temporal compartmentalization of the cellular metabolism and the dynamic regulation of many physiological activities. Numerous examples of biochemical self-organization are considered here, which show that practically all the main physiological processes in the cell exhibit this type of dynamic molecular organization. Finally, we focus on the biochemical self-assembly which, at a primary level of organization, is a basic but important mechanism for the order in the cell allowing biomolecules in a disorganized state to form complex aggregates necessary for a plethora of essential structures and physiological functions. In total, more than 500 references have been compiled in this review. Due to these main sources of order, systemic functional structures emerge in the cell, driving the metabolic functionality towards the biological complexity.

From Lesions to Lessons: Two Decades of Filamentous Plant Pathogen Genomics

Many filamentous microorganisms, such as fungi and oomycetes, have evolved the ability to colonize plants and cause devastating crop diseases. Coevolutionary conflicts with their hosts have shaped the genomes of these plant pathogens. Over the past 20 years, genomics and genomics-enabled technologies have revealed remarkable diversity in genome size, architecture, and gene regulatory mechanisms. Technical and conceptual advances continue to provide novel insights into evolutionary dynamics, diversification of distinct genomic compartments, and facilitated molecular disease diagnostics. In this review, we discuss how genomics has advanced our understanding of genome organization and plant-pathogen coevolution and provide a perspective on future developments in the field. [Formula: see text] Copyright © 2025 The Author(s). This is an open access article distributed under the CC BY 4.0 International license.

Multivalent nucleosome scaffolding by bromodomain and extraterminal domain tandem bromodomains

Promoter-promoter and enhancer-promoter interactions are enriched in histone acetylation and central to chromatin organization in active genetic regions. Bromodomains are epigenetic "readers" that recognize and bind histone acetylation. Bromodomains often exist in tandem or with other reader domains. Cellular knockdown of the bromodomain and extraterminal domain (BET) protein family disrupts chromatin organization, but the mechanisms through which BET proteins preserve chromatin structure are largely unknown. We hypothesize that BET proteins maintain overall chromatin structure by employing their tandem bromodomains to multivalently scaffold acetylated nucleosomes in an intranucleosomal or internucleosomal manner. To test this hypothesis biophysically, we used small-angle X-ray scattering, electron paramagnetic resonance, and Rosetta protein modeling to show that a disordered linker separates BET tandem bromodomain acetylation binding sites by 15 to 157 Å. Most of these modeled distances are sufficient to span the length of a nucleosome (>57 Å). Focusing on the BET family member BRD4, we employed bioluminescence resonance energy transfer and isothermal titration calorimetry to show that BRD4 bromodomain binding of multiple acetylation sites on a histone tail does not increase BRD4-histone tail affinity, suggesting that BET bromodomain intranucleosome binding is not biologically relevant. Using sucrose gradients and amplified luminescent proximity homogeneous (AlphaScreen) assays, we provide the first direct biophysical evidence that BET bromodomains can scaffold multiple acetylated nucleosomes. Taken together, our results demonstrate that BET bromodomains are capable of multivalent internucleosome scaffolding in vitro. The knowledge gained provides implications for how BET bromodomain-mediated acetylated internucleosome scaffolding may maintain cellular chromatin interactions in active genetic regions.