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1.
Mol Cell ; 82(21): 4080-4098.e12, 2022 11 03.
Article in English | MEDLINE | ID: mdl-36272410

ABSTRACT

Growing evidence suggests prevalence of transcriptional condensates on chromatin, yet their mechanisms of formation and functional significance remain largely unclear. In human cancer, a series of mutations in the histone acetylation reader ENL create gain-of-function mutants with increased transcriptional activation ability. Here, we show that these mutations, clustered in ENL's structured acetyl-reading YEATS domain, trigger aberrant condensates at native genomic targets through multivalent homotypic and heterotypic interactions. Mechanistically, mutation-induced structural changes in the YEATS domain, ENL's two disordered regions of opposing charges, and the incorporation of extrinsic elongation factors are all required for ENL condensate formation. Extensive mutagenesis establishes condensate formation as a driver of oncogenic gene activation. Furthermore, expression of ENL mutants beyond the endogenous level leads to non-functional condensates. Our findings provide new mechanistic and functional insights into cancer-associated condensates and support condensate dysregulation as an oncogenic mechanism.


Subject(s)
Neoplasms , Nuclear Bodies , Humans , Protein Domains , Chromatin/genetics , Mutation , Neoplasms/genetics
2.
Cell ; 159(3): 558-71, 2014 Oct 23.
Article in English | MEDLINE | ID: mdl-25417107

ABSTRACT

The recognition of modified histones by "reader" proteins constitutes a key mechanism regulating gene expression in the chromatin context. Compared with the great variety of readers for histone methylation, few protein modules that recognize histone acetylation are known. Here, we show that the AF9 YEATS domain binds strongly to histone H3K9 acetylation and, to a lesser extent, H3K27 and H3K18 acetylation. Crystal structural studies revealed that AF9 YEATS adopts an eight-stranded immunoglobin fold and utilizes a serine-lined aromatic "sandwiching" cage for acetyllysine readout, representing a novel recognition mechanism that is distinct from that of known acetyllysine readers. ChIP-seq experiments revealed a strong colocalization of AF9 and H3K9 acetylation genome-wide, which is important for the chromatin recruitment of the H3K79 methyltransferase DOT1L. Together, our studies identified the evolutionarily conserved YEATS domain as a novel acetyllysine-binding module and established a direct link between histone acetylation and DOT1L-mediated H3K79 methylation in transcription control.


Subject(s)
Histone Code , Methyltransferases/chemistry , Methyltransferases/metabolism , Nuclear Proteins/chemistry , Nuclear Proteins/metabolism , Acetylation , Amino Acid Sequence , Gene Expression Regulation , Histone Acetyltransferases/chemistry , Histone Acetyltransferases/metabolism , Histone-Lysine N-Methyltransferase , Histones/metabolism , Humans , Methylation , Models, Molecular , Molecular Sequence Data , Protein Processing, Post-Translational , Protein Structure, Tertiary , Saccharomyces cerevisiae/metabolism , Saccharomyces cerevisiae Proteins/chemistry , Saccharomyces cerevisiae Proteins/metabolism , Sequence Alignment , Transcription, Genetic
3.
Nature ; 620(7974): 669-675, 2023 Aug.
Article in English | MEDLINE | ID: mdl-37468628

ABSTRACT

Context-dependent dynamic histone modifications constitute a key epigenetic mechanism in gene regulation1-4. The Rpd3 small (Rpd3S) complex recognizes histone H3 trimethylation on lysine 36 (H3K36me3) and deacetylates histones H3 and H4 at multiple sites across transcribed regions5-7. Here we solved the cryo-electron microscopy structures of Saccharomyces cerevisiae Rpd3S in its free and H3K36me3 nucleosome-bound states. We demonstrated a unique architecture of Rpd3S, in which two copies of Eaf3-Rco1 heterodimers are asymmetrically assembled with Rpd3 and Sin3 to form a catalytic core complex. Multivalent recognition of two H3K36me3 marks, nucleosomal DNA and linker DNAs by Eaf3, Sin3 and Rco1 positions the catalytic centre of Rpd3 next to the histone H4 N-terminal tail for deacetylation. In an alternative catalytic mode, combinatorial readout of unmethylated histone H3 lysine 4 and H3K36me3 by Rco1 and Eaf3 directs histone H3-specific deacetylation except for the registered histone H3 acetylated lysine 9. Collectively, our work illustrates dynamic and diverse modes of multivalent nucleosomal engagement and methylation-guided deacetylation by Rpd3S, highlighting the exquisite complexity of epigenetic regulation with delicately designed multi-subunit enzymatic machineries in transcription and beyond.


Subject(s)
Histones , Lysine , Methylation , Multiprotein Complexes , Nucleosomes , Saccharomyces cerevisiae Proteins , Saccharomyces cerevisiae , Acetylation , Cryoelectron Microscopy , DNA, Fungal/genetics , DNA, Fungal/metabolism , Epigenesis, Genetic , Histones/chemistry , Histones/metabolism , Lysine/metabolism , Nucleosomes/chemistry , Nucleosomes/metabolism , Saccharomyces cerevisiae/genetics , Saccharomyces cerevisiae/metabolism , Saccharomyces cerevisiae Proteins/metabolism , Multiprotein Complexes/chemistry , Multiprotein Complexes/metabolism
4.
Cell ; 153(5): 1012-24, 2013 May 23.
Article in English | MEDLINE | ID: mdl-23706739

ABSTRACT

Histone acetylation plays critical roles in chromatin remodeling, DNA repair, and epigenetic regulation of gene expression, but the underlying mechanisms are unclear. Proteasomes usually catalyze ATP- and polyubiquitin-dependent proteolysis. Here, we show that the proteasomes containing the activator PA200 catalyze the polyubiquitin-independent degradation of histones. Most proteasomes in mammalian testes ("spermatoproteasomes") contain a spermatid/sperm-specific α subunit α4 s/PSMA8 and/or the catalytic ß subunits of immunoproteasomes in addition to PA200. Deletion of PA200 in mice abolishes acetylation-dependent degradation of somatic core histones during DNA double-strand breaks and delays core histone disappearance in elongated spermatids. Purified PA200 greatly promotes ATP-independent proteasomal degradation of the acetylated core histones, but not polyubiquitinated proteins. Furthermore, acetylation on histones is required for their binding to the bromodomain-like regions in PA200 and its yeast ortholog, Blm10. Thus, PA200/Blm10 specifically targets the core histones for acetylation-mediated degradation by proteasomes, providing mechanisms by which acetylation regulates histone degradation, DNA repair, and spermatogenesis.


Subject(s)
DNA Repair , Histones/metabolism , Nuclear Proteins/metabolism , Proteasome Endopeptidase Complex/metabolism , Spermatogenesis , Testis/metabolism , Acetylation , Amino Acid Sequence , Animals , DNA Breaks, Double-Stranded , Humans , Male , Mice , Molecular Sequence Data , Nuclear Proteins/chemistry , Protein Structure, Tertiary , Saccharomyces cerevisiae/metabolism , Saccharomyces cerevisiae Proteins/metabolism , Sequence Alignment
5.
Mol Cell ; 76(4): 646-659.e6, 2019 11 21.
Article in English | MEDLINE | ID: mdl-31543422

ABSTRACT

Eukaryotic chromosomes contain compartments of various functions, which are marked by and enriched with specific histone modifications. However, the molecular mechanisms by which these histone marks function in chromosome compartmentalization are poorly understood. Constitutive heterochromatin is a largely silent chromosome compartment characterized in part by H3K9me2 and 3. Here, we show that heterochromatin protein 1 (HP1), an H3K9me2 and 3 "reader," interacts with SUV39H1, an H3K9me2 and 3 "writer," and with TRIM28, an abundant HP1 scaffolding protein, to form complexes with increased multivalent engagement of H3K9me2 and 3-modified chromatin. H3K9me2 and 3-marked nucleosomal arrays and associated complexes undergo phase separation to form macromolecule-enriched liquid droplets. The droplets are reminiscent of heterochromatin as they are highly dense chromatin-containing structures that are resistant to DNase and exclude the general transcription factor TFIIB. Our data suggest a general mechanism by which histone marks regulate chromosome compartmentalization by promoting phase separation.


Subject(s)
Chromatin Assembly and Disassembly , Heterochromatin/metabolism , Histones/metabolism , Lipid Droplets/metabolism , Nucleosomes/metabolism , Protein Processing, Post-Translational , Chromobox Protein Homolog 5 , Chromosomal Proteins, Non-Histone/genetics , Chromosomal Proteins, Non-Histone/metabolism , HEK293 Cells , Heterochromatin/genetics , Humans , Methylation , Methyltransferases/genetics , Methyltransferases/metabolism , Multiprotein Complexes , Nucleosomes/genetics , Repressor Proteins/genetics , Repressor Proteins/metabolism , Time Factors , Tripartite Motif-Containing Protein 28/genetics , Tripartite Motif-Containing Protein 28/metabolism
6.
Mol Cell ; 76(3): 516-527.e7, 2019 11 07.
Article in English | MEDLINE | ID: mdl-31492635

ABSTRACT

The PTEN tumor suppressor is frequently mutated or deleted in cancer and regulates glucose metabolism through the PI3K-AKT pathway. However, whether PTEN directly regulates glycolysis in tumor cells is unclear. We demonstrate here that PTEN directly interacts with phosphoglycerate kinase 1 (PGK1). PGK1 functions not only as a glycolytic enzyme but also as a protein kinase intermolecularly autophosphorylating itself at Y324 for activation. The protein phosphatase activity of PTEN dephosphorylates and inhibits autophosphorylated PGK1, thereby inhibiting glycolysis, ATP production, and brain tumor cell proliferation. In addition, knockin expression of a PGK1 Y324F mutant inhibits brain tumor formation. Analyses of human glioblastoma specimens reveals that PGK1 Y324 phosphorylation levels inversely correlate with PTEN expression status and are positively associated with poor prognosis in glioblastoma patients. This work highlights the instrumental role of PGK1 autophosphorylation in its activation and PTEN protein phosphatase activity in governing glycolysis and tumorigenesis.


Subject(s)
Brain Neoplasms/enzymology , Glioblastoma/enzymology , Glucose/metabolism , Glycolysis , PTEN Phosphohydrolase/metabolism , Phosphoglycerate Kinase/metabolism , Adenosine Triphosphate/metabolism , Animals , Brain Neoplasms/genetics , Brain Neoplasms/pathology , Cell Line, Tumor , Cell Proliferation , Female , Glioblastoma/genetics , Glioblastoma/pathology , HEK293 Cells , Humans , Mice , Mice, Inbred BALB C , Mice, Nude , PTEN Phosphohydrolase/genetics , Phosphoglycerate Kinase/genetics , Phosphorylation , Prognosis , Signal Transduction , Time Factors , Tumor Burden , Tyrosine
7.
Cell ; 145(5): 692-706, 2011 May 27.
Article in English | MEDLINE | ID: mdl-21596426

ABSTRACT

Little is known about how combinations of histone marks are interpreted at the level of nucleosomes. The second PHD finger of human BPTF is known to specifically recognize histone H3 when methylated on lysine 4 (H3K4me2/3). Here, we examine how additional heterotypic modifications influence BPTF binding. Using peptide surrogates, three acetyllysine ligands are indentified for a PHD-adjacent bromodomain in BPTF via systematic screening and biophysical characterization. Although the bromodomain displays limited discrimination among the three possible acetyllysines at the peptide level, marked selectivity is observed for only one of these sites, H4K16ac, in combination with H3K4me3 at the mononucleosome level. In support, these two histone marks constitute a unique trans-histone modification pattern that unambiguously resides within a single nucleosomal unit in human cells, and this module colocalizes with these marks in the genome. Together, our data call attention to nucleosomal patterning of covalent marks in dictating critical chromatin associations.


Subject(s)
Antigens, Nuclear/metabolism , Histones/metabolism , Nerve Tissue Proteins/metabolism , Nucleosomes/metabolism , Transcription Factors/metabolism , Acetylation , Animals , Cell Nucleus/metabolism , Chromatin/chemistry , Chromatin/metabolism , Histone Code , Histones/chemistry , Humans , Models, Molecular , Nucleosomes/chemistry , Peptides/chemistry , Peptides/metabolism , Protein Processing, Post-Translational , Protein Structure, Tertiary , Xenopus
8.
Nature ; 583(7817): 625-630, 2020 07.
Article in English | MEDLINE | ID: mdl-32669713

ABSTRACT

The recent discovery of N6-methyladenine (N6-mA) in mammalian genomes suggests that it may serve as an epigenetic regulatory mechanism1. However, the biological role of N6-mA and the molecular pathways that exert its function remain unclear. Here we show that N6-mA has a key role in changing the epigenetic landscape during cell fate transitions in early development. We found that N6-mA is upregulated during the development of mouse trophoblast stem cells, specifically at regions of stress-induced DNA double helix destabilization (SIDD)2-4. Regions of SIDD are conducive to topological stress-induced unpairing of the double helix and have critical roles in organizing large-scale chromatin structures3,5,6. We show that the presence of N6-mA reduces the in vitro interactions by more than 500-fold between SIDD and SATB1, a crucial chromatin organizer that interacts with SIDD regions. Deposition of N6-mA also antagonizes SATB1 function in vivo by preventing its binding to chromatin. Concordantly, N6-mA functions at the boundaries between euchromatin and heterochromatin to restrict the spread of euchromatin. Repression of SIDD-SATB1 interactions mediated by N6-mA is essential for gene regulation during trophoblast development in cell culture models and in vivo. Overall, our findings demonstrate an unexpected molecular mechanism for N6-mA function via SATB1, and reveal connections between DNA modification, DNA secondary structures and large chromatin domains in early embryonic development.


Subject(s)
Adenine/analogs & derivatives , DNA/chemistry , DNA/metabolism , Embryonic Development , Matrix Attachment Region Binding Proteins/antagonists & inhibitors , Adenine/metabolism , Animals , Base Pairing , Embryonic Development/genetics , Euchromatin/genetics , Euchromatin/metabolism , Female , Humans , Male , Matrix Attachment Region Binding Proteins/genetics , Matrix Attachment Region Binding Proteins/metabolism , Mice , Stem Cells/cytology , Stem Cells/metabolism , Thermodynamics , Trophoblasts/cytology
9.
Nature ; 577(7788): 121-126, 2020 01.
Article in English | MEDLINE | ID: mdl-31853060

ABSTRACT

Modifications of histone proteins have essential roles in normal development and human disease. Recognition of modified histones by 'reader' proteins is a key mechanism that mediates the function of histone modifications, but how the dysregulation of these readers might contribute to disease remains poorly understood. We previously identified the ENL protein as a reader of histone acetylation via its YEATS domain, linking it to the expression of cancer-driving genes in acute leukaemia1. Recurrent hotspot mutations have been found in the ENL YEATS domain in Wilms tumour2,3, the most common type of paediatric kidney cancer. Here we show, using human and mouse cells, that these mutations impair cell-fate regulation by conferring gain-of-function in chromatin recruitment and transcriptional control. ENL mutants induce gene-expression changes that favour a premalignant cell fate, and, in an assay for nephrogenesis using murine cells, result in undifferentiated structures resembling those observed in human Wilms tumour. Mechanistically, although bound to largely similar genomic loci as the wild-type protein, ENL mutants exhibit increased occupancy at a subset of targets, leading to a marked increase in the recruitment and activity of transcription elongation machinery that enforces active transcription from target loci. Furthermore, ectopically expressed ENL mutants exhibit greater self-association and form discrete and dynamic nuclear puncta that are characteristic of biomolecular hubs consisting of local high concentrations of regulatory factors. Such mutation-driven ENL self-association is functionally linked to enhanced chromatin occupancy and gene activation. Collectively, our findings show that hotspot mutations in a chromatin-reader domain drive self-reinforced recruitment, derailing normal cell-fate control during development and leading to an oncogenic outcome.


Subject(s)
Cell Lineage , Chromatin/genetics , DNA-Binding Proteins/metabolism , Gain of Function Mutation , Transcription Factors/metabolism , Animals , Cell Differentiation , DNA-Binding Proteins/chemistry , DNA-Binding Proteins/genetics , HEK293 Cells , Humans , Mice , Nephrons/metabolism , Nephrons/pathology , Transcription Factors/chemistry , Transcription Factors/genetics
10.
Nature ; 583(7818): 852-857, 2020 07.
Article in English | MEDLINE | ID: mdl-32699416

ABSTRACT

Complex organisms can rapidly induce select genes in response to diverse environmental cues. This regulation occurs in the context of large genomes condensed by histone proteins into chromatin. The sensing of pathogens by macrophages engages conserved signalling pathways and transcription factors to coordinate the induction of inflammatory genes1-3. Enriched integration of histone H3.3, the ancestral histone H3 variant, is a general feature of dynamically regulated chromatin and transcription4-7. However, how chromatin is regulated at induced genes, and what features of H3.3 might enable rapid and high-level transcription, are unknown. The amino terminus of H3.3 contains a unique serine residue (Ser31) that is absent in 'canonical' H3.1 and H3.2. Here we show that this residue, H3.3S31, is phosphorylated (H3.3S31ph) in a stimulation-dependent manner along rapidly induced genes in mouse macrophages. This selective mark of stimulation-responsive genes directly engages the histone methyltransferase SETD2, a component of the active transcription machinery, and 'ejects' the elongation corepressor ZMYND118,9. We propose that features of H3.3 at stimulation-induced genes, including H3.3S31ph, provide preferential access to the transcription apparatus. Our results indicate dedicated mechanisms that enable rapid transcription involving the histone variant H3.3, its phosphorylation, and both the recruitment and the ejection of chromatin regulators.


Subject(s)
Histones/chemistry , Histones/metabolism , Transcription, Genetic , Up-Regulation/genetics , Animals , Cell Cycle Proteins/genetics , Cell Cycle Proteins/metabolism , Cells, Cultured , Co-Repressor Proteins/genetics , Co-Repressor Proteins/metabolism , DNA-Binding Proteins/genetics , DNA-Binding Proteins/metabolism , Histone-Lysine N-Methyltransferase/genetics , Histone-Lysine N-Methyltransferase/metabolism , Humans , I-kappa B Kinase/chemistry , I-kappa B Kinase/metabolism , Macrophages/metabolism , Male , Methylation , Mice , Models, Molecular , Phosphorylation
11.
Genes Dev ; 32(1): 58-69, 2018 01 01.
Article in English | MEDLINE | ID: mdl-29437725

ABSTRACT

Histone acetylation is associated with active transcription in eukaryotic cells. It helps to open up the chromatin by neutralizing the positive charge of histone lysine residues and providing binding platforms for "reader" proteins. The bromodomain (BRD) has long been thought to be the sole protein module that recognizes acetylated histones. Recently, we identified the YEATS domain of AF9 (ALL1 fused gene from chromosome 9) as a novel acetyl-lysine-binding module and showed that the ENL (eleven-nineteen leukemia) YEATS domain is an essential acetyl-histone reader in acute myeloid leukemias. The human genome encodes four YEATS domain proteins, including GAS41, a component of chromatin remodelers responsible for H2A.Z deposition onto chromatin; however, the importance of the GAS41 YEATS domain in human cancer remains largely unknown. Here we report that GAS41 is frequently amplified in human non-small cell lung cancer (NSCLC) and is required for cancer cell proliferation, survival, and transformation. Biochemical and crystal structural studies demonstrate that GAS41 binds to histone H3 acetylated on H3K27 and H3K14, a specificity that is distinct from that of AF9 or ENL. ChIP-seq (chromatin immunoprecipitation [ChIP] followed by high-throughput sequencing) analyses in lung cancer cells reveal that GAS41 colocalizes with H3K27ac and H3K14ac on the promoters of actively transcribed genes. Depletion of GAS41 or disruption of the interaction between its YEATS domain and acetylated histones impairs the association of histone variant H2A.Z with chromatin and consequently suppresses cancer cell growth and survival both in vitro and in vivo. Overall, our study identifies GAS41 as a histone acetylation reader that promotes histone H2A.Z deposition in NSCLC.


Subject(s)
Carcinoma, Non-Small-Cell Lung/metabolism , Histones/metabolism , Lung Neoplasms/metabolism , Transcription Factors/metabolism , Acetylation , Carcinoma, Non-Small-Cell Lung/genetics , Carcinoma, Non-Small-Cell Lung/pathology , Cell Line, Tumor , Cell Proliferation , Gene Amplification , Genes, cdc , Histones/physiology , Humans , Lung Neoplasms/genetics , Lung Neoplasms/pathology , Promoter Regions, Genetic , Protein Interaction Domains and Motifs , Transcription Factors/chemistry , Transcription Factors/genetics , Transcription Factors/physiology
12.
Brief Bioinform ; 25(1)2023 11 22.
Article in English | MEDLINE | ID: mdl-38145949

ABSTRACT

Prediction of drug-target interactions (DTIs) is essential in medicine field, since it benefits the identification of molecular structures potentially interacting with drugs and facilitates the discovery and reposition of drugs. Recently, much attention has been attracted to network representation learning to learn rich information from heterogeneous data. Although network representation learning algorithms have achieved success in predicting DTI, several manually designed meta-graphs limit the capability of extracting complex semantic information. To address the problem, we introduce an adaptive meta-graph-based method, termed AMGDTI, for DTI prediction. In the proposed AMGDTI, the semantic information is automatically aggregated from a heterogeneous network by training an adaptive meta-graph, thereby achieving efficient information integration without requiring domain knowledge. The effectiveness of the proposed AMGDTI is verified on two benchmark datasets. Experimental results demonstrate that the AMGDTI method overall outperforms eight state-of-the-art methods in predicting DTI and achieves the accurate identification of novel DTIs. It is also verified that the adaptive meta-graph exhibits flexibility and effectively captures complex fine-grained semantic information, enabling the learning of intricate heterogeneous network topology and the inference of potential drug-target relationship.


Subject(s)
Algorithms , Medicine , Benchmarking , Drug Delivery Systems , Semantics
13.
Plant Physiol ; 2024 Jun 14.
Article in English | MEDLINE | ID: mdl-38875008

ABSTRACT

Maintenance and homeostasis of the quiescent center (QC) in Arabidopsis (Arabidopsis thaliana) root apical meristems are critical for stem cell organization and root development. Despite great progress in relevant research, the molecular mechanisms that determine the root stem cell fate and QC still need further exploration. In Arabidopsis, SUPPRESSOR OF FRIGIDA 4 (SUF4) encodes a C2H2-type zinc finger protein that represses flowering by transcriptional activation of FLOWERING LOCUS C (FLC) through the FRIGIDA (FRI) pathway, and EARLY BOLTING IN SHORT DAYS (EBS) is a bivalent histone reader that prevents premature flowering. Here, we found that SUF4 directly interacts with EBS in vivo and in vitro. Loss of function of SUF4 and/or EBS resulted in disorganization of the QC, aberrant cell division, and stunted root growth. RNA-seq and reverse transcription quantitative real-time polymerase chain reaction analysis revealed that SUF4 and EBS coregulate many root development-related genes. A series of biochemical analyses demonstrated that SUF4 directly binds to the promoter of SCARECROW (SCR), which encodes a key regulator of root development. Chromatin immunoprecipitation assay indicated that both SUF4 and EBS are recruited to the SCR locus in an interdependent manner to promote H3K4me3 levels and suppress H3K27me3 levels, thereby activating the expression of SCR. These findings improve our understanding of the function of SUF4 and EBS and provide insights into the molecular mechanism that couples a transcription factor and a histone methylation reader to modulate QC specification and root development in Arabidopsis.

14.
Cell ; 141(7): 1183-94, 2010 Jun 25.
Article in English | MEDLINE | ID: mdl-20541251

ABSTRACT

The MLL1 gene is a frequent target for recurrent chromosomal translocations, resulting in transformation of hematopoietic precursors into leukemia stem cells. Here, we report on structure-function studies that elucidate molecular events in MLL1 binding of histone H3K4me3/2 marks and recruitment of the cyclophilin CyP33. CyP33 contains a PPIase and a RRM domain and regulates MLL1 function through HDAC recruitment. We find that the PPIase domain of CyP33 regulates the conformation of MLL1 through proline isomerization within the PHD3-Bromo linker, thereby disrupting the PHD3-Bromo interface and facilitating binding of the MLL1-PHD3 domain to the CyP33-RRM domain. H3K4me3/2 and CyP33-RRM target different surfaces of MLL1-PHD3 and can bind simultaneously to form a ternary complex. Furthermore, the MLL1-CyP33 interaction is required for repression of HOXA9 and HOXC8 genes in vivo. Our results highlight the role of PHD3-Bromo cassette as a regulatory platform, orchestrating MLL1 binding of H3K4me3/2 marks and cyclophilin-mediated repression through HDAC recruitment.


Subject(s)
Cyclophilins/metabolism , Histone Deacetylases/metabolism , Myeloid-Lymphoid Leukemia Protein/chemistry , Amino Acid Sequence , Cell Line , Crystallography, X-Ray , Histone-Lysine N-Methyltransferase , Histones/metabolism , Humans , Methylation , Models, Molecular , Molecular Sequence Data , Nuclear Magnetic Resonance, Biomolecular , Proline/chemistry , Protein Interaction Domains and Motifs
15.
Nature ; 567(7749): 535-539, 2019 03.
Article in English | MEDLINE | ID: mdl-30867594

ABSTRACT

Chemical modifications of histones can mediate diverse DNA-templated processes, including gene transcription1-3. Here we provide evidence for a class of histone post-translational modification, serotonylation of glutamine, which occurs at position 5 (Q5ser) on histone H3 in organisms that produce serotonin (also known as 5-hydroxytryptamine (5-HT)). We demonstrate that tissue transglutaminase 2 can serotonylate histone H3 tri-methylated lysine 4 (H3K4me3)-marked nucleosomes, resulting in the presence of combinatorial H3K4me3Q5ser in vivo. H3K4me3Q5ser displays a ubiquitous pattern of tissue expression in mammals, with enrichment observed in brain and gut, two organ systems responsible for the bulk of 5-HT production. Genome-wide analyses of human serotonergic neurons, developing mouse brain and cultured serotonergic cells indicate that H3K4me3Q5ser nucleosomes are enriched in euchromatin, are sensitive to cellular differentiation and correlate with permissive gene expression, phenomena that are linked to the potentiation of TFIID4-6 interactions with H3K4me3. Cells that ectopically express a H3 mutant that cannot be serotonylated display significantly altered expression of H3K4me3Q5ser-target loci, which leads to deficits in differentiation. Taken together, these data identify a direct role for 5-HT, independent from its contributions to neurotransmission and cellular signalling, in the mediation of permissive gene expression.


Subject(s)
Gene Expression Regulation , Histones/chemistry , Histones/metabolism , Lysine/metabolism , Protein Processing, Post-Translational , Serotonin/metabolism , Transcription Factor TFIID/metabolism , Animals , Cell Differentiation , Cell Line , Female , GTP-Binding Proteins/metabolism , Glutamine/chemistry , Glutamine/metabolism , Humans , Methylation , Mice , Mice, Inbred C57BL , Protein Binding , Protein Glutamine gamma Glutamyltransferase 2 , Serotonergic Neurons/cytology , Transglutaminases/metabolism
16.
Nature ; 573(7773): 281-286, 2019 09.
Article in English | MEDLINE | ID: mdl-31485078

ABSTRACT

Enzymes that catalyse CpG methylation in DNA, including the DNA methyltransferases 1 (DNMT1), 3A (DNMT3A) and 3B (DNMT3B), are indispensable for mammalian tissue development and homeostasis1-4. They are also implicated in human developmental disorders and cancers5-8, supporting the critical role of DNA methylation in the specification and maintenance of cell fate. Previous studies have suggested that post-translational modifications of histones are involved in specifying patterns of DNA methyltransferase localization and DNA methylation at promoters and actively transcribed gene bodies9-11. However, the mechanisms that control the establishment and maintenance of intergenic DNA methylation remain poorly understood. Tatton-Brown-Rahman syndrome (TBRS) is a childhood overgrowth disorder that is defined by germline mutations in DNMT3A. TBRS shares clinical features with Sotos syndrome (which is caused by haploinsufficiency of NSD1, a histone methyltransferase that catalyses the dimethylation of histone H3 at K36 (H3K36me2)8,12,13), which suggests that there is a mechanistic link between these two diseases. Here we report that NSD1-mediated H3K36me2 is required for the recruitment of DNMT3A and maintenance of DNA methylation at intergenic regions. Genome-wide analysis shows that the binding and activity of DNMT3A colocalize with H3K36me2 at non-coding regions of euchromatin. Genetic ablation of Nsd1 and its paralogue Nsd2 in mouse cells results in a redistribution of DNMT3A to H3K36me3-modified gene bodies and a reduction in the methylation of intergenic DNA. Blood samples from patients with Sotos syndrome and NSD1-mutant tumours also exhibit hypomethylation of intergenic DNA. The PWWP domain of DNMT3A shows dual recognition of H3K36me2 and H3K36me3 in vitro, with a higher binding affinity towards H3K36me2 that is abrogated by TBRS-derived missense mutations. Together, our study reveals a trans-chromatin regulatory pathway that connects aberrant intergenic CpG methylation to human neoplastic and developmental overgrowth.


Subject(s)
DNA (Cytosine-5-)-Methyltransferases/metabolism , DNA Methylation , DNA, Intergenic/metabolism , Histones/metabolism , Animals , Cell Line , DNA Methyltransferase 3A , Genome-Wide Association Study , Growth Disorders/genetics , Growth Disorders/physiopathology , Humans , Mice , Protein Binding , Protein Domains , Protein Transport , Sotos Syndrome/genetics , Sotos Syndrome/physiopathology
17.
Anal Chem ; 96(4): 1795-1802, 2024 01 30.
Article in English | MEDLINE | ID: mdl-38241199

ABSTRACT

Cytokines are essential components of the immune system and are recognized as significant biomarkers. However, detection of a single cytokine is not precise and reliable enough to satisfy the requirements for diagnosis. Herein, we developed a pattern recognition-based method for the multiplexed sensing of cytokines, which involves three-color-emitting boronic acid-decorated carbon dots (BCDs) and arginine-modified titanium carbide (Ti3C2 MXenes) as the sensor array. Initially, the fluorescence signals of the three BCDs were quenched by Ti3C2 MXenes. In the presence of cytokines, the fluorescence intensity of the BCDs was restored or further quenched by different cytokines. The fluorescence response occurs in two steps: first, boronic acid interacts with cis-diol functional groups of cytokines, and second, arginine headgroup selectively interacts with glycans. By exploiting the different competing binding of the BCDs and the cytokines toward Ti3C2 MXenes, seven cytokines and their mixtures can be effectively discriminated at a concentration of 20 ng mL-1. Furthermore, our sensor array demonstrated an excellent performance in classifying human oral cancer saliva samples from healthy individuals with clinically relevant specificity. The noninvasive method offers a rapid approach to cytokine analysis, benefiting early and timely clinical diagnosis and treatment.


Subject(s)
Cytokines , Mouth Neoplasms , Humans , Carbon , Boronic Acids , Mouth Neoplasms/diagnosis , Arginine
18.
Anal Chem ; 96(8): 3436-3444, 2024 02 27.
Article in English | MEDLINE | ID: mdl-38372258

ABSTRACT

Cerebral ischemia-reperfusion injury (CIRI), a cause of cerebral dysfunction during cerebral infarction treatment, is closely associated with mitochondrial viscosity and hydrogen peroxide (H2O2). However, the accurate measurement of mitochondrial viscosity and H2O2 levels in CIRI is challenging because of the lack of sufficient selectivity and blood-brain barrier (BBB) penetration of existing monitoring tools related to CIRI, hampering the exploration of the role of mitochondrial viscosity and H2O2 in CIRI. To address this issue, we designed an activatable fluorescent probe, mitochondria-targeting styryl-quinolin-ium (Mito-IQS), with excellent properties including high selectivity, mitochondrial targeting, and BBB penetration, for the visualization of mitochondrial viscosity and H2O2 in the brain. Based on the real-time monitoring capabilities of the probe, bursts of mitochondrial viscosity and H2O2 levels were visualized during CIRI. This probe can be used to monitor the therapeutic effects of butylphthalein treatment. More importantly, in vivo experiments further confirmed that CIRI was closely associated with the mitochondrial viscosity and H2O2 levels. This discovery provides new insights and tools for the study of CIRI and is expected to accelerate the process of CIRI diagnosis, treatment, and drug design.


Subject(s)
Brain Ischemia , Reperfusion Injury , Humans , Hydrogen Peroxide , Fluorescent Dyes , Viscosity , Mitochondria
19.
Small ; : e2400780, 2024 Mar 30.
Article in English | MEDLINE | ID: mdl-38554020

ABSTRACT

Developing efficient homojunctions on g-C3N4 promises metal-free photocatalysis to realize truly sustainable artificial photosynthesis. However, current designs are limited by hindered charge separation due to inevitable grain boundaries and random formation of ineffective homojunctions embedded within the photocatalyst. Here, efficient photocatalysis is driven by introducing effective surface homojunctions on chemically and structurally identical g-C3N4 through leveraging its size-dependent electronic properties. Using a top-down approach, the surface layer of bulk g-C3N4 is partially exfoliated to create sheet-like g-C3N4 nanostructures on the bulk material. This hierarchical design establishes a subtle band energy offset between the macroscopic and nanoscopic g-C3N4, generating homojunctions while maintaining the chemical and structural integrities of the original g-C3N4. The optimized g-C3N4 homojunction demonstrates superior photocatalytic degradation of antibiotic pollutants at >96% efficiency in 2 h, even in different real water samples. It achieves reaction kinetics (≈0.041 min-1) up to fourfold better than standalone materials and their physical mixture. Mechanistic studies highlight the importance of the unique design in boosting photocatalysis by effectively promoting interfacial photocarrier manipulation and utilization directly at the point-of-catalysis, without needing co-catalysts or sacrificial agents. This work presents enormous opportunities for developing advanced and green photocatalytic platforms for sustainable light-driven environmental, energy, and chemical applications.

20.
Small ; 20(24): e2309983, 2024 Jun.
Article in English | MEDLINE | ID: mdl-38174596

ABSTRACT

Plasmon-mediated catalysis utilizing hybrid photocatalytic ensembles promises effective light-to-chemical transformation, but current approaches suffer from weak electromagnetic field enhancements from polycrystalline and isotropic plasmonic nanoparticles as well as poor utilization of precious co-catalyst. Here, efficient plasmon-mediated catalysis is achieved by introducing a unique catalyst-on-hotspot nanoarchitecture obtained through the strategic positioning of co-photocatalyst onto plasmonic hotspots to concentrate light energy directly at the point-of-reaction. Using environmental remediation as a proof-of-concept application, the catalyst-on-hotspot design (edge-AgOcta@Cu2O) enhances photocatalytic advanced oxidation processes to achieve superior organic-pollutant degradation at ≈81% albeit having lesser Cu2O co-photocatalyst than the fully deposited design (full-AgOcta@Cu2O). Mass-normalized rate constants of edge-AgOcta@Cu2O reveal up to 20-fold and 3-fold more efficient utilization of Cu2O and Ag nanoparticles, respectively, compared to full-AgOcta@Cu2O and standalone catalysts. Moreover, this design also exhibits catalytic performance >4-fold better than emerging hybrid photocatalytic platforms. Mechanistic studies unveil that the light-concentrating effect facilitated by the dense electromagnetic hotspots is crucial to promote the generation and utilization of energetic photocarriers for enhanced catalysis. By enabling the plasmonic focusing of light onto co-photocatalyst at the single-particle level, the unprecedented design offers valuable insights in enhancing light-driven chemical reactions and realizing efficient energy/catalyst utilizations for diverse chemical, environmental, and energy applications.

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