Diverse Modifications Research Articles

Structurally stable copolymer ultrafiltration membranes prepared via vinyl chloride suspension copolymerization and tannic acid in-situ modification integration

Polyvinyl chloride ultrafiltration membranes, widely used in various industries, are hindered by their high susceptibility to contamination. To address this concern, researchers have investigated diverse modification methods, encompassing surface modification and physical blending. Although surface modification provides stability, but it is intricate, expensive, and may result in pore clogging. Physical blending is a simpler approach but lacks durability and stability. Tannic acid (TA), a natural compound, has attracted attention for its potential in membrane modification due to its diverse benefits. However, the existing methods, such as TA-metal networks, encounter challenges of weakened stability and reduced permeability of membrane. To solve these issues, this research presents a novel approach that integrates suspension copolymerization, polyaddition, and a sol–gel process to fabricate structurally stable copolymer ultrafiltration membranes. Active sites for sol–gel reactions were embedded into the copolymer through copolymerization. Subsequently, TA was added to the copolymer casting solution, and isocyanate propyltriethoxysilane was decorated onto TA through a polyaddition reaction. Following this, a non-solvent induced phase separation method was used for membrane fabrication. During the formation of the membrane, a sol–gel reaction occurred between the copolymer and the modified TA, ensuring both stable chemical cross-linking. The membrane demonstrates excellent permeability, fouling resistance, and long-term operational stability. This innovative approach not only addresses compatibility and leakage issues associated with traditional methods but also ensures the stable integration of hydrophilic functional monomers within the copolymer matrix. The proposed method holds promise for advancing applications of ultrafiltration membrane technology in various complex environments.

Shakespeare Tragedy, Comedy and Historical Play

This particular research paper sheds light on common recognizable characteristics of Shakespeare tragedy, comedy and historical play. Shakespeare, the dramatist of all time, brought tragedy and comedy developed by classic Greek dramatists: Aeschylus, Sophocles, Euripides and Aristophanes to a new level in the Elizabeth period. Within his theatre life which expands for 22 years, he produced ten tragedies, seventeen comedies and ten historic plays, which are staged with diverse modification all over the world, being translated to almost all the languages that are spoken in very nook and corner in the world. Shakespeare whom quoted next to the Bible is undoubtedly a social reality; his tragedy, comedy and historical plays have become the most timeless and placeless plays which touch the hearts of the audiences irrespective of social political and geographical differences. His tragedy showcases the downfall of the hero/heroine of high socio standing due to a tragic flaw, which finally causes the death of the protagonist either by being killed or committing suicide. His comedy is much more different from one another, although almost all of then end in poetic justice. His historical plays are based on the English history from 12th century to 16th century (from 1399 to 1485) and actual kings who ruled Great Britain in the particular period. However, Shakespeare added more dramatic effects into these historical plays constantly reminding the fact that he is not a historian yet a dramatist.

Chemical Synthesis of Modified RNA.

Ribonucleic acids (RNAs) play a vital role in living organisms. Many of their cellular functions depend critically on chemical modification. Methods to modify RNA in a controlled manner-both in vitro and in vivo-are thus essential to evaluate and understand RNA biology at the molecular and mechanistic levels. The diversity of modifications, combined with the size and uniformity of RNA (made up of only 4 nucleotides) makes its site-specific modification a challenging task that needs to be addressed by complementary approaches. One such approach is solid-phase RNA synthesis. We discuss recent developments in this field, starting with new protection concepts in the ongoing effort to overcome current size limitations. We continue with selected modifications that have posed significant challenges for their incorporation into RNA. These include deazapurine bases required for atomic mutagenesis to elucidate mechanistic aspects of catalytic RNAs, and RNA containing xanthosine, N4-acetylcytidine, 5-hydroxymethylcytidine, 3-methylcytidine, 2'-OCF3, and 2'-N3 ribose modifications. We also discuss the all-chemical synthesis of 5'-capped mRNAs and the enzymatic ligation of chemically synthesized oligoribonucleotides to obtain long RNA with multiple distinct modifications, such as those needed for single-molecule FRET studies. Finally, we highlight promising developments in RNA-catalyzed RNA modification using cofactors that transfer bioorthogonal functionalities.

Chemical Synthesis of Modified RNA

AbstractRibonucleic acids (RNAs) play a vital role in living organisms. Many of their cellular functions depend critically on chemical modification. Methods to modify RNA in a controlled manner—both in vitro and in vivo—are thus essential to evaluate and understand RNA biology at the molecular and mechanistic levels. The diversity of modifications, combined with the size and uniformity of RNA (made up of only 4 nucleotides) makes its site‐specific modification a challenging task that needs to be addressed by complementary approaches. One such approach is solid‐phase RNA synthesis. We discuss recent developments in this field, starting with new protection concepts in the ongoing effort to overcome current size limitations. We continue with selected modifications that have posed significant challenges for their incorporation into RNA. These include deazapurine bases required for atomic mutagenesis to elucidate mechanistic aspects of catalytic RNAs, and RNA containing xanthosine, N4‐acetylcytidine, 5‐hydroxymethylcytidine, 3‐methylcytidine, 2′‐OCF3, and 2′‐N3 ribose modifications. We also discuss the all‐chemical synthesis of 5′‐capped mRNAs and the enzymatic ligation of chemically synthesized oligoribonucleotides to obtain long RNA with multiple distinct modifications, such as those needed for single‐molecule FRET studies. Finally, we highlight promising developments in RNA‐catalyzed RNA modification using cofactors that transfer bioorthogonal functionalities.

Cytochrome P450 Mining for Bufadienolide Diversification.

Bufadienolides are a class of steroids with a distinctive α-pyrone ring at C17, mostly produced by toads and consisting of over 100 orthologues. They exhibit potent cardiotonic and antitumor activities and are active ingredients of the traditional Chinese medicine Chansu and Cinobufacini. Direct extraction from toads is costly, and chemical synthesis is difficult, limiting the accessibility of active bufadienolides with diverse modifications and trace content. In this work, based on the transcriptome and genome analyses, using a yeast-based screening platform, we obtained eight cytochrome P450 (CYP) enzymes from toads, which catalyze the hydroxylation of bufalin and resibufogenin at different sites. Moreover, a reported fungal CYP enzyme Sth10 was found functioning in the modification of bufalin and resibufogenin at multiple sites. A total of 15 bufadienolides were produced and structurally identified, of which six were first discovered. All of the compounds were effective in inhibiting the proliferation of tumor cells, especially 19-hydroxy-bufalin (2) and 1β-hydroxy-bufalin (3), which were generated from bufalin hydroxylation catalyzed by CYP46A35. The catalytic efficiency of CYP46A35 was improved about six times and its substrate diversity was expanded to progesterone and testosterone, the common precursors for steroid drugs, achieving their efficient and site-specific hydroxylation. These findings elucidate the key modification process in the synthesis of bufadienolides by toads and provide an effective way for the synthesis of unavailable bufadienolides with site-specific modification and active potentials.

Integration of Modified Classical Conjugate Gradient Methods for Unconstrained Optimization

The integration of modified classical conjugate gradient methods (CGMs) for unconstrained optimization represents a crucial and evolving area of research within the field of optimization algorithms. Over time, numerous studies have put forth diverse modifications and novel approaches to enhance the effectiveness of classical CGMs. These modifications aim to address specific challenges and improve the overall performance of optimization algorithms in unconstrained scenarios. In order to tackle unconstrained optimization challenges and improve our understanding of their synergies, this ongoing study aims to unify different modified classical CGMs. Conventional CGMs have proven effective for optimization tasks, and a range of different approaches have been produced by carefully modifying these techniques. The main goal of this paper is to combine these modified versions, with particular attention to those that have similar numerators. The integration process involves systematically merging the advantageous aspects of these modified methods to develop not only innovative but also more resilient approaches to unconstrained optimization problems. The ultimate goal of this unification effort is to capitalize on the strengths inherent in different approaches to create a cohesive framework that significantly improves overall optimization performance. To thoroughly assess the efficacy of the integrated methods, a series of comprehensive performance tests are conducted. These tests include a meticulous comparison of outcomes with those of classical CGMs, providing valuable insights into the relative strengths and weaknesses of the modified approaches across diverse optimization scenarios. The evaluation criteria encompass convergence rates, solution accuracy, and computational efficiency. The conclusive outcome demonstrates that the unified approaches consistently outperform individual methods across all three crucial evaluation criteria.

Epitranscriptomic orchestrations: Unveiling the regulatory paradigm of m6A, A-to-I editing, and m5C in breast cancer via long noncoding RNAs and microRNAs.

Breast cancer (BC) poses a persistent global health challenge, particularly in countries with elevated human development indices linked to factors such as increased life expectancy, education, and wealth. Despite therapeutic progress, challenges persist, and the role of epitranscriptomic RNA modifications in BC remains inadequately understood. The epitranscriptome, comprising diverse posttranscriptional modifications on RNA molecules, holds the potential to intricately modulate RNA function and regulation, implicating dysregulation in various diseases, including BC. Noncoding RNAs (ncRNAs),acting as posttranscriptional regulators, influence physiological and pathological processes, including cancer. RNA modifications in long noncoding RNAs (lncRNAs)and microRNAs (miRNAs)add an extra layer to gene expression control. This review delves into recent insights into epitranscriptomic RNA modifications, such as N-6-methyladenosine (m6A), adenine-to-inosine (A-to-I) editing, and 5-methylcytosine (m5C), specifically in the context of lncRNA and miRNAs in BC, highlighting their potential implications in BC development and progression. Understanding this intricate regulatory landscape is vital for deciphering the molecular mechanisms underlying BC and identifying potential therapeutic targets.

Dynein Light Intermediate Chains Exhibit Different Arginine Methylation Patterns.

The motor protein dynein is integral to retrograde transport along microtubules and interacts with numerous cargoes through the recruitment of cargo-specific adaptor proteins. This interaction is mediated by dynein light intermediate chain subunits LIC1 (DYNC1LI1) and LIC2 (DYNC1LI2), which govern the adaptor binding and are present in distinct dynein complexes with overlapping and unique functions. Using bioinformatics, we analyzed the C-terminal domains (CTDs) of LIC1 and LIC2, revealing similar structural features but diverse post-translational modifications (PTMs). The methylation status of LIC2 and the proteins involved in this modification were examined through immunoprecipitation and immunoblotting analyses. The specific methylation sites on LIC2 were identified through a site-directed mutagenesis analysis, contributing to a deeper understanding of the regulatory mechanisms of the dynein complex. We found that LIC2 is specifically methylated at the arginine 397 residue, a reaction that is catalyzed by protein arginine methyltransferase 1 (PRMT1). The distinct PTMs of the LIC subunits offer a versatile mechanism for dynein to transport diverse cargoes efficiently. Understanding how these PTMs influence the functions of LIC2, and how they differ from LIC1, is crucial for elucidating the role of dynein-related transport pathways in a range of diseases. The discovery of the arginine 397 methylation site on LIC2 enhances our insight into the regulatory PTMs of dynein functions.

Evolution of staining methods in neuroanatomy: Impetus for emanation of neuron doctrine during the turn of 20th century.

The nervous system is distinctive as compared to other tissue systems in human body owing to intricate structural organization. Histological studies played a key role in unveiling complex details of nervous tissue. However, the process of developing suitable staining method for nerve cells was arduous and spanned across almost half a century. The present study explored details of the journey involving quest for propitious staining method in neuroanatomy culminating in promulgation of neuron doctrine at the onset of 20th century. Initial efforts involving hematoxylin (including its diverse modifications) and subsequent adoption of analogous dye-based stains (like Nissl's method) had limited success in visualization of different parts of a nerve cell and structural details of nervous tissue. This was due to inability of dye-based stains to penetrate the connective tissue sheath of nervous tissue. Eventually, advent of metallic stains in form of silver impregnation method (Golgi stain), reduced silver impregnation method with gold stain (Cajal's stain) and silver carbonate staining method of Río-Hortega unraveled the structure of nervous tissue. The evolution of staining methods catalyzed the refinement of theories pertinent to constitution of nervous tissue. Golgi's staining led to emergence of reticular theory (neurons exist as a network) and Nissl's staining was the basis of the concept of Nervösen Grau (nerve cells and glial cells are embedded in mass of gray matter). Finally, Cajal's staining method successfully elucidated the complex anatomy of nerve terminals and resulted in emanation of neuron doctrine (neurons exists as individual units with adjacent connections).

N6-methylation in the development, diagnosis, and treatment of gastric cancer.

Gastric cancer (GC) ranks third among cancers in terms of mortality rate worldwide. A clear understanding of the mechanisms underlying the genesis and progression of GC will contribute to clinical decision making. N6-methyladenosine (m6A) is the most abundant among diverse mRNA modification types and regulates multiple facets of RNA metabolism. In recent years, emerging studies have shown that m6A modifications are involved in gastric carcinoma tumorigenesis and progression and can potentially be valuable new prospects for diagnosis and prognosis. This article reviews the recent progress regarding m6A in GC.

Does progress in microfracture techniques necessarily translate into clinical effectiveness?

Multitudinous advancements have been made to the traditional microfracture (MFx) technique, which have involved delivery of various acellular 2nd generation MFx and cellular MFx-III components to the area of cartilage defect. The relative benefits and pitfalls of these diverse modifications of MFx technique are still not widely understood. To comparatively analyze the functional, radiological, and histological outcomes, and complications of various generations of MFx available for the treatment of cartilage defects. A systematic review was performed using PubMed, EMBASE, Web of Science, Cochrane, and Scopus. Patients of any age and sex with cartilage defects undergoing any form of MFx were considered for analysis. We included only randomized controlled trials (RCTs) reporting functional, radiological, histological outcomes or complications of various generations of MFx for the management of cartilage defects. Network meta-analysis (NMA) was conducted in Stata and Cochrane's Confidence in NMA approach was utilized for appraisal of evidence. Forty-four RCTs were included in the analysis with patients of mean age of 39.40 (± 9.46) years. Upon comparing the results of the other generations with MFX-I as a constant comparator, we noted a trend towards better pain control and functional outcome (KOOS, IKDC, and Cincinnati scores) at the end of 1-, 2-, and 5-year time points with MFx-III, although the differences were not statistically significant (P > 0.05). We also noted statistically significant Magnetic resonance observation of cartilage repair tissue score in the higher generations of microfracture (weighted mean difference: 17.44, 95% confidence interval: 0.72, 34.16, P = 0.025; without significant heterogeneity) at 1 year. However, the difference was not maintained at 2 years. There was a trend towards better defect filling on MRI with the second and third generation MFx, although the difference was not statistically significant (P > 0.05). The higher generations of traditional MFx technique utilizing acellular and cellular components to augment its potential in the management of cartilage defects has shown only marginal improvement in the clinical and radiological outcomes.

Exploring Cereal Metagenomics: Unravelling Microbial Communities for Improved Food Security.

Food security is an urgent global challenge, with cereals playing a crucial role in meeting the nutritional requirements of populations worldwide. In recent years, the field of metagenomics has emerged as a powerful tool for studying the microbial communities associated with cereal crops and their impact on plant health and growth. This chapter aims to provide a comprehensive overview of cereal metagenomics and its role in enhancing food security through the exploration of beneficial and pathogenic microbial interactions. Furthermore, we will examine how the integration of metagenomics with other tools can effectively address the adverse effects on food security. For this purpose, we discuss the integration of metagenomic data and machine learning in providing novel insights into the dynamic interactions shaping plant-microbe relationships. We also shed light on the potential applications of leveraging microbial diversity and epigenetic modifications in improving crop resilience and yield sustainability. Ultimately, cereal metagenomics has revolutionized the field of food security by harnessing the potential of beneficial interactions between cereals and their microbiota, paving the way for sustainable agricultural practices.

Interpretable Multi-Scale Deep Learning for RNA Methylation Analysis across Multiple Species.

RNA modification plays a crucial role in cellular regulation. However, traditional high-throughput sequencing methods for elucidating their functional mechanisms are time-consuming and labor-intensive, despite extensive research. Moreover, existing methods often limit their focus to specific species, neglecting the simultaneous exploration of RNA modifications across diverse species. Therefore, a versatile computational approach is necessary for interpretable analysis of RNA modifications across species. A multi-scale biological language-based deep learning model is proposed for interpretable, sequential-level prediction of diverse RNA modifications. Benchmark comparisons across species demonstrate the model's superiority in predicting various RNA methylation types over current state-of-the-art methods. The cross-species validation and attention weight visualization also highlight the model's capability to capture sequential and functional semantics from genomic backgrounds. Our analysis of RNA modifications helps us find the potential existence of "biological grammars" in each modification type, which could be effective for mapping methylation-related sequential patterns and understanding the underlying biological mechanisms of RNA modifications.

Chemoenzymatic Installation of Site-Specific Chemical Groups on DNA Enhances the Catalytic Activity.

Functional DNAs are valuable molecular tools in chemical biology and analytical chemistry but suffer from low activities due to their limited chemical functionalities. Here, we present a chemoenzymatic method for site-specific installation of diverse functional groups on DNA, and showcase the application of this method to enhance the catalytic activity of a DNA catalyst. Through chemoenzymatic introduction of distinct chemical groups, such as hydroxyl, carboxyl, and benzyl, at specific positions, we achieve significant enhancements in the catalytic activity of the RNA-cleaving deoxyribozyme 10-23. A single carboxyl modification results in a 100-fold increase, while dual modifications (carboxyl and benzyl) yield an approximately 700-fold increase in activity when an RNA cleavage reaction is catalyzed on a DNA-RNA chimeric substrate. The resulting dually modified DNA catalyst, CaBn, exhibits a kobs of 3.76 min-1 in the presence of 1 mM Mg2+ and can be employed for fluorescent imaging of intracellular magnesium ions. Molecular dynamics simulations reveal the superior capability of CaBn to recruit magnesium ions to metal-ion-binding site 2 and adopt a catalytically competent conformation. Our work provides a broadly accessible strategy for DNA functionalization with diverse chemical modifications, and CaBn offers a highly active DNA catalyst with immense potential in chemistry and biotechnology.

Gut microbiota and epigenetics in colorectal cancer: implications for carcinogenesis and therapeutic intervention.

Colorectal cancer (CRC) is a leading cause of cancer-related deaths worldwide. The occurrence of CRC is associated with various genetic and epigenetic mutations in intestinal epithelial cells that transform them into adenocarcinomas. There is increasing evidenceindicating thegut microbiota playsa crucial role in the regulation of host physiological processes. Alterations in gut microbiota composition are responsible for initiating carcinogenesis through diverse epigenetic modifications, including histone modifications, ncRNAs and DNA methylation. This work was designedto comprehensively reviewrecent findings to provide insight into the associations between the gut microbiota and CRC at an epigenetic level. These scientific insights can be used in the future to develop effective strategies for early detection and treatment of CRC.

Dynamic and distinct histone modifications facilitate human trophoblast lineage differentiation

The placenta serves as an essential organ for fetal growth throughout pregnancy. Histone modification is a crucial regulatory mechanism involved in numerous biological processes and development. Nevertheless, there remains a significant gap in our understanding regarding the epigenetic regulations that influence trophoblast lineage differentiation, a fundamental aspect of placental development. Here, through comprehensive mapping of H3K4me3, H3K27me3, H3K9me3, and H3K27ac loci during the differentiation of trophoblast stem cells (TSCs) into syncytiotrophoblasts (STs) and extravillous trophoblasts (EVTs), we reveal dynamic reconfiguration in H3K4me3 and H3K27ac patterns that establish an epigenetic landscape conducive to proper trophoblast lineage differentiation. We observe that broad H3K4me3 domains are associated with trophoblast lineage-specific gene expression. Unlike embryonic stem cells, TSCs lack robust bivalent domains. Notably, the repression of ST- and EVT-active genes in TSCs is primarily attributed to the weak H3K4me3 signal rather than bivalent domains. We also unveil the inactivation of TSC enhancers precedes the activation of ST enhancers during ST formation. Our results provide a comprehensive global map of diverse histone modifications, elucidating the dynamic histone modifications during trophoblast lineage differentiation.

Association between anthropization and rodent reservoirs of zoonotic pathogens in Northwestern Mexico.

The world is facing a major pulse of ecological and social changes that may favor the risk of zoonotic outbreaks. Such risk facilitation may occur through the modification of the host's community diversity and structure, leading to an increase in pathogen reservoirs and the contact rate between these reservoirs and humans. Here, we examined whether anthropization alters the relative abundance and richness of zoonotic reservoir and non-reservoir rodents in three Socio-Ecological Systems. We hypothesized that anthropization increases the relative abundance and richness of rodent reservoirs while decreasing non-reservoir species. We first developed an Anthropization index based on 15 quantitative socio-ecological variables classified into five groups: 1) Vegetation type, 2) Urbanization degree, 3) Water quality, 4) Potential contaminant sources, and 5) Others. We then monitored rodent communities in three regions of Northwestern Mexico (Baja California, Chihuahua, and Sonora). A total of 683 rodents of 14 genera and 27 species were captured, nine of which have been identified as reservoirs of zoonotic pathogens (359 individuals, 53%). In all regions, we found that as anthropization increased, the relative abundance of reservoir rodents increased; in contrast, the relative abundance of non-reservoir rodents decreased. In Sonora, reservoir richness increased with increasing anthropization, while in Baja California and Chihuahua non-reservoir richness decreased as anthropization increased. We also found a significant positive relationship between the anthropization degree and the abundance of house mice (Mus musculus) and deer mice (Peromyscus maniculatus), the most abundant reservoir species in the study. These findings support the hypothesis that reservoir species of zoonotic pathogens increase their abundance in disturbed environments, which may increase the risk of pathogen exposure to humans, while anthropization creates an environmental filtering that promotes the local extinction of non-reservoir species.

Multimodal probing of T-cell recognition with hexapod heterostructures.

Studies using antigen-presenting systems at the single-cell and ensemble levels can provide complementary insights into T-cell signaling and activation. Although crucial for advancing basic immunology and immunotherapy, there is a notable absence of synthetic material toolkits that examine T cells at both levels, and especially those capable of single-molecule-level manipulation. Here we devise a biomimetic antigen-presenting system (bAPS) for single-cell stimulation and ensemble modulation of T-cell recognition. Our bAPS uses hexapod heterostructures composed of a submicrometer cubic hematite core (α-Fe2O3) and nanostructured silica branches with diverse surface modifications. At single-molecule resolution, we show T-cell activation by a single agonist peptide-loaded major histocompatibility complex; distinct T-cell receptor (TCR) responses to structurally similar peptides that differ by only one amino acid; and the superior antigen recognition sensitivity of TCRs compared with that of chimeric antigen receptors (CARs). We also demonstrate how the magnetic field-induced rotation of hexapods amplifies the immune responses in suspended T and CAR-T cells. In addition, we establish our bAPS as a precise and scalable method for identifying stimulatory antigen-specific TCRs at the single-cell level. Thus, our multimodal bAPS represents a unique biointerface tool for investigating T-cell recognition, signaling and function.

Abstract B041: Identification of m3C modification sites within mRNAs of pancreatic cancer cells by long-read direct RNA sequencing

Abstract Chemical modification is a precise and effective way to control the biogenesis, stability, and function of biological molecules, such as nucleic acids, proteins, and lipids. More than 170 different types of modifications have been discovered in coding and non-coding RNAs, constituting a diverse RNA modification landscape, called epitranscriptome. RNA modifications were mediated by three types of proteins: writers, erasers, and readers. Recently, RNA modification machinery has been dysregulated in several types of cancers and may be promising targets for cancer therapy. 3-methylcytidine (m3C), which is catalyzed by METTL2A, 2B, 6, and 8, is found at position 32 of cytoplasmic tRNAs in organisms ranging from yeast to humans, however, their functions and regulatory machinery in mRNA and non-coding RNA has not been clarified because there were no effective anti- m3C antibodies. Here we discovered that the expression of m3C writers was higher in pancreatic tumors than in noncancerous tissues. We further found that METTL2A expression is associated with a poor prognosis in pancreatic cancer patients. We also showed that METTL2A depletion led to a reduction in the growth of AsPC1 cells. We next attempted to identify the m3C sites in cellular transcripts regulated by METTL2A in AsPC1 cells using long-read direct RNA sequencing. We corrected the transcriptome using ESPRESSO and searched for the RNA modifications using Nanocompore. We then found that METTL2A targets the NYCYN motif in mRNAs and mitochondrial rRNAs. Moreover, we found that transcripts with METTL2A-mediated m3C modification were upregulated in AsPC-1 cells knocked down by METTL2A. Our study provides evidence for METTL2A-mediated down-regulation of target mRNAs via m3C modification in the survival of pancreatic tumor cells. Citation Format: Shuhei Mitsutomi, Anzu Sugawara, Kenji Takahashi, Yusuke Mizukami, Nobuyoshi Akimitsu, Kenzui Taniue. Identification of m3C modification sites within mRNAs of pancreatic cancer cells by long-read direct RNA sequencing [abstract]. In: Proceedings of the AACR Special Conference in Cancer Research: Translating Cancer Evolution and Data Science: The Next Frontier; 2023 Dec 3-6; Boston, Massachusetts. Philadelphia (PA): AACR; Cancer Res 2024;84(3 Suppl_2):Abstract nr B041.

Development of Complementary Photo-arginine/lysine to Promote Discovery of Arg/Lys hPTMs Interactomes.

Arginine and lysine, frequently appearing as a pair on histones, have been proven to carry diverse modifications and execute various epigenetic regulatory functions. However, the most context-specific and transient effectors of these marks, while significant, have evaded study as detection methods have thus far not reached a standard to capture these ephemeral events. Herein, a pair of complementary photo-arginine/δ-photo-lysine (R-dz/K-dz) probes is developed and involve these into histone peptide, nucleosome, and chromatin substrates to capture and explore the interactomes of Arg and Lys hPTMs. By means of these developed tools, this study identifies that H3R2me2a can recruit MutS protein homolog 6 (MSH6), otherwise repelDouble PHD fingers 2 (DPF2), Retinoblastoma binding protein 4/7 (RBBP4/7). And it is disclosed that H3R2me2a inhibits the chromatin remodeling activity of the cBAF complex by blocking the interaction between DPF2 (one component of cBAF) and the nucleosome. In addition, the novel pairs of H4K5 PTMs and respective readers are highlighted, namely H4K5me-Lethal(3)malignant brain tumor-like protein 2 (L3MBTL2), H4K5me2-L3MBTL2, and H4K5acK8ac-YEATS domain-containing protein 4 (YEATS4). These powerful tools pave the way for future investigation of related epigenetic mechanisms including but not limited to hPTMs.