Histone Modifications Research Articles

Epigenetic Regulation of Stromal and Immune Cells and Therapeutic Targets in the Tumor Microenvironment.

The tumor microenvironment (TME) plays a pivotal role in neoplastic initiation and progression. Epigenetic machinery, governing the expression of core oncogenes and tumor suppressor genes in transformed cells, significantly contributes to tumor development at both primary and distant sites. Recent studies have illuminated how epigenetic mechanisms integrate external cues and downstream signals, altering the phenotype of stromal cells and immune cells. This remolds the area surrounding tumor cells, ultimately fostering an immunosuppressive microenvironment. Therefore, correcting the TME by targeting the epigenetic modifications holds substantial promise for cancer treatment. This review synthesizes recent research that elucidates the impact of specific epigenetic regulations-ranging from DNA methylation to histone modifications and chromatin remodeling-on stromal and immune cells within the TME. Notably, we highlight their functional roles in either promoting or restricting tumor progression. We also discuss the potential applications of epigenetic agents for cancer treatment, envisaging their ability to normalize the ecosystem. This review aims to assist researchers in understanding the dynamic interplay between epigenetics and the TME, paving the way for better epigenetic therapy.

Unraveled: The role of Arabidopsis GTE4-EML in transcription via two distinct histone modifications.

Unraveled: The role of Arabidopsis GTE4-EML in transcription via two distinct histone modifications.

ZAR1/2‐Regulated Epigenetic Modifications are Essential for Age‐Associated Oocyte Quality Maintenance and Zygotic Activation

AbstractThe developmental competence and epigenetic progression of oocytes gradually become dysregulated with increasing maternal age. However, the mechanisms underlying age‐related epigenetic regulation in oocytes remain poorly understood. Zygote arrest proteins 1 and 2 (ZAR1/2) are two maternal factors with partially redundant roles in maintaining oocyte quality, mainly known by regulating mRNA stability. In addition to this known function, it is found that ZAR1/2 is required for oocyte epigenetic maturation and zygotic reprogramming. Zar1/2‐deleted oocytes exhibited reduced levels of multiple histone modifications and of the expression of corresponding histone modifiers, along with over‐condensed chromatin, leading to compromised minor zygotic genome activation and deficient embryo development following fertilization. Cytoplasmic ZAR1/2 participated in intranuclear epigenetic maturation by binding the transcripts encoding histone modifiers and regulating their stability and translational activity. Moreover, oocytes from aged mice exhibited similar histone‐modification deficiencies as the Zar1/2‐deleted oocytes. ZAR1/2 mRNA and protein levels are downregulated in oocytes from mice and women with advanced ages, suggesting ZAR1/2 as regulators of epigenetic changes with reproductive aging. This study presents a new nucleo‐cytoplasmic interaction mechanism that is involved in preventing oocyte epigenetic aging. Further, ZAR1/2 represents potential gene targets for diagnosis and clinical interventions in age‐associated deficiencies in oocyte and embryo development.

DNA supercoiling modulates eukaryotic transcription in a gene-orientation dependent manner.

Transcription introduces torsional stress in the DNA fiber causing it to transition from a relaxed to a supercoiled state that can propagate across several kilobases and modulate the binding and activity of DNA-associated proteins. As a result, transcription at one locus has the potential to impact nearby transcription events. In this study, we asked how DNA supercoiling affects histone modifications and transcription of neighboring genes in the multicellular eukaryote Caenorhabditis elegans . We acutely depleted the two major topoisomerases and measured nascent transcription by Global Run-on sequencing (GRO-seq), RNA Polymerase II occupancy by ChIP-seq, gene expression by RNA-seq and four transcription-associated histone modifications by Cut & Tag. Depletion of topoisomerases I and II led to genome-wide changes in transcription dynamics, with minor disruptions to the histone modification landscape. Our results showed that C. elegans topoisomerase I is required for transcription elongation and is partially redundant with topoisomerase II. Analysis of transcription changes with respect to neighboring genes suggest that negative supercoiling promotes the transcription of genes with a divergent neighbor and positive supercoiling suppresses transcription of convergent genes. Additionally, topoisomerase depletion caused coordinated changes in the expression of divergent gene pairs, suggesting that negative supercoiling drives their synchronized expression. Conversely, the coordinated expression of convergent genes was disrupted, suggesting that excessive positive supercoiling inhibits transcription. Overall, our data supports a model in which DNA supercoiling generated by transcription at one site propagates along the eukaryotic chromatin fiber, influencing nearby transcription in an orientation-dependent manner.

Single-cell mapping of regulatory DNA:Protein interactions.

Gene expression is coordinated by a multitude of transcription factors (TFs), whose binding to the genome is directed through multiple interconnected epigenetic signals, including chromatin accessibility and histone modifications. These complex networks have been shown to be disrupted during aging, disease, and cancer. However, profiling these networks across diverse cell types and states has been limited due to the technical constraints of existing methods for mapping DNA:Protein interactions in single cells. As a result, a critical gap remains in understanding where TFs or other chromatin remodelers bind to DNA and how these interactions are perturbed in pathological contexts. To address this challenge, we developed a transformative single-cell immuno-tethering DNA:Protein mapping technology. By coupling a species-specific antibody-binding nanobody to a cytosine base editing enzyme, this approach enables profiling of even weak or transient factor binding to DNA, a task that was previously unachievable in single cells. Thus, our Docking & Deamination followed by sequencing (D&D-seq) technique induces cytosine-to-uracil edits in genomic regions bound by the target protein, offering a novel means to capture DNA:Protein interactions with unprecedented resolution. Importantly, this technique can be seamlessly incorporated into common single-cell multiomics workflows, enabling multimodal analysis of gene regulation in single cells. We tested the ability of D&D-seq to record TF binding both in bulk and at the single-cell level by profiling CTCF and GATA family members, obtaining high specificity and efficiency, with clear identification of TF footprint and signal retention in the targeted cell subpopulations. Furthermore, the deamination reaction showed minimal off-target activity, with high concordance to bulk ChIP-seq reference data. Applied to primary human peripheral blood mononuclear cells (PBMCs), D&D-seq successfully identified CTCF binding sites and enabled integration with advanced machine-learning algorithms for predicting 3D chromatin structure. Furthermore, we integrated D&D-seq with single-cell genotyping to assess the impact of IDH2 mutations on CTCF binding in a human clonal hematopoiesis sample, uncovering altered binding and chromatin co-accessibility patterns in mutant cells. Altogether, D&D-seq represents an important technological advance enabling the direct mapping of TF or chromatin remodeler binding to the DNA in primary human samples, opening new avenues for understanding chromatin and transcriptional regulation in health and disease.

Arsenic Exposure Triggers Nonalcoholic Fatty Liver Disease through Repressing S-Adenosylmethionine-Dependent Histone Methylation in Rats.

Arsenic (As) is a toxic metalloid widespread in the environment, and its exposure has been associated with a variety of adverse health outcomes. As exposure is demonstrated to cause nonalcoholic fatty liver disease (NAFLD), and the underlying epigenetic mechanisms remain largely unknown. This study aimed to investigate the roles of histone modifications in low-level As exposure-induced NAFLD in rats. The results showed that exposure to As caused lipid accumulation and upregulated the expression of lipid metabolism-related genes Fabp1, Srebf1, and Apoc3, while downregulated Acox1 and Cpt1a in rat liver. In addition, it was found that inorganic arsenite (iAsIII) was methylated to DMA, and the S-adenosylmethionine (SAM) level was decreased, which would contribute to the repression of H3K9me1/2 in rat liver after exposure. The in vitro studies revealed that SAM supplementation attenuated lipid accumulation by restoring H3K9me1/2 in HepG2 cells, which further confirmed our animal results. Therefore, it is suggested that As methylation depleted SAM, which inhibited H3K9me1/2 and activated Fabp1, Srebf1, and Apoc3 expressions, leading to NAFLD upon inorganic As exposure. Overall, these data shed new light on the role of SAM-mediated histone methylation in As-triggered NAFLD, which could be useful for the prevention and intervention of hepatotoxicity induced by environmental As exposure.

3-methyl-4-nitrophenol disturbs the maternal-to-zygotic transition of early embryos by damaging mitochondrial function and histone modification.

3-methyl-4-nitrophenol (PNMC), a chemical prevalent in various industries for drug, dye, and leather production, also serves as a primary byproduct of organophosphate insecticides. Despite its global recognition as an endocrine disruptor with documented reproductive toxicity, its detrimental impact on preimplantation embryonic development has yet to be thoroughly investigated. In this study, through the in vitro culture of mice embryos, it was initially observed that even low concentrations of PNMC exposure led to a significant reduction in blastocyst formation and a sharp decline in the ratio of inner cell mass within the blastocysts. SMART-seq2 transcriptome sequencing further confirmed that PNMC treatment disrupted global gene expression in 2-cell embryos, with differentially expressed genes enriched in multiple signaling pathways, including those related to autophagy, apoptosis, fertilization, embryonic development, transcription, and mRNA processing. Integration of transcriptome data with open databases revealed that both zygotic genome activation genes and maternal factors experienced significant transcript-level disruptions. Moreover, the study demonstrated that these gene expression changes were closely associated with mitochondrial dysfunction, evidenced by diminished mitochondrial membrane potential, reduced ATP production, aberrant expression of mitochondria-related genes, increased ROS accumulation, and heightened DNA damage in PNMC-treated embryos. Additionally, PNMC exposure induced defects in histone modification, as shown by altered levels of H3K9me3 and H3K27me3, H3K9ac and H3K27ac. Lastly, the findings indicated that PNMC triggered apoptosis in embryos, validated by elevated BAX and CASPASE3 expression, alongside positive TUNEL staining. In summary, PNMC exposure impairs the maternal-to-zygotic transition, likely through mitochondrial dysfunction and histone modification, culminating in developmental arrest and apoptosis in mouse preimplantation embryos.

Roles for the long non-coding RNA Pax6os1/PAX6-AS1 in pancreatic beta cell function.

Long non-coding RNAs (lncRNAs) are emerging as crucial regulators of beta cell function. Here, we show that an lncRNA-transcribed antisense to Pax6, annotated as Pax6os1/PAX6-AS1, was upregulated by high glucose concentrations in human as well as murine beta cell lines and islets. Elevated expression was also observed in islets from mice on a high-fat diet and patients with type 2 diabetes. Silencing Pax6os1/PAX6-AS1 in MIN6 or EndoC-βH1 cells increased several beta cell signature genes' expression. Pax6os1/PAX6-AS1 was shown to bind to EIF3D, indicating a role in translation of specific mRNAs, as well as histones H3 and H4, suggesting a role in histone modifications. Important interspecies differences were found, with a stronger phenotype in humans. Only female Pax6os1 null mice fed a high-fat diet showed slightly enhanced glucose clearance. In contrast, silencing PAX6-AS1 in human islets enhanced glucose-stimulated insulin secretion and increased calcium dynamics, whereas overexpression of the lncRNA resulted in the opposite phenotype.

MobiChIP: a compatible library construction method of single-cell ChIP-seq based droplets.

To illustrate epigenetic heterogeneity, versatile tools of single-cell ChIP-seq (scChIP-seq) are essential for both convenience and accuracy. We developed MobiChIP, a compatible ChIP-seq library construction method based on current sequencing platforms for single-cell applications. MobiChIP efficiently captures fragments from tagmented nuclei across various species and allows sample mixing from different tissues or species. This strategy offers robust nucleosome amplification and flexible sequencing without customized primers. MobiChIP reveals regulatory landscapes of chromatin with active (H3K27ac) and repressive (H3K27me3) histone modification in peripheral blood mononuclear cells (PBMCs) and accurately identifies epigenetic repression of the Hox gene cluster, outperforming ATAC-seq. Meanwhile, we also integrated scChIP-seq with scRNA-seq to further illustrate cellular genetic and epigenetic heterogeneity.

Revisiting epigenetic regulation in cancer: Evolving trends and translational implications.

Cancer is a leading cause of mortality worldwide. The evolving role of epigenetics and tumor microenvironments of cancer pose significant challenges to the management of cancer. Besides genetics, epigenetic changes play a crucial role in the alteration of cellular machinery, progression, metastasis, epithelial-mesenchymal transition, and chemoresistance. Epigenetic changes such as DNA and RNA methylation, histone modifications, and chromatin modeling directly or indirectly influence the different stages of cancer from initiation to chemoresistant phenotype. In addition, alterations in the epigenetic machinery, such as hypo- or hyperactivation of proteins involved in epigenetic modifications, can lead to different health complications, including cancer. Recently, epi-drugs or epigenetic drugs offer emerging hope for the treatment and management of this deadly disease. Various epigenetic drugs targeting factors responsible for epigenetic modifications in cancer are currently under clinical trials. This chapter provides an overview of epigenetic modifications, their clinical implications, and the potential of epigenetic drugs for cancer treatment.

Metabolic and epigenetic regulation of macrophage polarization in atherosclerosis: Molecular mechanisms and targeted therapies.

Atherosclerosis, a multifactorial progressive inflammatory disease, is the common pathology underlying cardiovascular and cerebrovascular diseases. The macrophage plasticity is involved in the pathogenesis of atherosclerosis. With the advance of metabolomics and epigenetics, metabolites/metabolic and epigenetic modification such as DNA methylation, histone modification and noncoding RNA, play a crucial role in macrophage polarization and the progression of atherosclerosis. Herein, we provide a comprehensive review of the essential role of metabolic and epigenetic regulation, as well as the crosstalk between the two in regulating macrophage polarization in atherosclerosis. We also highlight the potential therapeutic strategies of regulating macrophage polarization via epigenetic and metabolic modifications for atherosclerosis, and offer recommendations to advance our knowledge of the roles of metabolic-epigenetic crosstalk in macrophage polarization in the context of atherosclerosis. Fundamental studies that elucidate the mechanisms by which metabolic and epigenetic regulation of macrophage polarization influence atherosclerosis will pave the way for novel therapeutic approaches.

Epigenetic modifications and emerging therapeutic targets in cardiovascular aging and diseases.

The complex mechanisms underlying the development of cardiovasculardiseases remain not fully elucidated. Epigenetics, which modulates gene expression without DNA sequence changes, is shedding light on these mechanisms and their heritable effects. This review focus on epigenetic regulation in cardiovascular aging and diseases, detailing specific epigenetic enzymes such as DNA methyltransferases (DNMTs), histone acetyltransferases (HATs), and histone deacetylases (HDACs), which serve as writers or erasers that modify the epigenetic landscape. We also discuss the readers of these modifications, such as the 5-methylcytosine binding domain proteins, and the erasers ten-eleven translocation (TET) proteins. The emerging role of RNA methylation, particularly N6-methyladenosine (m6A), in cardiovascular pathogenesis is also discussed. We summarize potential therapeutic targets, such as key enzymes and their inhibitors, including DNMT inhibitors like 5-azacytidine and decitabine, HDAC inhibitors like belinostat and givinotide, some of which have been approved by the FDA for various malignancies, suggesting their potential in treating cardiovascular diseases. Furthermore, we highlight the role of novel histone modifications and their associated enzymes, which are emerging as potential therapeutic targets in cardiovascular diseases. Thus, by incorporating the recent studies involving patients with cardiovascular aging and diseases, we aim to provide a more detailed and updated review that reflects the advancements in the field of epigenetic modification in cardiovascular diseases.

BPZ inhibits early mouse embryonic development by disrupting maternal-to-zygotic transition and mitochondrial function.

The use of Bisphenol A (BPA) has been widely restricted due to its adverse health effects. Bisphenol Z (BPZ) is used as an alternative to BPA, and humans are widely exposed to BPZ through various routes. Recent studies have shown that BPZ exposure adversely affects mouse oocyte meiotic maturation. This study investigates the impact of BPZ exposure on early mouse embryonic development alongside an exploration of the underlying mechanisms. The findings reveal that exposure to BPZ leads to a reduction in early embryo quality and hinders developmental progression. RNA sequencing analysis has identified 593 differentially expressed genes as a result of BPZ exposure, highlighting considerable changes in early embryonic gene expression. Mechanistically, BPZ exposure inhibits the activation of the zygotic genome and impedes maternal mRNA degradation, thereby interfering with maternal-to-zygotic transition (MZT). Further analysis indicates compromised mitochondrial function, as evidenced by abnormal distribution, diminished membrane potential, and lower ATP levels. Consequently, BPZ-exposed embryos exhibit elevated levels of reactive oxygen species, superoxide anions, and oxidative DNA damage. Moreover, BPZ exposure is associated with an increase in γ-H2A.X expression. Additionally, BPZ exposure alters the expression levels of histone modifications, including H3K27me2, H3K27me3, H3K9me3, and H3K27ac, in early embryos. Collectively, BPZ exposure significantly impairs early embryo quality by disrupting mitochondrial function, inducing oxidative stress and DNA damage, altering histone modifications, and inhibiting MZT, ultimately resulting in hindered blastocyst formation. These findings underscore the profound adverse effects of BPZ on early embryonic development, indicating the need for caution when considering it as a safe alternative to BPA.

Epigenetic therapeutics attenuate kidney injury and fibrosis by restoring the expression of epigenetically reprogrammed fibrogenic genes and signaling pathways

Kidney fibrosis is a commonly observed pathological condition during development of chronic kidney disease. Therapeutic options currently available are effective only in slowing the progression of kidney fibrosis and there is no cure for this disease. Aberrant expression and excessive accumulation of extracellular matrix (ECM) proteins in the peritubular space is a characteristic pathological feature of fibrotic kidney. However, the molecular basis of aberrant regulation of fibrotic genes in kidneys is not clear. In this context, this study aimed to evaluate the role of epigenetic reprogramming in kidney fibrosis. Folic acid (FA)-induced acute kidney injury (AKI) and kidney fibrosis in mice as an in vivo model and long-term arsenic or FA-exposed fibrogenic HK-2 cells as an in vitro model were used to evaluate the role of DNA methylation and histone modifications in fibrosis. DNA demethylating agent 5aza2 deoxycytidine (5-aza-2-dC) and histone deacetylase inhibitor Trichostatin A (TSA) were used to treat FA-injected mice. Results of histopathological and immunofluorescence staining of kidney tissue, serum albumin- creatinine levels, body weight, and gene expression analysis revealed significant protective effects of 5-aza-2-dC and TSA in FA-induced AKI and fibrosis. Insignificant change in the expression of N-cadherin whereas a significant decrease in E-cadherin as well as an increase in the expression of Vimentin and α-SMA suggest partial EMT associated with fibrosis. Aberrant expression of epithelial-mesenchymal-transition (EMT) and ECM-regulators (MMP2, Smad7, and TIMP3) as well as fibrogenic signaling pathways (Notch, TGF-beta, and Wnt signaling), and their restoration by 5-aza-2-dC and TSA treatments suggest epigenetic reprogramming of these genes and signaling pathways during FA-induced fibrosis. In summary, this study provides new information on the role of epigenetic reprogramming of fibrogenic genes and signaling pathways during the development of kidney fibrosis. Attenuation of fibrosis after 5-aza-2-dC and TSA treatments suggest the promise of these epigenetic-based therapeutics in the clinical management of this disease.

Neurobiology, Molecular Pathways, and Environmental Influences in Antisocial Traits and Personality Disorders.

Personality disorders (PDs) are psychiatric conditions characterized by enduring patterns of cognition, emotion, and behaviour that deviate significantly from cultural norms, causing distress or impairment. The aetiology of PDs is complex, involving both genetic and environmental factors. Genetic studies estimate the heritability of PDs at 30% to 60%, implicating genes involved in neurotransmitter regulation, such as those for serotonin transporters and dopamine receptors. Environmental factors, including childhood trauma and chronic stress, interact with genetic predispositions to induce epigenetic modifications like DNA methylation and histone modifications, contributing to PD development. Neurobiological research has identified structural and functional abnormalities in brain regions related to emotional regulation and social cognition, such as the amygdala, prefrontal cortex, and limbic system. These abnormalities are linked to impaired emotion processing and interpersonal functioning in PDs. This review focuses on how environmental factors shape maladaptive behaviours and endophenotypes central to many PDs. It explores the interaction between the Ras-ERK, p38, and mTOR molecular pathways in response to environmental stimuli, and examines the role of oxidative stress and mitochondrial metabolism in these processes. Also reviewed are various types of PDs and existing animal models that replicate key endophenotypes, highlighting changes in neurotransmitters and neurohormones. Identifying molecular biomarkers can lead to the development of "enviromimetic" drugs, which mimic environmental influences to activate molecular pathways, facilitating targeted, personalized treatments based on the molecular profiles of individuals with PDs. Ultimately, understanding the molecular mechanisms of PDs promises to enhance diagnostic accuracy, prognosis, and therapeutic outcomes for affected individuals.

Remodeling the Epigenome Through Meditation: Effects on Brain, Body, and Well-being.

Epigenetic mechanisms are key processes that constantly reshape genome activity carrying out physiological responses to environmental stimuli. Such mechanisms regulate gene activity without modifying the DNA sequence, providing real-time adaptation to changing environmental conditions. Both favorable and unfavorable lifestyles have been shown to influence body and brain by means of epigenetics, leaving marks on the genome that can either be rapidly reversed or persist in time and even be transmitted trans-generationally. Among virtuous habits, meditation seemingly represents a valuable way of activating inner resources to cope with adverse experiences. While unhealthy habits, stress, and traumatic early-life events may favor the onset of diseases linked to inflammation, neuroinflammation, and neuroendocrine dysregulation, the practice of mindfulness-based techniques was associated with the alleviation of many of the above symptoms, underlying the importance of lifestyles for health and well-being. Meditation influences brain and body systemwide, eliciting structural/morphological changes as well as modulating the levels of circulating factors and the expression of genes linked to the HPA axis and the immune and neuroimmune systems. The current chapter intends to give an overview of pioneering research showing how meditation can promote health through epigenetics, by reshaping the profiles of the three main epigenetic markers, namely DNA methylation, histone modifications, and non-coding RNAs.

JARID1D-dependent androgen receptor and JunD signaling activation of osteoclast differentiation inhibits prostate cancer bone metastasis through demethylating H3K4.

Rationale: Bone metastasis and skeletal-related complications are primary causes of mortality in advanced-stage prostate cancer (PCa). Epigenetic regulation, particularly histone modification, plays a key role in this process; however, the underlying mechanisms remain elusive. Methods and Results: In mouse models, JARID1D was an important mediator of both visceral and bone metastases. Chromatin immunoprecipitation (ChIP) and immunofluorescence (IF) techniques showed that the H3K4me3 demethylation activity of JARID1D is a key factor in the dynamic regulation of androgen receptor (AR) expression. Further analysis using western blotting and bone culture systems indicated that knocking down JARID1D enhanced the expression of monoamine oxidase A (MAOA) through the AR signaling pathway, leading to increased secretion of the nuclear factor kappa B (NF-κB) ligand receptor activator (RANKL) by PCa cells. This in turn promotes osteoclast differentiation and facilitates bone metastasis. In addition, single-cell sequencing results indicated that a reduction in JARID1D levels directly affected osteoclasts, stimulated JunD transcription, and accelerated PCa bone metastasis progression. Finally, both in vivo and in vitro experiments confirmed that the JARID1D agonist JIB-04 effectively blocked these molecular pathways, thereby delaying the onset of bone metastasis in PCa. Conclusions: These insights provide a theoretical foundation for targeting JARID1D and related molecules in the treatment of PCa bone metastasis.

Characterizations of Nuclear Organization and Chromatin Modifications in Mature Embryos from Arabidopsis Dry Seeds.

Embryo development and seed germination are characterized by important alterations in nuclear and chromatin organization. It is however challenging to analyze these dynamic changes because the Arabidopsis embryo is embedded in the seed coat and a layer of endosperm tissue and is therefore difficult to access. Here, we describe a protocol to analyze nuclear organization in whole-mount dry seed embryos from Arabidopsis thaliana and to investigate the distribution of histone variants and modifications using immunostaining on isolated embryo nuclei. This protocol should be useful to elucidate the dry seed-specific chromatin organization and to follow dynamic changes in nuclear organization during seed germination.

In silico protein structural analysis of PRMT5 and RUVBL1 mutations arising in human cancers.

DNA double strand breaks (DSBs) can be generated spontaneously during DNA replication and are repaired primarily by Homologous Recombination (HR). However, efficient repair requires chromatin remodeling to allow the recombination machinery access to the break. TIP60 is a complex conserved from yeast to humans that is required for histone acetylation and modulation of HR activity at DSBs. Two enzymatic activities within the TIP60 complex, KAT5 (a histone acetyltransferase) and RUVBL1 (an AAA+ ATPase) are required for efficient HR repair. Post-translational modification of RUVBL1 by the PRMT5 methyltransferase activates the complex acetyltransferase activity and facilitates error free HR repair. In S. pombe a direct interaction between PRMT5 and the acetyltransferase subunit of the TIP60 complex (KAT5) was also identified. The TIP60 complex has been partially solved experimentally in both humans and S. cerevisiae, but not S. pombe. Here, we used in silico protein structure analysis to investigate structural conservation between S. pombe and human PRMT5 and RUVBL1. We found that there is more similarity in structure conservation between S. pombe and human proteins than between S. cerevisiae and human. Next, we queried the COSMIC database to analyze how mutations occurring in human cancers affect the structure and function of these proteins. Artificial intelligence algorithms that predict how likely mutations are to promote cellular transformation and immortalization show that RUVBL1 mutations should have a more drastic effect than PRMT5. Indeed, in silico protein structural analysis shows that PRMT5 mutations are less likely to destabilize enzyme function. Conversely, most RUVBL1 mutations occur in a region required for interaction with its partner (RUVBL2). These data suggests that cancer mutations could destabilize the TIP60 complex. Sequence conservation analysis between S. pombe and humans shows that the residues identified in cancer cells are highly conserved, suggesting that this may be an essential process in eukaryotic DSB repair. These results shed light on mechanisms of DSB repair and also highlight how S. pombe remains a great model system for analyzing DSB repair processes that are tractable in human cells.

Chromatin Immunoprecipitation for Standard, Rare, or Weakly Binding Proteins.

Various proteins interact with specific genome regions, playing crucial roles in gene regulation. Chromatin Immunoprecipitation (ChIP) is the most commonly used method to study protein-DNA interactions in vivo. By combining ChIP with high-throughput sequencing, ChIP-seq allows for studying the genome-wide localization of proteins. Although several ChIP protocols are available for plant tissues, they are primarily designed for histone modifications and abundant proteins with high DNA-binding affinity, which are considered as the "standard targets." Here we describe a ChIP protocol for plant tissues not only optimized for the standard targets but also adapted for proteins with low abundances or weak DNA-binding ability. Successful execution of the protocol enables reliable generation of DNA templates for quantitative PCR or libraries for next-generation sequencing, which makes it an effective tool for analyzing genomic interactions of a wide range of proteins.