Manuel M. Müller

Inhibition of PRC2 Activity by a Gain-of-Function H3 Mutation Found in Pediatric Glioblastoma

EZ Inhibition Missense mutations in the core constituents of the genome packaging material, chromatin, have been implicated in several of human cancers. Nucleosomes are made up of histones, and a mutation of lysine 27 (K27) to methionine in the N-terminal tail of histone variants H3.3 and H3.1 has been identified in various pediatric gliomas. Lewis et al. (p. 857, published online 28 March; see the Perspective by Morgan and Shilatifard) show that the polycomb enzyme complex, which can epigenetically modify K27 by addition of a methyl group—and which is often a silencing signal—is itself potently inhibited by replacement of the H3.3/3.1 K27 by methionine. The inhibition of the EZH2 subunit causes an overall reduction of K27 methylation. Methionine mutants of other methylated lysine residues in histone H3 cause similar reductions in methylation levels of the cognate lysine, altering the epigenetic profiles of such cancer cells. Mutations of histones in some cancers result in inhibition of enzymes that lay down epigenetic marks on chromatin. [Also see Perspective by Morgan and Shilatifard] Sequencing of pediatric gliomas has identified missense mutations Lys27Met (K27M) and Gly34Arg/Val (G34R/V) in genes encoding histone H3.3 (H3F3A) and H3.1 (HIST3H1B). We report that human diffuse intrinsic pontine gliomas (DIPGs) containing the K27M mutation display significantly lower overall amounts of H3 with trimethylated lysine 27 (H3K27me3) and that histone H3K27M transgenes are sufficient to reduce the amounts of H3K27me3 in vitro and in vivo. We find that H3K27M inhibits the enzymatic activity of the Polycomb repressive complex 2 through interaction with the EZH2 subunit. In addition, transgenes containing lysine-to-methionine substitutions at other known methylated lysines (H3K9 and H3K36) are sufficient to cause specific reduction in methylation through inhibition of SET-domain enzymes. We propose that K-to-M substitutions may represent a mechanism to alter epigenetic states in a variety of pathologies.

A rationally designed aldolase foldamer.

Current strategies for creating enzyme-like catalysts range from rational[1] and computational design[2] to evolutionary searches of large molecular libraries.[3] Sequence-specific polymers are particularly attractive starting points for these efforts because of their ability to adopt three-dimensional structures that preorganize functional groups for catalysis. Although natural enzymes are constructed from α-amino acids, many other backbone structures can give rise to well-defined secondary and tertiary structures. Such non-natural oligomers, often referred to as “foldamers”, have the potential to display properties akin to those of proteins.[4–8]

Accelerated chromatin biochemistry using DNA-barcoded nucleosome libraries

Elucidating the molecular details of how chromatin-associated factors deposit, remove and recognize histone post-translational modification (PTM) signatures remains a daunting task in the epigenetics field. We introduce a versatile platform that greatly accelerates biochemical investigations into chromatin recognition and signaling. This technology is based on the streamlined semisynthesis of DNA-barcoded nucleosome libraries with distinct combinations of PTMs. Chromatin immunoprecipitation of these libraries, once they have been treated with purified chromatin effectors or the combined chromatin recognizing and modifying activities of the nuclear proteome, is followed by multiplexed DNA-barcode sequencing. This ultrasensitive workflow allowed us to collect thousands of biochemical data points revealing the binding preferences of various nuclear factors for PTM patterns and how preexisting PTMs, alone or synergistically, affect further PTM deposition via cross-talk mechanisms. We anticipate that the high throughput and sensitivity of the technology will help accelerate the decryption of the diverse molecular controls that operate at the level of chromatin.

Histones: at the crossroads of peptide and protein chemistry.

In eukaryotic cells, inheritable information is stored in a nucleoprotein complex referred to as chromatin.1 This genome architecture serves two key purposes. On the one hand, wrapping DNA (approximately 145–147 basepairs) twice around a spool composed of two copies each of the highly basic core histones H2A, H2B, H3, and H4 leads to compaction of DNA strands (Figure ​(Figure1a,b).1a,b). These assemblies are called nucleosomes. Contacts between individual nucleosomes are often mediated by cationic tails at the N- and C-termini of all histone proteins that protrude from the core and further tighten the chromatin fiber (Figure ​(Figure1c).1c). Additional packing is achieved through attachment of histone H1 to the DNA that links neighboring nucleosomes or by nonhistone proteins that are able to bridge units within or between chromatin fibers.2 The second pivotal function of storing genetic information as a DNA–protein complex is the additional layer of regulation that this feature provides.3−5 For instance, the very presence of histones on DNA sequences can occlude access to these sites by transcription factors and other DNA binding proteins.6 Thus, nucleosome positioning, shaped in part by DNA sequence preferences and shifted by ATP-powered molecular motors (referred to as chromatin remodelers), directly affects chromatin transactions.7 Beyond their location, the biochemical makeup of nucleosomes provides further opportunity for regulation. Canonical histones can be replaced with closely resembling variants, and all histones are dynamically decorated with post-translational modifications (PTMs). These biochemical marks can be as small as just a few atoms, such as methyl (Lys, Arg, Gln), acetyl (Lys), or phosphoryl groups (Ser, Thr), or as large as an entire protein in the case of ubiquitin or SUMO. Upon attachment by dedicated transferase enzymes, PTMs can directly alter the biophysical properties of the target protein, provide a docking site for specific interaction partners, interfere with binding events of other factors, or act through a combination of these mechanisms. In this way, signaling through histone PTMs serves to orchestrate chromatin-templated processes, including fine-tuning transcriptional outputs. Remarkably, transcriptional states can be inherited through cell division cycles, thus providing a mode of epigenetic memory.8,9 Not surprisingly, misregulation of the inputs and outputs of chromatin signaling occurs in many diseases, especially cancer.10−13 Figure 1 Chromatin architecture in eukaryotic cells. (a) Structure of a mononucleosome. DNA (gray) is wrapped around two copies each of H2A (orange), H2B (red), H3 (blue), and H4 (green); pdb code: 1kx5. (b) Electrostatic surface rendering of a histone octamer. ...

Strategy for “Detoxification” of a Cancer-Derived Histone Mutant Based on Mapping Its Interaction with the Methyltransferase PRC2

The histone methyltransferase PRC2 plays a central role in genomic stability and cellular development. Consequently, its misregulation has been implicated in several cancers. Recent work has shown that a histone H3 mutant, where the PRC2 substrate residue Lys27 is replaced by methionine, is also associated with cancer phenotypes and functions as an inhibitor of PRC2. Here we investigate the mechanism of this PRC2 inhibition through kinetic studies and photo-cross-linking. Efficient inhibition is dependent on (1) hydrophobic lysine isosteres blocking the active site, (2) proximal residues, and (3) the H3 tail forming extensive contacts with the EZH2 subunit of PRC2. We further show that naturally occurring post-translational modifications of the same H3 tail, both proximal and distal to K27M, can greatly diminish the inhibition of PRC2. These results suggest that this potent gain of function mutation may be “detoxified” by modulating alternate chromatin modification pathways.

A two-state activation mechanism controls the histone methyltransferase Suv39h1

Specialized chromatin domains contribute to nuclear organization and regulation of gene expression. Gene-poor regions are di- and trimethylated at lysine 9 of histone H3 (H3K9me2/3) by the histone methyltransferase, Suv39h1. This enzyme harnesses a positive feedback loop to spread H3K9me2/3 over extended heterochromatic regions. However, little is known about how feedback loops operate on complex biopolymers such as chromatin, in part because of the difficulty in obtaining suitable substrates. Here we describe the synthesis of multi-domain ‘designer chromatin’ templates and their application to dissecting the regulation of human Suv39h1. We uncovered a two-step activation switch where H3K9me3 recognition and subsequent anchoring of the enzyme to chromatin allosterically promotes methylation activity, and confirmed that this mechanism contributes to chromatin recognition in cells. We propose that this mechanism serves as a paradigm in chromatin biochemistry since it enables highly dynamic sampling of chromatin state combined with targeted modification of desired genomic regions.

Building Proficient Enzymes with Foldamer Prostheses

Foldamers are non-natural oligomers that adopt stable conformations reminiscent of those found in proteins. To evaluate the potential of foldameric subunits for catalysis, semisynthetic enzymes containing foldamer fragments constructed from α- and β-amino acid residues were designed and characterized. Systematic variation of the α→β substitution pattern and types of β-residue afforded highly proficient hybrid catalysts, thus demonstrating the feasibility of expanding the enzyme-engineering toolkit with non-natural backbones.

Directed evolution of a model primordial enzyme provides insights into the development of the genetic code.

The contemporary proteinogenic repertoire contains 20 amino acids with diverse functional groups and side chain geometries. Primordial proteins, in contrast, were presumably constructed from a subset of these building blocks. Subsequent expansion of the proteinogenic alphabet would have enhanced their capabilities, fostering the metabolic prowess and organismal fitness of early living systems. While the addition of amino acids bearing innovative functional groups directly enhances the chemical repertoire of proteomes, the inclusion of chemically redundant monomers is difficult to rationalize. Here, we studied how a simplified chorismate mutase evolves upon expanding its amino acid alphabet from nine to potentially 20 letters. Continuous evolution provided an enhanced enzyme variant that has only two point mutations, both of which extend the alphabet and jointly improve protein stability by >4 kcal/mol and catalytic activity tenfold. The same, seemingly innocuous substitutions (Ile→Thr, Leu→Val) occurred in several independent evolutionary trajectories. The increase in fitness they confer indicates that building blocks with very similar side chain structures are highly beneficial for fine-tuning protein structure and function.

Design, selection, and characterization of a split chorismate mutase

Split proteins are versatile tools for detecting protein–protein interactions and studying protein folding. Here, we report a new, particularly small split enzyme, engineered from a thermostable chorismate mutase (CM). Upon dissecting the helical‐bundle CM from Methanococcus jannaschii into a short N‐terminal helix and a 3‐helix segment and attaching an antiparallel leucine zipper dimerization domain to the individual fragments, we obtained a weakly active heterodimeric mutase. Using combinatorial mutagenesis and in vivo selection, we optimized the short linker sequences connecting the leucine zipper to the enzyme domain. One of the selected CMs was characterized in detail. It spontaneously assembles from the separately inactive fragments and exhibits wild‐type like CM activity. Owing to the availability of a well characterized selection system, the simple 4‐helix bundle topology, and the small size of the N‐terminal helix, the heterodimeric CM could be a valuable scaffold for enzyme engineering efforts and as a split sensor for specifically oriented protein–protein interactions.

ISWI chromatin remodellers sense nucleosome modifications to determine substrate preference

ATP-dependent chromatin remodellers regulate access to genetic information by controlling nucleosome positions in vivo. However, the mechanism by which remodellers discriminate between different nucleosome substrates is poorly understood. Many chromatin remodelling proteins possess conserved protein domains that interact with nucleosomal features. Here we used a quantitative high-throughput approach, based on the use of a DNA-barcoded mononucleosome library, to profile the biochemical activity of human ISWI family remodellers in response to a diverse set of nucleosome modifications. We show that accessory (non-ATPase) subunits of ISWI remodellers can distinguish between differentially modified nucleosomes, directing remodelling activity towards specific nucleosome substrates according to their modification state. Unexpectedly, we show that the nucleosome acidic patch is necessary for maximum activity of all ISWI remodellers evaluated. This dependence also extends to CHD and SWI/SNF family remodellers, suggesting that the acidic patch may be generally required for chromatin remodelling. Critically, remodelling activity can be regulated by modifications neighbouring the acidic patch, signifying that it may act as a tunable interaction hotspot for ATP-dependent chromatin remodellers and, by extension, many other chromatin effectors that engage this region of the nucleosome surface.