Purification and assay protocols for obtaining highly active Jumonji C demethylases

2-Hydroxyglutarate modulates histone methylation at specific loci and alters gene expression via Rph1 inhibition

2-Hydroxyglutarate (2-HG) is an oncometabolite that accumulates in certain cancers. Gain-of-function mutations in isocitrate dehydrogenase lead to 2-HG accumulation at the expense of alpha-ketoglutarate. Elevated 2-HG levels inhibit histone and DNA demethylases, causing chromatin structure and gene regulation changes with tumorigenic consequences. We investigated the effects of elevated 2-HG levels in Saccharomyces cerevisiae, a yeast devoid of DNA methylation and heterochromatin-associated histone methylation. Our results demonstrate genetic background-dependent gene expression changes and altered H3K4 and H3K36 methylation at specific loci. Analysis of histone demethylase deletion strains indicated that 2-HG inhibits Rph1 sufficiently to induce extensive gene expression changes. Rph1 is the yeast homolog of human KDM4 demethylases and, among the yeast histone demethylases, was the most sensitive to the inhibitory effect of 2-HG in vitro. Interestingly, Rph1 deficiency favors gene repression and leads to further down-regulation of already silenced genes marked by low H3K4 and H3K36 trimethylation, but abundant in H3K36 dimethylation. Our results provide novel insights into the genome-wide effects of 2-HG and highlight Rph1 as its preferential demethylase target.

Ascorbic Acid Reprograms Epigenome and Epitranscriptome by Reducing Fe(III) in the Catalytic Cycle of Dioxygenases

Ascorbic acid (ASC) has been reported to stimulate DNA iterative oxidase ten-eleven translocation (TET) enzymes, Jumonji C-domain-containing histone demethylases, and potentially RNA m6A demethylases FTO and ALKBH5 as a cofactor. Although ascorbic acid has been widely investigated in reprogramming DNA and histone methylation status in vitro, in cultured cells and mouse models, its specific role in the catalytic cycle of dioxygenases remains enigmatic. Here, we systematically investigated the stimulation of ASC toward TET2, ALKBH3, histone demethylases, and FTO. We find that ASC reprograms epitranscriptome by erasing the hypermethylated m6A sites in mRNA. Biochemistry and electron spin resonance assays demonstrate that ASC enters the active pocket of dioxygenases and reduces Fe(III), either incorporated upon protein synthesis or generated upon rebounding the hydroxyl radical during oxidation, into Fe(II). Finally, we propose a remedied model for the catalytic cycle of dioxygenases by adding in the essential cofactor, ASC, which refreshes and regenerates inactive dioxygenase through recycling Fe(III) into Fe(II) in a dynamic "hit-and-run" manner.

Allele-Specific Chemical Rescue of Histone Demethylases Using Abiotic Cofactors

Closely related protein families evolved from common ancestral genes present a significant hurdle in developing member- and isoform-specific chemical probes, owing to their similarity in fold and function. In this piece of work, we explore an allele-specific chemical rescue strategy to activate a "dead" variant of a wildtype protein using synthetic cofactors and demonstrate its successful application to the members of the alpha-ketoglutarate (αKG)-dependent histone demethylase 4 (KDM4) family. We show that a mutation at a specific residue in the catalytic site renders the variant inactive toward the natural cosubstrate. In contrast, αKG derivatives bearing appropriate stereoelectronic features endowed the mutant with native-like demethylase activity while remaining refractory to a set of wild type dioxygenases. The orthogonal enzyme-cofactor pairs demonstrated site- and degree-specific lysine demethylation on a full-length chromosomal histone in the cellular milieu. Our work offers a strategy to modulate a specific histone demethylase by identifying and engineering a conserved phenylalanine residue, which acts as a gatekeeper in the KDM4 subfamily, to sensitize the enzyme toward a novel set of αKG derivatives. The orthogonal pairs developed herein will serve as probes to study the role of degree-specific lysine demethylation in mammalian gene expression. Furthermore, this approach to overcome active site degeneracy is expected to have general application among all human αKG-dependent dioxygenases.

Histone Demethylase JMJD2D: A Novel Player in Colorectal and Hepatocellular Cancers

Simple Summary

Histone demethylase JMJD2D is a multifunctional epigenetic factor coordinating androgen receptor activation, DNA damage repair, DNA replication, cell cycle regulation, and inflammation modulation. JMJD2D is also a well-established epigenetic facilitator in the progression of multiple malignant tumors, especially in colorectal cancer (CRC) and hepatocellular cancer (HCC). This review aims to summarize the mechanisms of JMJD2D in promoting CRC and HCC progression, which provides novel ideas for targeting JMJD2D in oncotherapy. JMJD2D promotes gene transcription by reducing H3K9 methylation and serves as a coactivator to enhance the activities of multiple carcinogenic pathways, including Wnt/β-catenin, Hedgehog, HIF1, JAK-STAT3, and Notch signaling; or acts as an antagonist of the tumor suppressor p53.

Abstract

Posttranslational modifications (PTMs) of histones are well-established contributors in a variety of biological functions, especially tumorigenesis. Histone demethylase JMJD2D (also known as KDM4D), a member of the JMJD2 subfamily, promotes gene transcription by antagonizing H3K9 methylation. JMJD2D is an epigenetic factor coordinating androgen receptor activation, DNA damage repair, DNA replication, and cell cycle regulation. Recently, the oncogenic role of JMJD2D in colorectal cancer (CRC) and hepatocellular cancer (HCC) has been recognized. JMJD2D serves as a coactivator of β-catenin, Gli1/2, HIF1α, STAT3, IRF1, TCF4, and NICD or an antagonist of p53 to promote the progression of CRC and HCC. In this review, we summarize the molecular mechanisms of JMJD2D in promoting the progression of CRC and HCC as well as the constructive role of its targeting inhibitors in suppressing tumorigenesis and synergistically enhancing the efficacy of anti-PD-1/PD-L1 immunotherapy.

Evaluation of Jumonji C lysine demethylase substrate preference to guide identification of in vitro substrates

Within the realm of lysine methylation, the discovery of lysine methyltransferase (KMTs) substrates has been burgeoning because of established systematic substrate screening protocols. Here, we describe a protocol enabling the systematic identification of JmjC KDM substrate preference and in vitro substrates. Systematically designed peptide libraries containing methylated lysine residues are used to characterize enzyme-substrate preference and identify new candidate substrates in vitro.

For complete details on the use and execution of this protocol, please refer to Hoekstra and Biggar (2021).

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Use of a permutated substrate library to define JmjC KDM recognition motifs

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JmjC KDM activity is measured via luminescent detection of succinate

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Recognition motifs enable prediction of novel in vitro substrates of JmjC KDMs

Dissecting contributions of catalytic and reader domains in regulation of histone demethylation

Histone demethylases catalyze the removal of methyl marks from histones, an activity associated with transcriptional regulation and DNA damage repair. As these processes are critical for normal physiology, deregulation of histone demethylases is disease causative, and their function and regulation are targets for therapeutic intervention. The larger of two histone demethylase families are Jumonji C (JmjC) demethylases. The members of the JmjC family share a conserved catalytic domain, and often contain non-catalytic domains that "read" the modification state of chromatin. By binding to specific histone modifications, reader domains assist in recruitment and promote accumulation of demethylases at their targets, as well as regulate their activity and substrate specificity. Here, we present protocols for the investigation of this functional coupling between reader and catalytic domains in human histone demethylase KDM5A. Although we use KDM5A and its PHD1 domain as our model system, the procedures presented herein can be applied for the biochemical characterization of other JmjC demethylases and chromatin readers.

Allele-Specific Inhibition of Histone Demethylases

Histone demethylases play a critical role in mammalian gene expression by removing methyl groups from lysine residues in degree- and site-specific manner. To specifically interrogate members and isoforms of this class of enzymes, we have developed demethylase variants with an expanded active site. The mutant enzymes are capable of performing lysine demethylation with wild-type proficiency, but are sensitive to inhibition by cofactor-competitive molecules embellished with a complementary steric "bump". The selected inhibitors show more than 20-fold selectivity over the wild-type demethylase, thus overcoming issues typical to pharmacological and genetic approaches. The mutant-inhibitor pairs are shown to act on a physiologically relevant full-length substrate. By engineering a conserved amino acid to achieve member-specific perturbation, this study provides a general approach for studying histone demethylases in diverse cellular processes.

Phospho-H1 Decorates the Inter-chromatid Axis and Is Evicted along with Shugoshin by SET during Mitosis

Precise control of sister chromatid separation during mitosis is pivotal to maintaining genomic integrity. Yet, the regulatory mechanisms involved are not well understood. Remarkably, we discovered that linker histone H1 phosphorylated at S/T18 decorated the inter-chromatid axial DNA on mitotic chromosomes. Sister chromatid resolution during mitosis required the eviction of such H1S/T18ph by the chaperone SET, with this process being independent of and most likely downstream of arm-cohesin dissociation. SET also directed the disassembly of Shugoshins in a polo-like kinase 1-augmented manner, aiding centromere resolution. SET ablation compromised mitotic fidelity as evidenced by unresolved sister chromatids with marked accumulation of H1S/T18ph and centromeric Shugoshin. Thus, chaperone-assisted eviction of linker histones and Shugoshins is a fundamental step in mammalian mitotic progression. Our findings also elucidate the functional implications of the decades-old observation of mitotic linker histone phosphorylation, serving as a paradigm to explore the role of linker histones in bio-signaling processes.

Purification, Biochemical Analysis, and Structure Determination of JmjC Lysine Demethylases

Jumonji C (JmjC) lysine demethylases (KDMs) catalyze the site- and state-specific demethylation of lysine residues in histone and nonhistone protein substrates. These enzymes have been implicated in diverse genomic processes, including epigenetic gene regulation, DNA damage response, DNA replication, and regulation of heterochromatin structure. In addition, a number of JmjC KDMs contribute to the incidence of numerous cancers, rendering them targets for the development of novel chemotherapeutic drugs. Using the JMJD2 KDM subfamily as representative examples, this chapter outlines strategies for purifying highly active, recombinant JmjC KDMs lacking inhibitory transition metal ions, characterizing kinetic parameters of these enzymes using a coupled fluorescent assay, and determining crystal structures of the enzymes in complex with methylated histone peptides. Together, these approaches provide a foundation for structural and biochemical characterization of the JmjC KDMs and facilitate efforts to identify small molecule inhibitors through high-throughput screening and structure-guided design.

Substrate Specificity Profiling of Histone-Modifying Enzymes by Peptide Microarray

The dynamic addition and removal of covalent posttranslational modifications (PTMs) on histone proteins serves as a major mechanism regulating chromatin-templated biological processes in eukaryotic genomes. Histone PTMs and their combinations function by directly altering the physical structure of chromatin and as rheostats for effector protein interactions. In this chapter, we detail microarray-based methods for analyzing the substrate specificity of lysine methyltransferase and demethylase enzymes on immobilized synthetic histone peptides. Consistent with the "histone code" hypothesis, we reveal a strong influence of adjacent and, surprisingly, distant histone PTMs on the ability of histone-modifying enzymes to methylate or demethylate their substrates. This platform will greatly facilitate future investigations into histone substrate specificity and mechanisms of PTM signaling that regulate the catalytic properties of histone-modifying enzymes.

Synthetic histone code

Chromatin is the universal template of genetic information in all eukaryotic cells. This complex of DNA and histone proteins not only packages and organizes genomes but also regulates gene expression. A multitude of posttranslational histone modifications and their combinations are thought to constitute a code for directing distinct structural and functional states of chromatin. Methods of protein chemistry, including protein semisynthesis, amber suppression technology, and cysteine bioconjugation, have enabled the generation of so-called designer chromatin containing histones in defined and homogeneous modification states. Several of these approaches have matured from proof-of-concept studies into efficient tools and technologies for studying the biochemistry of chromatin regulation and for interrogating the histone code. We summarize pioneering experiments and recent developments in this exciting field of chemical biology.

In vitro histone demethylase assays

Histone methylation plays pivotal roles in modulating chromatin structure and dynamics and in turn regulates genomic processes that require access to the DNA template. The methylation status at different sites is dynamically regulated by histone methyltransferases and demethylases. During the past decade, two classes of proteins have been characterized to actively remove methyl groups from lysine residues through different mechanisms. The LSD1/KDM1 family of amine oxidases require flavin adenine dinucleotide (FAD) for reaction, while the larger Jumonji C (JmjC) family of hydroxylases utilize Fe(II) and α-ketoglutarate as cofactors to demethylate histones. Since their discoveries, histone demethylases have been implicated in the precise control of gene expression program during development, cell identity, and fate decision. Several demethylases have also been linked to various human diseases such as neurological disorders and cancer. This chapter describes several in vitro assay conditions and detection methods for two classes of histone demethylases. We also discuss the protocols to prepare various substrates for different histone demethylase assays.

Towards understanding methyllysine readout

BACKGROUND

Lysine methylation is the most versatile covalent posttranslational modification (PTM) found in histones and non-histone proteins. Over the past decade a number of methyllysine-specific readers have been discovered and their interactions with histone tails have been structurally and biochemically characterized. More recently innovative experimental approaches have emerged that allow for studying reader interactions in the context of the full nucleosome and nucleosomal arrays.

SCOPE OF REVIEW

In this review we give a brief overview of the known mechanisms of histone lysine methylation readout, summarize progress recently made in exploring interactions with methylated nucleosomes, and discuss the latest advances in the development of small molecule inhibitors of the methyllysine-specific readers.

MAJOR CONCLUSIONS

New studies reveal various reader-nucleosome contacts outside the methylated histone tail, thus offering a better model for association of histone readers to chromatin and broadening our understanding of the functional implications of these interactions. In addition, some progress has been made in the design of antagonists of these interactions.

GENERAL SIGNIFICANCE

Specific lysine methylation patterns are commonly associated with certain chromatin states and genomic elements, and are linked to distinct biological outcomes such as transcription activation or repression. Disruption of patterns of histone modifications is associated with a number of diseases, and there is tremendous therapeutic potential in targeting histone modification pathways. Thus, investigating binding of readers of these modifications is not only important for elucidating fundamental mechanisms of chromatin regulation, but also necessary for the design of targeted therapeutics. This article is part of a Special Issue entitled: Molecular mechanisms of histone modification function.

Reconstitution of nucleosome demethylation and catalytic properties of a Jumonji histone demethylase

Jumonji histone demethylases catalyze removal of methyl marks from lysine residues in histone proteins within nucleosomes. Here, we show that the catalytic domain of demethylase JMJD2A (cJMJD2A) utilizes a distributive mechanism to remove the histone H3 lysine 9 trimethyl mark. By developing a method to assess demethylation of homogeneous, site-specifically methylated nucleosomes, we determined that the kinetic parameters for demethylation of nucleosomes by cJMJD2A are comparable to those of peptide substrates. These findings imply that other domains of the demethylase or its protein partners may contribute to nucleosome recognition in vivo and, in this way, may further regulate demethylation activity and processivity. The quantitative assays of nucleosome demethylation developed in our work provide a platform for future work with complex chromatin substrates and full-length demethylases.

Posttranslational modifications of the histone 3 tail and their impact on the activity of histone lysine demethylases in vitro

Posttranslational modifications (PTMs) of the histone H3 tail such as methylation, acetylation and phosphorylation play important roles in epigenetic signaling. Here we study the effect of some of these PTMs on the demethylation rates of methylated lysine 9 in vitro using peptide substrates mimicking histone H3. Various combinations with other PTMs were employed to study possible cross-talk effects by comparing enzyme kinetic characteristics. We compared the kinetics of histone tail substrates for truncated histone lysine demethylases KDM4A and KDM4C containing only the catalytic core (cc) and some combinations were characterized on full length (FL) KDM4A and KDM4C. We found that the substrates combining trimethylated K4 and K9 resulted in a significant increase in the catalytic activity for FL-KDM4A. For the truncated versions of KDM4A and KDM4C a two-fold increase in the catalytic activity toward bis-trimethylated substrates could be observed. Furthermore, a significant difference in the catalytic activity between dimethylated and trimethylated substrates was found for full length demethylases in line with what has been reported previously for truncated demethylases. Histone peptide substrates phosphorylated at T11 could not be demethylated by neither truncated nor full length KDM4A and KDM4C, suggesting that phosphorylation of threonine 11 prevents demethylation of the H3K9me3 mark on the same peptide. Acetylation of K14 was also found to influence demethylation rates significantly. Thus, for truncated KDM4A, acetylation on K14 of the substrate leads to an increase in enzymatic catalytic efficiency (k_cat/K_m), while for truncated KDM4C it induces a decrease, primarily caused by changes in K_m. This study demonstrates that demethylation activities towards trimethylated H3K9 are significantly influenced by other PTMs on the same peptide, and emphasizes the importance of studying these interactions at the peptide level to get a more detailed understanding of the dynamics of epigenetic marks.

Quantitative analysis of histone demethylase probes using fluorescence polarization

We previously reported methylstat as a selective inhibitor of jumonji C domain-containing histone demethylases (JHDMs). Herein, we describe the synthesis of a fluorescent analogue of methylstat and its application as a tracer in fluorescence polarization assays. Using this format, we have evaluated the binding affinities of several known JHDM probes, as well as the native cofactor and substrate of JHDM1A. This fluorophore allowed a highly robust and miniaturized competition assay sufficient for high-throughput screening.

Structural and functional analysis of JMJD2D reveals molecular basis for site-specific demethylation among JMJD2 demethylases

JMJD2 lysine demethylases (KDMs) participate in diverse genomic processes. Most JMJD2 homologs display dual selectivity toward H3K9me3 and H3K36me3, with the exception of JMJD2D, which is specific for H3K9me3. Here, we report the crystal structures of the JMJD2D⋅2-oxoglutarate⋅H3K9me3 ternary complex and JMJD2D apoenzyme. Utilizing structural alignments with JMJD2A, molecular docking, and kinetic analysis with an array of histone peptide substrates, we elucidate the specific signatures that permit efficient recognition of H3K9me3 by JMJD2A and JMJD2D, and the residues in JMJD2D that occlude H3K36me3 demethylation. Surprisingly, these results reveal that JMJD2A and JMJD2D exhibit subtle yet important differences in H3K9me3 recognition, despite the overall similarity in the substrate-binding conformation. Further, we show that H3T11 phosphorylation abrogates demethylation by JMJD2 KDMs. Together, these studies reveal the molecular basis for JMJD2 site specificity and provide a framework for structure-based design of selective inhibitors of JMJD2 KDMs implicated in disease.

Kinetic analysis of iron-dependent histone demethylases: α-ketoglutarate substrate inhibition and potential relevance to the regulation of histone demethylation in cancer cells

The Jumonji C domain-containing histone demethylases (JmjC-HDMs) are α-ketoglutarate (αKG)-dependent, O(2)-activating, non-heme iron enzymes that play an important role in epigenetics. Reported herein is a detailed kinetic analysis of three JmjC-HDMs, including the cancer-relevant JMJD2C, that was achieved by employing three enzyme activity assays. A continuous O(2) consumption assay reveals that HDMs have low affinities for O(2), suggesting that these enzymes can act as oxygen sensors in vivo. An interesting case of αKG substrate inhibition was found, and the kinetic data suggest that αKG inhibits JMJD2C competitively with respect to O(2). JMJD2C displays an optimal activity in vitro at αKG concentrations similar to those found in cancer cells, with implications for the regulation of histone demethylation activity in cancer versus normal cells.

Crystal structure and functional analysis of JMJD5 indicate an alternate specificity and function

JMJD5 is a Jumonji C (JmjC) protein that has been implicated in breast cancer tumorigenesis, circadian rhythm regulation, embryological development, and osteoclastogenesis. Recently, JMJD5 (also called KDM8) has been reported to demethylate dimethylated Lys-36 in histone H3 (H3K36me2), regulating genes that control cell cycle progression. Here, we report high-resolution crystal structures of the human JMJD5 catalytic domain in complex with the substrate 2-oxoglutarate (2-OG) and the inhibitor N-oxalylglycine (NOG). The structures reveal a β-barrel fold that is conserved in the JmjC family and a long shallow cleft that opens into the enzyme's active site. A comparison with other JmjC enzymes illustrates that JMJD5 shares sequence and structural homology with the asparaginyl and histidinyl hydroxylase FIH-1 (factor inhibiting hypoxia-inducible factor 1 [HIF-1]), the lysyl hydroxylase JMJD6, and the RNA hydroxylase TYW5 but displays limited homology to JmjC lysine demethylases (KDMs). Contrary to previous findings, biochemical assays indicate that JMJD5 does not display demethylase activity toward methylated H3K36 nor toward the other methyllysines in the N-terminal tails of histones H3 and H4. Together, these results imply that JMJD5 participates in roles independent of histone demethylation and may function as a protein hydroxylase given its structural homology with FIH-1 and JMJD6.

A method to site-specifically incorporate methyl-lysine analogues into recombinant proteins

The site-specific and degree-specific methylation of histone lysine residues is important for the regulation of chromatin. To study the biochemical roles of lysine methylation, several approaches have been developed to reconstitute chromatin fibers in vitro with well-defined methylation patterns. Here, we describe the installation of methyl-lysine analogues (MLAs) as a simple and scalable method to introduce mono-, di-, or trimethylation at specific sites of recombinantly expressed histones. In this method, a histone is engineered to harbor a lysine-to-cysteine mutation at the desired site of modification. These mutant histones are treated with halo-ethylamines that react with the cysteine side chain, providing high yields of N-methylated aminoethylcysteines, analogues of N-methylated lysine residues. These MLA histones have been used to construct well-defined chromatin templates to study the direct biochemical consequences of histone lysine methylation in a variety of contexts.