Examining histone modification crosstalk using immobilized libraries established from ligation-ready nucleosomes

Deciphering the interplay of histone post-translational modifications in cancer: Co-targeting histone modulators for precision therapy

Chromatin undergoes dynamic regulation through reversible histone post-translational modifications (PTMs), orchestrated by "writers," "erasers," and "readers" enzymes. Dysregulation of these histone modulators is well implicated in shaping the cancer epigenome and providing avenues for precision therapies. The approval of six drugs for cancer therapy targeting histone modulators, along with the ongoing clinical trials of numerous candidates, represents a significant advancement in the field of precision medicine. Recently, it became apparent that histone PTMs act together in a coordinated manner to control gene expression. The intricate crosstalk of histone PTMs has been reported to be dysregulated in cancer, thus emerging as a critical factor in the complex landscape of cancer development. This formed the foundation of the swift emergence of co-targeting different histone modulators as a new strategy in cancer therapy. This review dissects how histone PTMs, encompassing acetylation, phosphorylation, methylation, SUMOylation and ubiquitination, collaboratively influence the chromatin states and impact cellular processes. Furthermore, we explore the significance of histone modification crosstalk in cancer and discuss the potential of targeting histone modification crosstalk in cancer management. Moreover, we underscore the significant strides made in developing dual epigenetic inhibitors, which hold promise as emerging candidates for effective cancer therapy.

MRG15 activates histone methyltransferase activity of ASH1L by recruiting it to the nucleosomes

ASH1L is a histone methyltransferase that regulates gene expression through methylation of histone H3 on lysine K36. While the catalytic SET domain of ASH1L has low intrinsic activity, several studies found that it can be vastly enhanced by the interaction with MRG15 protein and proposed allosteric mechanism of releasing its autoinhibited conformation. Here, we found that full-length MRG15, but not the MRG domain alone, can enhance the activity of the ASH1L SET domain. In addition, we showed that catalytic activity of MRG15-ASH1L depends on nucleosome binding mediated by MRG15 chromodomain. We found that in solution MRG15 binds to ASH1L, but has no impact on the conformation of the SET domain autoinhibitory loop or the S-adenosylmethionine cofactor binding site. Moreover, MRG15 binding did not impair the potency of small molecule inhibitors of ASH1L. These findings suggest that MRG15 functions as an adapter that enhances ASH1L catalytic activity by recruiting nucleosome substrate.

Arginine anchor points govern H3 tail dynamics

Chromatin is dynamically reorganized spatially and temporally, and the post-translational modification of histones is a key component of this regulation. The basic subunit of chromatin is the nucleosome core particle, consisting of two copies each of the histones H2A, H2B, H3, and H4 around which ∼147 base pairs of DNA wrap. The intrinsically disordered histone termini, or tails, protrude from the core and are heavily post-translationally modified. Previous studies have shown that the histone tails exist in dynamic ensembles of DNA-bound states within the nucleosome. Histone tail interactions with DNA are involved in nucleosome conformation and chromatin organization. Charge-modulating histone post-translational modifications (PTMs) are poised to perturb the dynamic interactions between histone tails and DNA. Arginine side chains form favorable interactions with DNA and are sites of charge-modulating PTMs such as citrullination. Our current focus is on the H3 tail, the longest histone tail. Four arginine residues are relatively evenly spaced along the H3 tail sequence, suggesting multivalent interactions with DNA poised for regulation by PTMs. In this study, we use NMR nuclear spin relaxation experiments to investigate the contribution of arginine residues to H3 tail dynamics within the nucleosome core particle. By neutralizing arginine via mutation to glutamine, we begin to work towards a comprehensive understanding of the contribution of individual residues to H3 tail dynamics. We find that neutralization of arginine residues results in increased regional mobility of the H3 tails, with implications for understanding the direct effects of arginine citrullination. Altogether, these studies support a role for dynamics within the histone language and emphasize the importance of charge-modulating histone PTMs in regulating chromatin dynamics, starting at the level of the basic subunit of chromatin.

Chemical Biology Approaches to Identify and Profile Interactors of Chromatin Modifications

In eukaryotes, DNA is packaged with histone proteins in a complex known as chromatin. Both the DNA and histone components of chromatin can be chemically modified in a wide variety of ways, resulting in a complex landscape often referred to as the "epigenetic code". These modifications are recognized by effector proteins that remodel chromatin and modulate transcription, translation, and repair of the underlying DNA. In this Review, we examine the development of methods for characterizing proteins that interact with these histone and DNA modifications. "Mark first" approaches utilize chemical, peptide, nucleosome, or oligonucleotide probes to discover interactors of a specific modification. "Reader first" approaches employ arrays of peptides, nucleosomes, or oligonucleotides to profile the binding preferences of interactors. These complementary strategies have greatly enhanced our understanding of how chromatin modifications effect changes in genomic regulation, bringing us ever closer to deciphering this complex language.

Histone tail electrostatics modulate E2-E3 enzyme dynamics: a gateway to regulate ubiquitination machinery

BRCA1 (Breast Cancer-Associated Protein 1) is a human tumor suppressor that functions as an ubiquitin (Ub) ligase enzyme (E3) and plays a key role in genomic stability and DNA repair. Heterodimerization of BRCA1 with BARD1 (BRCA1-associated RING domain protein 1) is known to increase its Ub ligase activity and is important for its stability, and cooperative activation of UbcH5c (Ub conjugating enzyme (E2)). Recent studies demonstrate the importance of ubiquitination of the nucleosomal H2A C-terminal tail by BRCA1/BARD1-UbcH5c in which its mutations inhibit ubiquitination, predispose cells to chromosomal instability and greatly increase the likelihood of breast and ovarian cancer development. Due to the lack of molecular-level insight on the flexible and dis-ordered H2A C-tail, its ubiquitination mechanism by BRCA1/BARD1-UbcH5c and its function and relationship to cancer susceptibility remain elusive. Here, we use molecular dynamics simulations to provide molecular-level insights into the dynamics of the less-studied H2A C-tail and BRCA1/BARD1-UbcH5c on the nucleosome surface and their effect on ubiquitination. Our results precisely identify the key interactions and residues that trigger conformational transitions of BRCA1/BARD1-UbcH5c, and characterize the important role of histone electrostatics in their dynamics. We provide a mechanistic basis for the H2A C-tail lysine approach to UbcH5c and show the role of H2A C-tail and UbcH5c dynamics in lysine ubiquitination. Furthermore, our data demonstrate the potential for ubiquitination based on the lysine position of the C-tail. Altogether, the findings of this study provide unrevealed insights into the mechanism of H2A C-tail ubiquitination and help us understand the communication between Ub ligase/Ub conjugating enzymes (E3/E2) and nucleosome to regulate ubiquitination machinery, paving the way for the development of effective treatments for cancer and chronic pain.

Depsipeptides Targeting Tumor Cells: Milestones from In Vitro to Clinical Trials

Cancer is currently considered one of the most threatening diseases worldwide. Diet could be one of the factors that can be enhanced to comprehensively address a cancer patient's condition. Unfortunately, most molecules capable of targeting cancer cells are found in uncommon food sources. Among them, depsipeptides have emerged as one of the most reliable choices for cancer treatment. These cyclic amino acid oligomers, with one or more subunits replaced by a hydroxylated carboxylic acid resulting in one lactone bond in a core ring, have broadly proven their cancer-targeting efficacy, some even reaching clinical trials and being commercialized as "anticancer" drugs. This review aimed to describe these depsipeptides, their reported amino acid sequences, determined structure, and the specific mechanism by which they target tumor cells including apoptosis, oncosis, and elastase inhibition, among others. Furthermore, we have delved into state-of-the-art in vivo and clinical trials, current methods for purification and synthesis, and the recognized disadvantages of these molecules. The information collated in this review can help researchers decide whether these molecules should be incorporated into functional foods in the near future.

Nucleosome Core Particle Reconstitution with Recombinant Histones and Widom 601 DNA

Reconstitution of nucleosomes from recombinant histones and DNA is a widely used tool for studying nucleosome structure, dynamics, and interactions. Preparation of reconstituted nucleosomes allows for the study of nucleosomes with defined compositions. Here, we describe methods for refolding recombinant human histones, reconstituting nucleosome core particles with 147 bp Widom 601 DNA, and purification via sucrose gradient.

Preparation of Recombinant Histones and Widom 601 DNA for Reconstitution of Nucleosome Core Particles

Expression and purification of individual histone proteins and amplification and purification of DNA are the initial steps toward reconstituting nucleosome core particles. Histone proteins are expressed in E. coli, extracted from inclusion bodies, and purified using ion-exchange chromatography. DNA containing the 147 base pair Widom 601 sequence is amplified in bacteria using a plasmid containing multiple copies of this strong nucleosome positioning sequence. Following alkaline lysis of bacteria, DNA is extracted using phenol and chloroform, released from the vector via restriction enzyme digestion, and purified in subsequent precipitation and ion-exchange chromatography steps. Here, we describe a combination of two protocols: one to express and purify recombinant human histones and the other to amplify and purify Widom 601 DNA.

A General Method to Edit Histone H3 Modifications on Chromatin Via Sortase-Mediated Metathesis

The post-translational modifications (PTMs) on the tail of histone H3 control chromatin structure and influence epigenetics and gene expression. The current chemical methods including unnatural amino acid incorporation and protein splicing enable preparations of the histone with diverse PTMs in cellular contexts, but they are not applicable to edit native chromatin. The manipulation of histone-modifying enzymes alter the endogenous histone PTMs but the lack of specificity of most histone-modifying enzymes prevents precise control of specific H3 tail PTM patterns. Here we report a new method to edit the N-tail of histone H3 via sortase mediated metathesis (SMM). The sortase can install desired PTM patterns into histone H3 on nucleosomes in vitro and in cellulo. This study expands the application scope of sortase from ligation to metathesis in live cells using cell-penetrating peptides (CPPs). In addition, it offers a strategy to edit PTMs of cellular histone H3 with potential for the development of precise epigenome editing.

Enzymatic nucleosome acetylation selectively affects activity of histone methyltransferases in vitro

Posttranslational modification of histones plays a critical role in regulation of gene expression. These modifications include methylation and acetylation that work in combination to establish transcriptionally active or repressive chromatin states. Histone methyltransferases (HMTs) often have variable levels of activity in vitro depending on the form of substrate used. For example, certain HMTs prefer nucleosomes extracted from human or chicken cells as substrate compared to recombinant nucleosomes reconstituted from bacterially produced histones. We considered that pre-existing histone modifications in the extracted nucleosomes can affect the efficiency of catalysis by HMTs, suggesting functional cross-talk between histone-modifying enzymes within a complex network of interdependent activities. Here we systematically investigated the effect of nucleosome acetylation by EP300, GCN5L2 (KAT2A) and MYST1 (MOF) on histone 3 lysine 4 (H3K4), H3K9 and H4K20 methylation of nucleosomes by nine HMTs (MLL1, MLL3, SET1B, G9a, SETDB1, SUV39H1, SUV39H2, SUV420H1 and SUV420H2) in vitro. Our full kinetic characterization data indicate that site-specific acetylation of nucleosomal histones by specific acetyltransferases can create nucleosomes that are better substrates for specific HMTs. This includes significant increases in catalytic efficiencies of SETDB1, G9a and SUV420H2 after nucleosome acetylation in vitro.

Visualizing Conformational Ensembles of the Nucleosome by NMR

The formation of chromatin not only compacts the eukaryotic genome into the nucleus but also provides a mechanism for the regulation of all DNA templated processes. Spatial and temporal modulation of the chromatin structure is critical in such regulation and involves fine-tuned functioning of the basic subunit of chromatin, the nucleosome. It has become apparent that the nucleosome is an inherently dynamic system, but characterization of these dynamics at the atomic level has remained challenging. NMR spectroscopy is a powerful tool for investigating the conformational ensemble and dynamics of proteins and protein complexes, and recent advances have made the study of large systems possible. Here, we review recent studies which utilize NMR spectroscopy to uncover the atomic level conformation and dynamics of the nucleosome and provide a better understanding of the importance of these dynamics in key regulatory events.

Chemical biology approaches to study histone interactors

Protein-protein interactions (PPIs) in the nucleus play key roles in transcriptional regulation and ensure genomic stability. Critical to this are histone-mediated PPI networks, which are further fine-tuned through dynamic post-translational modification. Perturbation to these networks leads to genomic instability and disease, presenting epigenetic proteins as key therapeutic targets. This mini-review will describe progress in mapping the combinatorial histone PTM landscape, and recent chemical biology approaches to map histone interactors. Recent advances in mapping direct interactors of histone PTMs as well as local chromatin interactomes will be highlighted, with a focus on mass-spectrometry based workflows that continue to illuminate histone-mediated PPIs in unprecedented detail.

Interrogating Epigenome toward Personalized Approach in Cutaneous Melanoma

Epigenetic alterations have emerged as essential contributors in the pathogenesis of various human diseases, including cutaneous melanoma (CM). Unlike genetic changes, epigenetic modifications are highly dynamic and reversible and thus easy to regulate. Here, we present a comprehensive review of the latest research findings on the role of genetic and epigenetic alterations in CM initiation and development. We believe that a better understanding of how aberrant DNA methylation and histone modifications, along with other molecular processes, affect the genesis and clinical behavior of CM can provide the clinical management of this disease a wide range of diagnostic and prognostic biomarkers, as well as potential therapeutic targets that can be used to prevent or abrogate drug resistance. We will also approach the modalities by which these epigenetic alterations can be used to customize the therapeutic algorithms in CM, the current status of epi-therapies, and the preliminary results of epigenetic and traditional combinatorial pharmacological approaches in this fatal disease.

Histone tails as signaling antennas of chromatin

Histone tails, representing the N-terminal or C-terminal regions flanking the histone core, play essential roles in chromatin signaling networks. Intrinsic disorder of histone tails and their propensity for post-translational modifications allow them to serve as hubs in coordination of epigenetic processes within the nucleosomal context. Deposition of histone variants with distinct histone tail properties further enriches histone tails' repertoire in epigenetic signaling. Given the advances in experimental techniques and in silico modelling, we review the most recent data on histone tails' effects on nucleosome stability and dynamics, their function in regulating chromatin accessibility and folding. Finally, we discuss different molecular mechanisms to understand how histone tails are involved in nucleosome recognition by binding partners and formation of higher-order chromatin structures.