Modern techniques in molecular biology, genomics, and mass spectrometry-based proteomics have identified a large number of novel histone posttranslational modifications (PTMs), many of whose ...functions are still under intense investigation. Here, we catalog histone PTMs under two classes: first, those whose functions have been fairly well studied and, second, those PTMs that have been more recently identified but whose functions remain unclear. We hope that this will be a useful resource for researchers from all biological or technical backgrounds, aiding in their chromatin and epigenetic pursuits.
Interactions between noncoding RNAs and chromatin proteins play important roles in gene regulation, but the molecular details of most of these interactions are unknown. Using protein-RNA ...photocrosslinking and mass spectrometry on embryonic stem cell nuclei, we identified and mapped, at peptide resolution, the RNA-binding regions in ∼800 known and previously unknown RNA-binding proteins, many of which are transcriptional regulators and chromatin modifiers. In addition to known RNA-binding motifs, we detected several protein domains previously unknown to function in RNA recognition, as well as non-annotated and/or disordered regions, suggesting that many functional protein-RNA contacts remain unexplored. We identified RNA-binding regions in several chromatin regulators, including TET2, and validated their ability to bind RNA. Thus, proteomic identification of RNA-binding regions (RBR-ID) is a powerful tool to map protein-RNA interactions and will allow rational design of mutants to dissect their function at a mechanistic level.
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•RBR-ID identifies RNA-binding regions by 4SU photocrosslinking and mass spectrometry•RBRs were mapped in 803 nuclear RNA-binding proteins (RBPs) in embryonic stem cells•Many previously unknown RBPs regulate chromatin structure and transcription•RBRs were found in disordered regions and domains associated with chromatin function
Using 4SU-mediated photocrosslinking and quantitative mass spectrometry, He et al. map RNA-binding regions in hundreds of known and unknown RNA-binding proteins in the nuclei of embryonic stem cells, suggesting that RNA binding is a common feature of chromatin-associated proteins and transcriptional regulators.
The histone lysine methyltransferase NSD2 (MMSET/WHSC1) is implicated in diverse diseases and commonly overexpressed in multiple myeloma due to a recurrent t(4;14) chromosomal translocation. However, ...the precise catalytic activity of NSD2 is obscure, preventing progress in understanding how this enzyme influences chromatin biology and myeloma pathogenesis. Here, we show that dimethylation of histone H3 at lysine 36 (H3K36me2) is the principal chromatin-regulatory activity of NSD2. Catalysis of H3K36me2 by NSD2 is sufficient for gene activation. In t(4;14)-positive myeloma cells, the normal genome-wide and gene-specific distribution of H3K36me2 is obliterated, creating a chromatin landscape that selects for a transcription profile favorable for myelomagenesis. Catalytically active NSD2 confers xenograft tumor formation upon t(4;14)-negative cells and promotes oncogenic transformation of primary cells in an H3K36me2-dependent manner. Together, our findings establish H3K36me2 as the primary product generated by NSD2 and demonstrate that genomic disorganization of this canonical chromatin mark by NSD2 initiates oncogenic programming.
► Dimethylation of H3K36 is the principal chromatin-regulatory activity of NSD2 ► NSD2, via H3K36me2 catalysis, promotes transcription and cell transformation ► NSD2 links genomic disorganization of H3K36me2 to oncogenic programming ► NSD2 catalytic activity is required for t(4;14)+ myeloma cell tumorigenicity
Monomethylation of histone H3 at lysine 4 (H3K4me1) and acetylation of histone H3 at lysine 27 (H3K27ac) are correlated with transcriptionally engaged enhancer elements, but the functional impact of ...these modifications on enhancer activity is not well understood. Here we used CRISPR/Cas9 genome editing to separate catalytic activity-dependent and independent functions of Mll3 (Kmt2c) and Mll4 (Kmt2d, Mll2), the major enhancer H3K4 monomethyltransferases. Loss of H3K4me1 from enhancers in Mll3/4 catalytically deficient cells causes partial reduction of H3K27ac, but has surprisingly minor effects on transcription from either enhancers or promoters. In contrast, loss of Mll3/4 proteins leads to strong depletion of enhancer Pol II occupancy and eRNA synthesis, concomitant with downregulation of target genes. Interestingly, downregulated genes exhibit reduced polymerase levels in gene bodies, but not at promoters, suggestive of pause-release defects. Altogether, our results suggest that enhancer H3K4me1 provides only a minor contribution to the long-range coactivator function of Mll3/4.
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•H3K4me1 at active enhancers is not required for transcription of nearby genes•Mll3/4 function as long-range coactivators independent of their catalytic activity•Mll3/4 facilitate Pol II loading and eRNA synthesis at enhancers•Loss of Mll3/4 from enhancers reduces Pol II density in bodies of adjacent genes
Dorighi et al. investigate the function of H3K4me1, an enhancer modification catalyzed by Mll3 and Mll4. They find that while H3K4me1 partially supports H3K27ac at active enhancers, it is largely dispensable for transcription. By contrast, Mll3/4 proteins themselves are required for enhancer Pol II loading, eRNA synthesis, and gene expression.
Lysine-specific demethylase 1 (LSD1) has been reported to repress and activate transcription by mediating histone H3K4me1/2 and H3K9me1/2 demethylation, respectively. The molecular mechanism that ...underlies this dual substrate specificity has remained unknown. Here we report that an isoform of LSD1, LSD1+8a, does not have the intrinsic capability to demethylate H3K4me2. Instead, LSD1+8a mediates H3K9me2 demethylation in collaboration with supervillin (SVIL), a new LSD1+8a interacting protein. LSD1+8a knockdown increases H3K9me2, but not H3K4me2, levels at its target promoters and compromises neuronal differentiation. Importantly, SVIL co-localizes to LSD1+8a-bound promoters, and its knockdown mimics the impact of LSD1+8a loss, supporting SVIL as a cofactor for LSD1+8a in neuronal cells. These findings provide insight into mechanisms by which LSD1 mediates H3K9me demethylation and highlight alternative splicing as a means by which LSD1 acquires selective substrate specificities (H3K9 versus H3K4) to differentially control specific gene expression programs in neurons.
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•LSD1+8a isoform does not have the intrinsic property to demethylate H3K4•LSD1+8a functions as a co-activator by demethylating the repressive H3K9me2 mark•LSD1+8a interacts with SVIL; LSD1+8a/SVIL-containing complex demethylates H3K9me2•SVIL regulates neuronal maturation by controlling LSD1+8a mediated H3K9 demethylation
Benoit Laurent et al. find that the neuro-enriched LSD1 isoform, LSD1+8a, mediates H3K9me2 demethylation in collaboration with the supervillin protein (SVIL), a new LSD1+8a partner. These findings highlight alternative splicing as a means by which LSD1 acquires selective substrate specificities (H3K9 versus H3K4) to control specific transcriptional programs in neurons.
Turnover and exchange of nucleosomal histones and their variants, a process long believed to be static in post-replicative cells, remains largely unexplored in brain. Here, we describe a novel ...mechanistic role for HIRA (histone cell cycle regulator) and proteasomal degradation-associated histone dynamics in the regulation of activity-dependent transcription, synaptic connectivity, and behavior. We uncover a dramatic developmental profile of nucleosome occupancy across the lifespan of both rodents and humans, with the histone variant H3.3 accumulating to near-saturating levels throughout the neuronal genome by mid-adolescence. Despite such accumulation, H3.3-containing nucleosomes remain highly dynamic—in a modification-independent manner—to control neuronal- and glial-specific gene expression patterns throughout life. Manipulating H3.3 dynamics in both embryonic and adult neurons confirmed its essential role in neuronal plasticity and cognition. Our findings establish histone turnover as a critical and previously undocumented regulator of cell type-specific transcription and plasticity in mammalian brain.
•H3.3 displays a unique saturating profile of nucleosome occupancy in postnatal brain•Histones turn over rapidly to promote activity-dependent neuronal transcription•Nucleosomal dynamics are required for synaptic development and behavioral plasticity•Histone turnover is critical for cell type-specific gene expression
Maze et al. demonstrate a critical role for histone turnover in the regulation of neuronal transcription and synaptic development. Histone dynamics are essential for cognitive plasticity and represent a novel epigenetic mechanism with far-reaching implications for human neurobiology and disease.
Chimeric antigen receptor (CAR) T cell therapy has shown promise in hematologic malignancies, but its application to solid tumors has been challenging
. Given the unique effector functions of ...macrophages and their capacity to penetrate tumors
, we genetically engineered human macrophages with CARs to direct their phagocytic activity against tumors. We found that a chimeric adenoviral vector overcame the inherent resistance of primary human macrophages to genetic manipulation and imparted a sustained pro-inflammatory (M1) phenotype. CAR macrophages (CAR-Ms) demonstrated antigen-specific phagocytosis and tumor clearance in vitro. In two solid tumor xenograft mouse models, a single infusion of human CAR-Ms decreased tumor burden and prolonged overall survival. Characterization of CAR-M activity showed that CAR-Ms expressed pro-inflammatory cytokines and chemokines, converted bystander M2 macrophages to M1, upregulated antigen presentation machinery, recruited and presented antigen to T cells and resisted the effects of immunosuppressive cytokines. In humanized mouse models, CAR-Ms were further shown to induce a pro-inflammatory tumor microenvironment and boost anti-tumor T cell activity.
Asymmetrically Modified Nucleosomes Voigt, Philipp; LeRoy, Gary; Drury, William J., III ...
Cell,
09/2012, Letnik:
151, Številka:
1
Journal Article
Recenzirano
Odprti dostop
Mononucleosomes, the basic building blocks of chromatin, contain two copies of each core histone. The associated posttranslational modifications regulate essential chromatin-dependent processes, yet ...whether each histone copy is identically modified in vivo is unclear. We demonstrate that nucleosomes in embryonic stem cells, fibroblasts, and cancer cells exist in both symmetrically and asymmetrically modified populations for histone H3 lysine 27 di/trimethylation (H3K27me2/3) and H4K20me1. Further, we obtained direct physical evidence for bivalent nucleosomes carrying H3K4me3 or H3K36me3 along with H3K27me3, albeit on opposite H3 tails. Bivalency at target genes was resolved upon differentiation of ES cells. Polycomb repressive complex 2-mediated methylation of H3K27 was inhibited when nucleosomes contain symmetrically, but not asymmetrically, placed H3K4me3 or H3K36me3. These findings uncover a potential mechanism for the incorporation of bivalent features into nucleosomes and demonstrate how asymmetry might set the stage to diversify functional nucleosome states.
SnapShot: Histone Modifications Huang, He; Sabari, Benjamin R.; Garcia, Benjamin A. ...
Cell,
10/2014, Letnik:
159, Številka:
2
Journal Article
Recenzirano
Odprti dostop
Histone proteins are decorated by a variety of protein posttranslational modifications called histone marks that modulate chromatin structure and function, contributing to the cellular gene ...expression program. This SnapShot summarizes the reported human, mouse, and rat histone marks, including recently identified lysine acylation marks.
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