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1.
Methods Mol Biol ; 2519: 155-161, 2023.
Artigo em Inglês | MEDLINE | ID: mdl-36066720

RESUMO

Posttranslational modifications (PTMs) of histones, such as lysine acetylation and ubiquitination, regulate chromatin structure and gene expression. In living organisms, histone PTMs are catalyzed by histone-modifying enzymes. Here, we describe an entirely chemical method to introduce histone modifications in living cells without genetic manipulation. The chemical catalyst PEG-LANA-DSSMe activates a thioester acetyl donor, N,S-diacetylcysteamine (NAC-Ac), and promotes regioselective, synthetic histone acetylation at H2BK120 in living cells.


Assuntos
Histonas , Processamento de Proteína Pós-Traducional , Acetilação , Catálise , Histonas/metabolismo , Lisina/metabolismo
2.
Methods Mol Biol ; 2519: 163-185, 2023.
Artigo em Inglês | MEDLINE | ID: mdl-36066721

RESUMO

Posttranslational modifications of histone are intimately related to chromatin/chromosome-mediated cellular events. Among all, the roles of histone modifications including acetylation, methylation, ubiquitination, and SUMOylation of lysine or arginine residue of nucleosome core histones in gene expression have been intensively studied. Genome-wide profiles of histone modification marks revealed their combinatorial organization in the functional features of chromatin. Analysis of histone modification by chromatin immunoprecipitation (ChIP) is one of the standard assays to examine chromatin states. Although high-throughput sequencing analysis (ChIP-seq) is now widely conducted, classical ChIP-qPCR analysis has advantages in investigation of multiple histone modification marks at a target site simply through the use of relatively small numbers of cells. Since ChIP-qPCR is devoid of biases caused by overamplification and inaccurate mapping of sequencing reads, it is a more reliable quantification method than genome-wide ChIP-seq especially for analyses of the low-mappability regions, which harbor many repetitive sequences and/or highly homologous segmental multiplications as found in gene clusters. We have recently analyzed histone H3 and H4 modifications of the Zscan4 family gene loci in an 880 kb gene cluster and found that the atypical enhancer-like structure is formed upon derepression of Zscan4. In this chapter, we describe the detailed protocols for histone modification ChIP-assay of repeat-enriched gene cluster regions. The protocol here we applied to mouse ES cells, but the protocol is perfectly applicable to human cultured cells and specimens.


Assuntos
Código das Histonas , Histonas , Animais , Cromatina/genética , Imunoprecipitação da Cromatina/métodos , Histonas/genética , Histonas/metabolismo , Humanos , Camundongos , Processamento de Proteína Pós-Traducional
3.
Epigenomics ; 14(5): 279-293, 2022 03.
Artigo em Inglês | MEDLINE | ID: mdl-35184601

RESUMO

Head and neck squamous cell carcinoma (HNSCC) is the sixth most prevalent form of cancer worldwide. Despite advancements made in treatment strategies, the fatality rate of HNSCC is very high. An accumulating body of evidence suggests that epigenetic modification of histones plays an influential role in the development and progression of the disease. In this review we discuss the role of epigenetic modifications in HNSCC and the inter-relationships of human papillomavirus oncoproteins and histone-modifying agents. Further, we explore the possibility of identifying these modifications as biomarkers for their use as drugs in treatment strategies.


Head and neck squamous cell carcinoma (HNSCC) is the most common kind of head and neck cancer. HNSCC can develop therapeutic resistance, making therapy more difficult. Many studies have found that epigenetic events play a key role in HNSCC. Better understanding epigenetic regulation could help discovery of biomarkers that help detect and diagnose HNSCC. This review will present recent studies, showing the importance of epigenetic regulation targeting histone modifications in the development of HNSCC.


Assuntos
Neoplasias de Cabeça e Pescoço , Histonas , Epigênese Genética , Neoplasias de Cabeça e Pescoço/tratamento farmacológico , Neoplasias de Cabeça e Pescoço/genética , Código das Histonas , Histonas/metabolismo , Humanos , Carcinoma de Células Escamosas de Cabeça e Pescoço/genética
4.
Microb Genom ; 8(9)2022 Sep.
Artigo em Inglês | MEDLINE | ID: mdl-36129736

RESUMO

Chemical modifications of DNA and histone proteins impact the organization of chromatin within the nucleus. Changes in these modifications, catalysed by different chromatin-modifying enzymes, influence chromatin organization, which in turn is thought to impact the spatial and temporal regulation of gene expression. While combinations of different histone modifications, the histone code, have been studied in several model species, we know very little about histone modifications in the fungal genus Aspergillus, whose members are generally well studied due to their importance as models in cell and molecular biology as well as their medical and biotechnological relevance. Here, we used phylogenetic analyses in 94 Aspergilli as well as other fungi to uncover the occurrence and evolutionary trajectories of enzymes and protein complexes with roles in chromatin modifications or regulation. We found that these enzymes and complexes are highly conserved in Aspergilli, pointing towards a complex repertoire of chromatin modifications. Nevertheless, we also observed few recent gene duplications or losses, highlighting Aspergillus species to further study the roles of specific chromatin modifications. SET7 (KMT6) and other components of PRC2 (Polycomb Repressive Complex 2), which is responsible for methylation on histone H3 at lysine 27 in many eukaryotes including fungi, are absent in Aspergilli as well as in closely related Penicillium species, suggesting that these lost the capacity for this histone modification. We corroborated our computational predictions by performing untargeted MS analysis of histone post-translational modifications in Aspergillus nidulans. This systematic analysis will pave the way for future research into the complexity of the histone code and its functional implications on genome architecture and gene regulation in fungi.


Assuntos
Aspergillus nidulans , Código das Histonas , Aspergillus nidulans/genética , Aspergillus nidulans/metabolismo , Cromatina , DNA , Código das Histonas/genética , Histonas/genética , Histonas/metabolismo , Lisina/genética , Lisina/metabolismo , Filogenia , Complexo Repressor Polycomb 2/genética , Complexo Repressor Polycomb 2/metabolismo , Proteômica
5.
Cell Rep ; 40(12): 111393, 2022 Sep 20.
Artigo em Inglês | MEDLINE | ID: mdl-36130491

RESUMO

The neuromuscular junction (NMJ) is an essential synapse whose loss is a key hallmark of the neurodegenerative disease spinal muscular atrophy (SMA). Here, we show that activity of the SMA-determining SMN protein in the assembly of U7 small nuclear ribonucleoprotein (snRNP)-which functions in the 3'-end processing of replication-dependent histone mRNAs-is required for NMJ integrity. Co-expression of U7-specific Lsm10 and Lsm11 proteins selectively enhances U7 snRNP assembly, corrects histone mRNA processing defects, and rescues key structural and functional abnormalities of neuromuscular pathology in SMA mice-including NMJ denervation, decreased synaptic transmission, and skeletal muscle atrophy. Furthermore, U7 snRNP dysfunction drives selective loss of the synaptic organizing protein Agrin at NMJs innervating vulnerable muscles of SMA mice. These findings reveal a direct contribution of U7 snRNP dysfunction to neuromuscular pathology in SMA and suggest a role for histone gene regulation in maintaining functional synaptic connections between motor neurons and muscles.


Assuntos
Atrofia Muscular Espinal , Doenças Neurodegenerativas , Agrina/metabolismo , Animais , Histonas/metabolismo , Camundongos , Atrofia Muscular Espinal/metabolismo , Doenças Neurodegenerativas/metabolismo , Junção Neuromuscular/metabolismo , RNA Mensageiro/metabolismo , Ribonucleoproteína Nuclear Pequena U7/química , Ribonucleoproteína Nuclear Pequena U7/metabolismo
6.
Cell Rep ; 40(11): 111329, 2022 Sep 13.
Artigo em Inglês | MEDLINE | ID: mdl-36103831

RESUMO

Linker histones are highly abundant chromatin-associated proteins with well-established structural roles in chromatin and as general transcriptional repressors. In addition, it has been long proposed that histone H1 exerts context-specific effects on gene expression. Here, we identify a function of histone H1 in chromatin structure and transcription using a range of genomic approaches. In the absence of histone H1, there is an increase in the transcription of non-coding RNAs, together with reduced levels of m6A modification leading to their accumulation on chromatin and causing replication-transcription conflicts. This strongly suggests that histone H1 prevents non-coding RNA transcription and regulates non-coding transcript turnover on chromatin. Accordingly, altering the m6A RNA methylation pathway rescues the replicative phenotype of H1 loss. This work unveils unexpected regulatory roles of histone H1 on non-coding RNA turnover and m6A deposition, highlighting the intimate relationship between chromatin conformation, RNA metabolism, and DNA replication to maintain genome performance.


Assuntos
Cromatina , Histonas , Histonas/metabolismo , Metilação , RNA não Traduzido/genética , RNA não Traduzido/metabolismo , Fatores de Transcrição/metabolismo
7.
Adv Exp Med Biol ; 1390: 277-293, 2022.
Artigo em Inglês | MEDLINE | ID: mdl-36107325

RESUMO

The androgen receptor (AR) is a ligand-activated transcription factor belonging to the nuclear receptor (NR) superfamily. As with other members of the NR family, transcriptional activity of the AR is regulated by interactions with coregulatory proteins, which either enhance (coactivators) or repress (corepressors) its transcriptional activity. AR associated coregulators are functionally diverse, but a large fraction are epigenetic histone and chromatin modifiers. Epigenetic coregulators are recruited to gene regulatory regions as part of multi-protein complexes, often acting in a dynamic and inter-dependent manner to remodel chromatin, thereby allowing or inhibiting the access of AR-associated transcriptional machinery to target genes; functional consequences being regulation of transcriptional output. Epigenetic modifiers, including those that function as AR coregulators, are frequently mutated or aberrantly expressed in prostate cancer and are implicated in disease progression. Some of these modifiers are being investigated as therapeutic targets in several cancer types and could potentially be used to modulate aberrant AR activity in prostate cancer. In this chapter we will summarise the functional role of epigenetic coregulators in AR signalling, their dysregulation during prostate cancer progression and the current status of drugs targeting these enzymes.


Assuntos
Neoplasias da Próstata , Receptores Androgênicos , Cromatina , Proteínas Correpressoras/genética , Proteínas Correpressoras/metabolismo , Epigênese Genética , Histonas/genética , Histonas/metabolismo , Humanos , Ligantes , Masculino , Neoplasias da Próstata/metabolismo , Receptores Androgênicos/genética , Receptores Androgênicos/metabolismo , Fatores de Transcrição/metabolismo
8.
PLoS One ; 17(9): e0273518, 2022.
Artigo em Inglês | MEDLINE | ID: mdl-36126055

RESUMO

The histone deacetylase (HDAC) inhibitor vorinostat, used with gemcitabine and other therapies, has been effective in treatment of experimental models of pancreatic cancer. In this study, we demonstrated that M344, an HDAC inhibitor, is efficacious against pancreatic cancer in vitro and in vivo, alone or with gemcitabine. By 24 hours post-treatment, M344 augments the population of pancreatic cancer cells in G1, and at a later time point (48 hours) it increases apoptosis. M344 inhibits histone H3 deacetylation and slows pancreatic cancer cell proliferation better than vorinostat, and it does not decrease the viability of a non-malignant cell line more than vorinostat. M344 also elevates pancreatic cancer cell major histocompatibility complex (MHC) class I molecule expression, potentially increasing the susceptibility of pancreatic cancer cells to T cell lysis. Taken together, our findings support further investigation of M344 as a pancreatic cancer treatment.


Assuntos
Inibidores de Histona Desacetilases , Neoplasias Pancreáticas , Linhagem Celular Tumoral , Inibidores de Histona Desacetilases/farmacologia , Inibidores de Histona Desacetilases/uso terapêutico , Histona Desacetilases/metabolismo , Histonas/metabolismo , Humanos , Ácidos Hidroxâmicos/farmacologia , Ácidos Hidroxâmicos/uso terapêutico , Neoplasias Pancreáticas/tratamento farmacológico , Vorinostat/farmacologia
9.
Genome Biol ; 23(1): 197, 2022 Sep 20.
Artigo em Inglês | MEDLINE | ID: mdl-36127735

RESUMO

BACKGROUND: It is challenging to determine the effect of DNA methylation on the epigenetic landscape and the function in higher organisms due to the lack of DNA methylation-free mutants. RESULTS: Here, the analysis of a recently generated Arabidopsis mutant completely devoid of DNA methylation reveals that DNA methylation underpins the genome-wide landscape of histone modifications. Complete loss of DNA methylation causes an upheaval of the histone modification landscape, including complete loss of H3K9me2 and widespread redistribution of active and H3K27me3 histone marks, mostly owing to the role of DNA methylation in initiating H3K9me2 deposition and excluding active marks and repressive mark H3K27me3; CG and non-CG methylation can act independently at some genomic regions while they act cooperatively at many other regions. The transcriptional reprogramming upon loss of all DNA methylation correlates with the extensive redistribution or switches of the examined histone modifications. Histone modifications retained or gained in the DNA methylation-free mutant serve as DNA methylation-independent transcriptional regulatory signals: active marks promote genome transcription, whereas the repressive mark H3K27me3 compensates for the lack of DNA hypermethylation/H3K9me2 at multiple transposon families. CONCLUSIONS: Our results show that an intact DNA methylome constitutes the scaffolding of the epigenomic landscape in Arabidopsis and is critical for controlled genome transcription and ultimately for proper growth and development.


Assuntos
Arabidopsis , Arabidopsis/genética , Arabidopsis/metabolismo , DNA , Metilação de DNA , Epigênese Genética , Epigenômica , Histonas/metabolismo , Humanos
10.
Nat Commun ; 13(1): 5542, 2022 Sep 21.
Artigo em Inglês | MEDLINE | ID: mdl-36130923

RESUMO

Polycomb (PcG) silencing is crucial for development, but how targets are specified remains incompletely understood. The cold-induced Polycomb Repressive Complex 2 (PRC2) silencing of Arabidopsis thaliana FLOWERING LOCUS C (FLC) provides an excellent system to elucidate PcG regulation. Association of the DNA binding protein VAL1 to FLC PcG nucleation regionis an important step. VAL1 co-immunoprecipitates APOPTOSIS AND SPLICING ASSOCIATED PROTEIN (ASAP) complex and PRC1. Here, we show that ASAP and PRC1 are necessary for co-transcriptional repression and chromatin regulation at FLC. ASAP mutants affect FLC transcription in warm conditions, but the rate of FLC silencing in the cold is unaffected. PRC1-mediated H2Aub accumulation increases at the FLC nucleation region during cold, but unlike the PRC2-delivered H3K27me3, does not spread across the locus. H2Aub thus involved in the transition to epigenetic silencing at FLC, facilitating H3K27me3 accumulation and long-term epigenetic memory. Overall, our work highlights the importance of VAL1 as an assembly platform co-ordinating activities necessary for epigenetic silencing at FLC.


Assuntos
Proteínas de Arabidopsis , Arabidopsis , Arabidopsis/metabolismo , Proteínas de Arabidopsis/genética , Proteínas de Arabidopsis/metabolismo , Cromatina/genética , Cromatina/metabolismo , Regulação da Expressão Gênica de Plantas , Inativação Gênica , Histonas/genética , Histonas/metabolismo , Proteínas de Domínio MADS/genética , Proteínas de Domínio MADS/metabolismo , Complexo Repressor Polycomb 2/genética , Complexo Repressor Polycomb 2/metabolismo , Proteínas do Grupo Polycomb/metabolismo
11.
Sci Rep ; 12(1): 15735, 2022 Sep 21.
Artigo em Inglês | MEDLINE | ID: mdl-36130958

RESUMO

Cocaine epigenetically regulates gene expression via changes in histone post-translational modifications (HPTMs). We previously found that the immediate early gene Nr4a1 is epigenetically activated by cocaine in mouse brain reward regions. However, few studies have examined multiple HPTMs at a single gene. Bivalent gene promoters are simultaneously enriched in both activating (H3K4me3 (K4)) and repressive (H3K27me3 (K27)) HPTMs. As such, bivalent genes are lowly expressed but poised for activity-dependent gene regulation. In this study, we identified K4&K27 bivalency at Nr4a1 following investigator-administered cocaine in male and female mice. We applied sequential chromatin immunoprecipitation and qPCR to define Nr4a1 bivalency and expression in striatum (STR), prefrontal cortex (PFC), and hippocampus (HPC). We used Pearson's correlation to quantify relationships within each brain region across treatment conditions for each sex. In female STR, cocaine increased Nr4a1 mRNA while maintaining Nr4a1 K4&K27 bivalency. In male STR, cocaine enriched repressive H3K27me3 and K4&K27 bivalency at Nr4a1 and maintained Nr4a1 mRNA. Furthermore, cocaine epigenetically regulated a putative NR4A1 target, Cartpt, in male PFC. This study defined the epigenetic regulation of Nr4a1 in reward brain regions in male and female mice following cocaine, and, thus, shed light on the biological relevance of sex to cocaine use disorder.


Assuntos
Cocaína , Histonas , Animais , Cromatina/genética , Cocaína/farmacologia , Epigênese Genética , Feminino , Histonas/genética , Histonas/metabolismo , Masculino , Camundongos , Membro 1 do Grupo A da Subfamília 4 de Receptores Nucleares/genética , Membro 1 do Grupo A da Subfamília 4 de Receptores Nucleares/metabolismo , RNA Mensageiro/genética
12.
Front Endocrinol (Lausanne) ; 13: 932286, 2022.
Artigo em Inglês | MEDLINE | ID: mdl-36133305

RESUMO

2-Hydroxyglutarate (2HG) overproducing tumors arise in a number of tissues, including the kidney. The tumorigenesis resulting from overproduced 2HG has been attributed to the ability of 2HG alter gene expression by inhibiting α-ketoglutarate (αKG)-dependent dioxygenases, including Ten-eleven-Translocation (TET) enzymes. Genes that regulate cellular differentiation are reportedly repressed, blocking differentiation of mesenchymal cells into myocytes, and adipocytes. In this report, the expression of the enzyme responsible for L2HG degradation, L-2HG dehydrogenase (L2HGDH), is knocked down, using lentiviral shRNA, as well as siRNA, in primary cultures of normal Renal Proximal Tubule (RPT) cells. The knockdown (KD) results in increased L-2HG levels, decreased demethylation of 5mC in genomic DNA, and increased methylation of H3 Histones. Consequences include reduced tubulogenesis by RPT cells in matrigel, and reduced expression of molecular markers of differentiation, including membrane transporters as well as HNF1α and HNF1ß, which regulate their transcription. These results are consistent with the hypothesis that oncometabolite 2HG blocks RPT differentiation by altering the methylation status of chromatin in a manner that impedes the transcriptional events required for normal differentiation. Presumably, similar alterations are responsible for promoting the expansion of renal cancer stem-cells, increasing their propensity for malignant transformation.


Assuntos
Dioxigenases , Histonas , Diferenciação Celular/genética , Cromatina , Dioxigenases/metabolismo , Epigênese Genética , Glutaratos , Histonas/metabolismo , Ácidos Cetoglutáricos/metabolismo , Rim/metabolismo , Proteínas de Membrana Transportadoras/metabolismo , Oxirredutases/metabolismo , RNA Interferente Pequeno
13.
Dis Markers ; 2022: 9883831, 2022.
Artigo em Inglês | MEDLINE | ID: mdl-36133436

RESUMO

Liver fibrosis results from the formation of fibrous scars of hepatic stellate cells by various chronic liver diseases. Considering that the liver is the most important metabolic organ in the human body, exploring the metabolic characteristics of liver fibrosis is expected to discover new markers and therapeutic targets. In this study, we first used mouse model to verify that both lactate content and histone acetylation levels were significantly increased in hepatic fibrosis mice. At the same time, it was confirmed that activated hepatic stellate cells (HSCs) cocultured with M1 macrophages can promote their transformation into M2 macrophages in hepatic stellate cell line and primary hepatic stellate cells. In addition, the addition of lactic acid to the medium in which M1 cells are cultured can promote their transformation into M2 macrophages. Therefore, we concluded that activated HSCs can promote the transformation of M1 to M2 macrophages through lactate accumulation, thereby causing liver fibrosis.


Assuntos
Células Estreladas do Fígado , Histonas , Acetilação , Animais , Células Estreladas do Fígado/metabolismo , Histonas/metabolismo , Humanos , Ácido Láctico , Fígado/patologia , Cirrose Hepática/metabolismo , Macrófagos/metabolismo , Camundongos
14.
Biochemistry ; 61(18): 1974-1987, 2022 Sep 20.
Artigo em Inglês | MEDLINE | ID: mdl-36070615

RESUMO

Human lysine methyltransferase 2D (hKMT2D) is an epigenetic writer catalyzing the methylation of histone 3 lysine 4. hKMT2D by itself has little catalytic activity and reaches full activation as part of the WRAD2 complex, additionally comprising binding partners WDR5, RbBP5, Ash2L, and DPY30. Here, a detailed mechanistic study of the hKMT2D SET domain and its WRAD2 interactions is described. We characterized the WRAD2 subcomplexes containing full-length components and the hKMT2D SET domain. By performing steady-state analysis as a function of WRAD2 concentration, we identified the inner stoichiometry and determined the binding affinities for complex formation. Ash2L and RbBP5 were identified as the binding partners critical for the full catalytic activity of the SET domain. Contrary to a previous report, product and dead-end inhibitor studies identified hKMT2D as a rapid equilibrium random Bi-Bi mechanism with EAP and EBQ dead-end complexes. Matrix-assisted laser desorption ionization time-of-flight mass spectrometry (MALDI-ToF MS) analysis showed that hKMT2D uses a distributive mechanism and gives further insights into how the WRAD2 components affect mono-, di-, and trimethylation. We also conclude that the Win motif of hKMT2D is not essential in complex formation, unlike other hKMT2 proteins.


Assuntos
Histona-Lisina N-Metiltransferase , Lisina , Histona-Lisina N-Metiltransferase/química , Histonas/metabolismo , Humanos , Peptídeos e Proteínas de Sinalização Intracelular/metabolismo , Cinética , Lisina/metabolismo , Metilação , Proteína de Leucina Linfoide-Mieloide/química
15.
Proc Natl Acad Sci U S A ; 119(38): e2205691119, 2022 Sep 20.
Artigo em Inglês | MEDLINE | ID: mdl-36095189

RESUMO

The human Mixed Lineage Leukemia-1 (MLL1) complex methylates histone H3K4 to promote transcription and is stimulated by monoubiquitination of histone H2B. Recent structures of the MLL1-WRAD core complex, which comprises the MLL1 methyltransferase, WDR5, RbBp5, Ash2L, and DPY-30, have revealed variability in the docking of MLL1-WRAD on nucleosomes. In addition, portions of the Ash2L structure and the position of DPY30 remain ambiguous. We used an integrated approach combining cryoelectron microscopy (cryo-EM) and mass spectrometry cross-linking to determine a structure of the MLL1-WRAD complex bound to ubiquitinated nucleosomes. The resulting model contains the Ash2L intrinsically disordered region (IDR), SPRY insertion region, Sdc1-DPY30 interacting region (SDI-motif), and the DPY30 dimer. We also resolved three additional states of MLL1-WRAD lacking one or more subunits, which may reflect different steps in the assembly of MLL1-WRAD. The docking of subunits in all four states differs from structures of MLL1-WRAD bound to unmodified nucleosomes, suggesting that H2B-ubiquitin favors assembly of the active complex. Our results provide a more complete picture of MLL1-WRAD and the role of ubiquitin in promoting formation of the active methyltransferase complex.


Assuntos
Leucemia , Nucleossomos , Microscopia Crioeletrônica , Histona-Lisina N-Metiltransferase/metabolismo , Histonas/metabolismo , Humanos , Peptídeos e Proteínas de Sinalização Intracelular/metabolismo , Proteína de Leucina Linfoide-Mieloide/genética , Proteína de Leucina Linfoide-Mieloide/metabolismo , Ubiquitina/metabolismo
16.
Proc Natl Acad Sci U S A ; 119(38): e2207177119, 2022 Sep 20.
Artigo em Inglês | MEDLINE | ID: mdl-36103578

RESUMO

IMPORTIN-4, the primary nuclear import receptor of core histones H3 and H4, binds the H3-H4 dimer and histone chaperone ASF1 prior to nuclear import. However, how H3-H3-ASF1 is recognized for transport cannot be explained by available crystal structures of IMPORTIN-4-histone tail peptide complexes. Our 3.5-Å IMPORTIN-4-H3-H4-ASF1 cryoelectron microscopy structure reveals the full nuclear import complex and shows a binding mode different from suggested by previous structures. The N-terminal half of IMPORTIN-4 clamps the globular H3-H4 domain and H3 αN helix, while its C-terminal half binds the H3 N-terminal tail weakly; tail contribution to binding energy is negligible. ASF1 binds H3-H4 without contacting IMPORTIN-4. Together, ASF1 and IMPORTIN-4 shield nucleosomal H3-H4 surfaces to chaperone and import it into the nucleus where RanGTP binds IMPORTIN-4, causing large conformational changes to release H3-H4-ASF1. This work explains how full-length H3-H4 binds IMPORTIN-4 in the cytoplasm and how it is released in the nucleus.


Assuntos
Chaperonas de Histonas , Histonas , Proteínas de Ciclo Celular/metabolismo , Microscopia Crioeletrônica , Citoplasma/metabolismo , Chaperonas de Histonas/metabolismo , Histonas/metabolismo , Carioferinas/metabolismo
17.
Front Endocrinol (Lausanne) ; 13: 965445, 2022.
Artigo em Inglês | MEDLINE | ID: mdl-36120466

RESUMO

Background: Hepatocellular carcinoma (HCC) is the third leading cause of death in the world, characterized by high morbidity, poor prognosis and high mortality. Histone modifications regulate intracellular gene expression at the post-transcriptional level, and disturbances in the regulatory pattern of histone modifications at individual locus or across the genome can lead to tumorigenesis of HCC. In this study, we constructed a prognosis-related histone phosphorylation regulated (HPR) genes signature and elucidated whether HPR genes can predict overall survival in HCC patients. Methods: Differentially expressed genes were screened using TCGA, ICGC and GEO databases, and a new risk signature was constructed by univariate Cox regression and Lasso regression analysis. Predictive nomograms were established by multivariate Cox regression of risk scores and clinical parameters, calibration curve and decision curve analysis were used to evaluate the models. The ssGSEA methods were used to determine the effect of risk scores on the tumor immune microenvironment. Data for HCC single-cell RNA sequencing (scRNA-seq) have been downloaded from Gene Expression Omnibus (GEO) to understand the role of HPR genes in tumorigenesis. Results: Our analyses of nine HPR genes provided prognostic insights. Overall survival in the low-risk and high-risk groups was statistically higher, respectively (P<0.001). Cox regression analysis revealed that the risk score is a significant predictor of HCC outcomes (HR=2. 2.62, 95%CI: 1.248-5.514, P=0.011). In addition, a nomogram combining risk scores with TNM stages was constructed and tested from calibration curves and decision curves (AUC=0.780). MHC-class-I genes, iDCs, Macrophages, Tfh, Treg, Th2 were overexpressed in the high-risk group. Conclusion: HPR genes risk score is closely related to the prognosis of HCC, tumor immune process and tumor cell progression.


Assuntos
Carcinoma Hepatocelular , Neoplasias Hepáticas , Biomarcadores Tumorais/metabolismo , Carcinogênese , Carcinoma Hepatocelular/diagnóstico , Carcinoma Hepatocelular/genética , Histonas/genética , Histonas/metabolismo , Humanos , Neoplasias Hepáticas/genética , Fosforilação , Prognóstico , Análise de Sequência de RNA , Microambiente Tumoral/genética
18.
Nat Commun ; 13(1): 5447, 2022 Sep 19.
Artigo em Inglês | MEDLINE | ID: mdl-36123357

RESUMO

Silencing of endogenous retroviruses (ERVs) is largely mediated by repressive chromatin modifications H3K9me3 and DNA methylation. On ERVs, these modifications are mainly deposited by the histone methyltransferase Setdb1 and by the maintenance DNA methyltransferase Dnmt1. Knock-out of either Setdb1 or Dnmt1 leads to ERV de-repression in various cell types. However, it is currently not known if H3K9me3 and DNA methylation depend on each other for ERV silencing. Here we show that conditional knock-out of Setdb1 in mouse embryonic endoderm results in ERV de-repression in visceral endoderm (VE) descendants and does not occur in definitive endoderm (DE). Deletion of Setdb1 in VE progenitors results in loss of H3K9me3 and reduced DNA methylation of Intracisternal A-particle (IAP) elements, consistent with up-regulation of this ERV family. In DE, loss of Setdb1 does not affect H3K9me3 nor DNA methylation, suggesting Setdb1-independent pathways for maintaining these modifications. Importantly, Dnmt1 knock-out results in IAP de-repression in both visceral and definitive endoderm cells, while H3K9me3 is unaltered. Thus, our data suggest a dominant role of DNA methylation over H3K9me3 for IAP silencing in endoderm cells. Our findings suggest that Setdb1-meditated H3K9me3 is not sufficient for IAP silencing, but rather critical for maintaining high DNA methylation.


Assuntos
Metilação de DNA , Retrovirus Endógenos , Animais , Cromatina/metabolismo , DNA/metabolismo , Endoderma/metabolismo , Retrovirus Endógenos/metabolismo , Histona Metiltransferases/metabolismo , Histonas/genética , Histonas/metabolismo , Camundongos
19.
J Biomed Sci ; 29(1): 71, 2022 Sep 19.
Artigo em Inglês | MEDLINE | ID: mdl-36123603

RESUMO

Chromatin remodeling is an essential cellular process for organizing chromatin structure into either open or close configuration at specific chromatin locations by orchestrating and modifying histone complexes. This task is responsible for fundamental cell physiology including transcription, DNA replication, methylation, and damage repair. Aberrations in this activity have emerged as epigenomic mechanisms in cancer development that increase tumor clonal fitness and adaptability amidst various selection pressures. Inactivating mutations in AT-rich interaction domain 1A (ARID1A), a gene encoding a large nuclear protein member belonging to the SWI/SNF chromatin remodeling complex, result in its loss of expression. ARID1A is the most commonly mutated chromatin remodeler gene, exhibiting the highest mutation frequency in endometrium-related uterine and ovarian carcinomas. As a tumor suppressor gene, ARID1A is essential for regulating cell cycle, facilitating DNA damage repair, and controlling expression of genes that are essential for maintaining cellular differentiation and homeostasis in non-transformed cells. Thus, ARID1A deficiency due to somatic mutations propels tumor progression and dissemination. The recent success of PARP inhibitors in treating homologous recombination DNA repair-deficient tumors has engendered keen interest in developing synthetic lethality-based therapeutic strategies for ARID1A-mutated neoplasms. In this review, we summarize recent advances in understanding the biology of ARID1A in cancer development, with special emphasis on its roles in DNA damage repair. We also discuss strategies to harness synthetic lethal mechanisms for future therapeutics against ARID1A-mutated cancers.


Assuntos
Neoplasias Ovarianas , Mutações Sintéticas Letais , Cromatina , Dano ao DNA , Proteínas de Ligação a DNA/genética , Proteínas de Ligação a DNA/metabolismo , Feminino , Histonas , Humanos , Proteínas Nucleares/metabolismo , Neoplasias Ovarianas/genética , Inibidores de Poli(ADP-Ribose) Polimerases , Fatores de Transcrição/genética , Fatores de Transcrição/metabolismo
20.
Medicine (Baltimore) ; 101(36): e30344, 2022 Sep 09.
Artigo em Inglês | MEDLINE | ID: mdl-36086687

RESUMO

Obesity is characterized by excessive accumulation of adiposity and has been implicated in a strong predisposition to metabolic disorders and cancer, constituting one of the major public health issues worldwide. The formation of new mature adipocytes through differentiation of progenitor or precursor cells during adipogenesis can lead to the expansion of adipose tissue. Recent studies have revealed that the intrinsic risk of obesity arises not only through genetic variants but also through epigenetic predisposition. Enhancer of zeste homolog 2 (EZH2) is an enzymatic catalytic component of polycomb repressive complex 2 that acts as an epigenetic modulator in the regulation of gene expression. EZH2 can modulate the expression of its target genes by the trimethylation of Lys-27 in histone 3 or methylation of non-histone proteins. Emerging evidence has shown the important role played by EZH2 in adipogenesis and obesity. This review provides the latest knowledge about the involvement of EZH2 in the process of adipogenesis and obesity involving adipocyte differentiation, extract key concepts, and highlight open questions toward a better understanding of EZH2 function and the molecular mechanisms underlying obesity.


Assuntos
Adipogenia , Proteína Potenciadora do Homólogo 2 de Zeste , Proteína Potenciadora do Homólogo 2 de Zeste/genética , Histonas/metabolismo , Humanos , Obesidade/genética , Complexo Repressor Polycomb 2/genética , Complexo Repressor Polycomb 2/metabolismo
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