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1. The EZH2 SANT1 domain is a histone reader providing sensitivity to the modification state of the H4 tail

   https://doi.org/10.1038/s41598-018-37699-w  

   Weaver, Tyler M. ; Liu, Jiachen ; Connelly, Katelyn E. ; Coble, Chris ; Varzavand, Katayoun ; Dykhuizen, Emily C. ; Musselman, Catherine A. ( January 2019 , Scientific Reports)

   SANT domains are found in a number of chromatin regulators. They contain approximately 50 amino acids and have high similarity to the DNA binding domain of Myb related proteins. Though some SANT domains associate with DNA others have been found to bind unmodified histone tails. There are two SANT domains in Enhancer of Zeste 2 (EZH2), the catalytic subunit of the Polycomb Repressive Complex 2 (PRC2), of unknown function. Here we show that the first SANT domain (SANT1) of EZH2 is a histone binding domain with specificity for the histone H4 N-terminal tail. Using NMR spectroscopy, mutagenesis, and molecular modeling we structurally characterize the SANT1 domain and determine the molecular mechanism of binding to the H4 tail. Though not important for histone binding, we find that the adjacent stimulation response motif (SRM) stabilizes SANT1 and transiently samples its active form in solution. Acetylation of H4K16 (H4K16ac) or acetylation or methylation of H4K20 (H4K20ac and H4K20me3) are seen to abrogate binding of SANT1 to H4, which is consistent with these modifications being anti-correlated with H3K27me3in-vivo. Our results provide significant insight into this important regulatory region of EZH2 and the first characterization of the molecular mechanism of SANT domain histone binding.

    

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2. New twists of a TAIL: novel insights into the histone binding properties of a highly conserved PHD finger cluster within the MLR family of H3K4 mono-methyltransferases

   https://doi.org/10.1093/nar/gkad698  

   Zraly, Claudia B. ; Schultz, Richard ; Diaz, Manuel O. ; Dingwall, Andrew K. ( August 2023 , Nucleic Acids Research)

   Enhancer activation by the MLR family of H3K4 mono-methyltransferases requires proper recognition of histones for the deposition of the mono-methyl mark. MLR proteins contain two clusters of PHD zinc finger domains implicated in chromatin regulation. The second cluster is the most highly conserved, preserved as an ancient three finger functional unit throughout evolution. Studies of the isolated 3rd PHD finger within this cluster suggested specificity for the H4 [aa16–20] tail region. We determined the histone binding properties of the full three PHD finger cluster b module (PHDb) from the Drosophila Cmi protein which revealed unexpected recognition of an extended region of H3. Importantly, the zinc finger spacer separating the first two PHDb fingers from the third is critical for proper alignment and coordination among fingers for maximal histone engagement. Human homologs, MLL3 and MLL4, also show conservation of H3 binding, expanding current views of histone recognition for this class of proteins. We further implicate chromatin remodeling by the SWI/SNF complex as a possible mechanism for the accessibility of PHDb to globular regions of histone H3 beyond the tail region. Our results suggest a two-tail histone recognition mechanism by the conserved PHDb domain involving a flexible hinge to promote interdomain coordination.

    

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3. Evaluation of acyllysine isostere interactions with the aromatic pocket of the AF9 YEATS domain

   https://doi.org/10.1002/pro.4533  

   Travis, Christopher R. ; Francis, Denver Y. ; Williams, Jr., David C. ; Waters, Marcey L. ( December 2022 , Protein Science)

   Amide−π interactions, in which an amide interacts with an aromatic group, are ubiquitous in biology, yet remain understudied relative to other noncovalent interactions. Recently, we demonstrated that an electrostatically tunable amide−π interaction is key to recognition of histone acyllysine by the AF9 YEATS domain, a reader protein which has emerged as a therapeutic target due to its dysregulation in cancer. Amide isosteres are commonly employed in drug discovery, often to prevent degradation by proteases, and have proven valuable in achieving selectivity when targeting epigenetic proteins. However, like amide−π interactions, interactions of amide isosteres with aromatic rings have not been thoroughly studied despite widespread use. Herein, we evaluate the recognition of a series of amide isosteres by the AF9 YEATS domain using genetic code expansion to evaluate the amide isostere−π interaction. We show that compared to the amide−π interaction with the native ligand, each isostere exhibits similar electrostatic tunability with an aromatic residue in the binding pocket, demonstrating that the isosteres maintain similar interactions with the aromatic residue. We identify a urea‐containing ligand that binds with enhanced affinity for the AF9 YEATS domain, offering a promising starting point for inhibitor development. Furthermore, we demonstrate that carbamate and urea isosteres of crotonyllysine are resistant to enzymatic removal by SIRT1, a protein that cleaves acyl post‐translational modifications, further indicating the potential of amide isosteres in YEATS domain inhibitor development. These results also provide experimental precedent for interactions of these common drug discovery moieties with aromatic rings that can inform computational methods.

    

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4. Not all Is SET for Methylation: Evolution of Eukaryotic Protein Methyltransferases

   https://doi.org/10.1007/978-1-0716-2481-4_1  

   Erlendson AA ; Freitag M ( June 2022 , Methods in molecular biology)

   Margueron R ; Holoch D (Ed.)

   Dynamic posttranslational modifications to canonical histones that constitute the nucleosome (H2A, H2B, H3, and H4) control all aspects of enzymatic transactions with DNA. Histone methylation has been studied heavily for the past 20 years, and our mechanistic understanding of the control and function of individual methylation events on specific histone arginine and lysine residues has been greatly improved over the past decade, driven by excellent new tools and methods. Here, we will summarize what is known about the distribution and some of the functions of protein methyltransferases from all major eukaryotic supergroups. The main conclusion is that protein, and specifically histone, methylation is an ancient process. Many taxa in all supergroups have lost some subfamilies of both protein arginine methyltransferases (PRMT) and the heavily studied SET domain lysine methyltransferases (KMT). Over time, novel subfamilies, especially of SET domain proteins, arose. We use the interactions between H3K27 and H3K36 methylation as one example for the complex circuitry of histone modifications that make up the “histone code,” and we discuss one recent example (Paramecium Ezl1) for how extant enzymes that may resemble more ancient SET domain KMTs are able to modify two lysine residues that have divergent functions in plants, fungi, and animals. Complexity of SET domain KMT function in the well-studied plant and animal lineages arose not only by gene duplication but also acquisition of novel DNA- and histone-binding domains in certain subfamilies. 

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5. The conformation of the histone H3 tail inhibits association of the BPTF PHD finger with the nucleosome

   https://doi.org/10.7554/eLife.31481  

   Morrison, Emma A ; Bowerman, Samuel ; Sylvers, Kelli L ; Wereszczynski, Jeff ; Musselman, Catherine A ( April 2018 , eLife)

   The human genome contains all the instructions needed to build the human body. However, each human cell does not read all of these instructions, which come in the form of genes encoded in the DNA. Instead, different subsets of genes are switched on in each type of cell, while the rest of the genes are switched off. DNA within human cells is wrapped around proteins called histones, to form hundreds of thousands of structures called nucleosomes. If the DNA that encodes a gene contains a lot of nucleosomes, the DNA is not very accessible and the gene will generally be off; removing the histones or rearranging the nucleosomes can turn the gene on. Each histone contains a region called a tail – because it protrudes like the tail of a cat – that can be chemically modified in dozens of different ways. Particular combinations of histone modifications are thought to signal how the nucleosomes should be arranged so that each gene is properly regulated. However, it is unclear how these combinations of modifications actually work because, historically, it has been difficult to study tails in the context of a nucleosome. Instead most studies had looked at tails that had been removed from the nucleosome. Now, Morrison et al. set out to investigate how one protein, called BPTF, recognizes a specific chemical modification on the tail of a histone, referred to as H3K4me3, in the context of a human nucleosome. Unexpectedly, the experiments showed that the histone-binding domain of BPTF, which binds to H3K4me3, was impeded when the tail was attached to the nucleosome but not when it was removed from the nucleosome. Morrison et al. went on to show that this was because the histone tail is tucked onto the rest of the nucleosome and not easily accessible. Further experiments revealed that additional chemical modifications made the tail more accessible, making it easier for the histone-binding domain to bind. Together these findings show that a combination of histone modifications acts to positively regulate the binding of a regulatory protein to H3K4me3 in the context of the nucleosome by actually regulating the nucleosome itself. The disruption of the histone signals is known to lead to a number of diseases, including cancer, autoimmune disease, and neurological disorders, and these findings could guide further research that may lead to new treatments. Yet first, much more work is needed to investigate how other histone modifications are recognized in the context of the nucleosome, and how the large number of possible combinations of histone signals affects this process. 

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