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1.
J Phys Chem Lett ; 10(22): 7200-7207, 2019 Nov 21.
Artigo em Inglês | MEDLINE | ID: mdl-31693374

RESUMO

DNA compaction is essential to ensure the packaging of the genetic material in living cells and also plays a key role in the epigenetic regulation of gene expression. In both humans and bacteria, DNA packaging is achieved by specific well-conserved proteins. Here, by means of all-atom molecular dynamics simulations, including the determination of relevant free-energy profiles, we rationalize the molecular bases for this remarkable process in bacteria, illustrating the crucial role played by positively charged amino acids of a small histone-like protein. We also present compelling evidence that this histone-like protein alone can induce strong bending of a DNA duplex around its core domain, a process that requires overcoming a major free-energy barrier.


Assuntos
Proteínas de Bactérias/química , Borrelia burgdorferi/química , Empacotamento do DNA , DNA Bacteriano/química , Histonas/química , Simulação de Dinâmica Molecular , Modelos Moleculares
2.
Nature ; 574(7779): 575-580, 2019 10.
Artigo em Inglês | MEDLINE | ID: mdl-31645732

RESUMO

The Warburg effect, which originally described increased production of lactate in cancer, is associated with diverse cellular processes such as angiogenesis, hypoxia, polarization of macrophages and activation of T cells. This phenomenon is intimately linked to several diseases including neoplasia, sepsis and autoimmune diseases1,2. Lactate, which is converted from pyruvate in tumour cells, is widely known as an energy source and metabolic by-product. However, its non-metabolic functions in physiology and disease remain unknown. Here we show that lactate-derived lactylation of histone lysine residues serves as an epigenetic modification that directly stimulates gene transcription from chromatin. We identify 28 lactylation sites on core histones in human and mouse cells. Hypoxia and bacterial challenges induce the production of lactate by glycolysis, and this acts as a precursor that stimulates histone lactylation. Using M1 macrophages that have been exposed to bacteria as a model system, we show that histone lactylation has different temporal dynamics from acetylation. In the late phase of M1 macrophage polarization, increased histone lactylation induces homeostatic genes that are involved in wound healing, including Arg1. Collectively, our results suggest that an endogenous 'lactate clock' in bacterially challenged M1 macrophages turns on gene expression to promote homeostasis. Histone lactylation thus represents an opportunity to improve our understanding of the functions of lactate and its role in diverse pathophysiological conditions, including infection and cancer.


Assuntos
Epigênese Genética , Glicólise/genética , Histonas/química , Histonas/metabolismo , Ácido Láctico/metabolismo , Acetilação , Sequência de Aminoácidos , Animais , Linhagem Celular Tumoral , Cromatina/química , Cromatina/genética , Cromatina/metabolismo , Homeostase , Humanos , Hipóxia/metabolismo , Lisina/química , Lisina/metabolismo , Macrófagos/metabolismo , Macrófagos/microbiologia , Masculino , Camundongos , Camundongos Endogâmicos C57BL , Reprodutibilidade dos Testes , Transcrição Genética
3.
Enzymes ; 45: 27-57, 2019.
Artigo em Inglês | MEDLINE | ID: mdl-31627880

RESUMO

Repair of damaged DNA plays a crucial role in maintaining genomic integrity and normal cell function. The base excision repair (BER) pathway is primarily responsible for removing modified nucleobases that would otherwise cause deleterious and mutagenic consequences and lead to disease. The BER process is initiated by a DNA glycosylase, which recognizes and excises the target nucleobase lesion, and is completed via downstream enzymes acting in a well-coordinated manner. A majority of our current understanding about how BER enzymes function comes from in vitro studies using free duplex DNA as a simplified model. In eukaryotes, however, BER is challenged by the packaging of genomic DNA into chromatin. The fundamental structural repeating unit of chromatin is the nucleosome, which presents a more complex substrate context than free duplex DNA for repair. In this chapter, we discuss how BER enzymes, particularly glycosylases, engage in the context of packaged DNA with insights obtained from both in vivo and in vitro studies. Furthermore, we review factors and mechanisms that can modify chromatin architecture and/or influence DNA accessibility to BER machinery, such as the geometric location of the damage site, nucleosomal DNA unwrapping, histone post-translational modifications, histone variant incorporation, and chromatin remodeling.


Assuntos
Cromatina/química , Cromatina/genética , Dano ao DNA , Reparo do DNA , DNA/química , DNA/metabolismo , Montagem e Desmontagem da Cromatina , DNA/genética , Histonas/química , Histonas/metabolismo , Nucleossomos/química , Nucleossomos/genética
4.
J Chem Theory Comput ; 15(10): 5659-5673, 2019 Oct 08.
Artigo em Inglês | MEDLINE | ID: mdl-31476125

RESUMO

Human heterochromatin protein 1 (HP1) is a key factor in heterochromatin formation and maintenance. Its chromo-shadow domain (CSD) homodimerizes, and the HP1 dimer acts as a hub, transiently interacting with diverse binding partner (BP) proteins. We analyze atomistic details of interactions of the HP1γ(CSD) dimer with one of its targets, the histone H3 N-terminal tail, using molecular dynamics (MD) simulations. The goal is to complement the available X-ray crystallography data and unravel potential dynamic effects in the molecular recognition. Our results suggest that HP1(CSD)-BP recognition involves structural dynamics of both partners, including structural communication between adjacent binding pockets that may fine-tune the sequence recognition. For example, HP1 Trp174 sidechain substates may help in distinguishing residues bound in the conserved HP1(CSD) ±2 hydrophobic pockets. Further, there is intricate competition between the binding of negatively charged HP1 C-terminal extension and solvent anions near the ±2 hydrophobic pockets, which is also influenced by the BP sequence. Phosphorylated H3 Y41 can interact with the same site. We also analyze the ability of several pair-additive force fields to describe the protein-protein interface. ff14SB and ff99SB-ILDN* provide the closest correspondence with the crystallographic model. The ff15ipq local dynamics are somewhat less consistent with details of the experimental structure, while larger perturbations of the interface commonly occur in CHARMM36m simulations. The balance of some interactions, mainly around the anion binding site, also depends on the ion parameters. Some differences between the simulated and experimental structures are attributable to crystal packing.


Assuntos
Proteínas Cromossômicas não Histona/química , Histonas/química , Cristalografia por Raios X , Dimerização , Histonas/metabolismo , Humanos , Simulação de Dinâmica Molecular , Conformação Proteica
5.
Sheng Li Xue Bao ; 71(4): 637-644, 2019 Aug 25.
Artigo em Chinês | MEDLINE | ID: mdl-31440761

RESUMO

Mixed linked leukemia 4 (MLL4) is a specific methyltransferase of histone 3 position lysine 4 (H3K4). It is also one of the important members of COMPASS/Set1-like protein complex. Both MLL4 protein itself and its mediated H3K4 methylation modification can cause changes in chromatin structure and function, thus regulating gene transcription and expression. With the studies of MLL4 protein in recent years, the roles of MLL4 gene, MLL4 protein and protein complex in the development of tissues and organs, tumor diseases and other physiological and pathophysiological processes have been gradually revealed. In this paper, the research progress of MLL4 gene, MLL4 protein characteristics, biological function and its effect on disease were reviewed, in order to further understand the effect of histone methyltransferase on gene expression regulation, as well as its non-enzyme dependent function. This paper may provide new ideas for the prevention, diagnosis and treatment of related diseases.


Assuntos
Proteínas de Ligação a DNA/fisiologia , Histona-Lisina N-Metiltransferase/fisiologia , Histonas/química , Humanos , Metilação
6.
Nat Commun ; 10(1): 2935, 2019 07 03.
Artigo em Inglês | MEDLINE | ID: mdl-31270335

RESUMO

Trace elements play important roles in human health, but little is known about their functions in humoral immunity. Here, we show an important role for iron in inducing cyclin E and B cell proliferation. We find that iron-deficient individuals exhibit a significantly reduced antibody response to the measles vaccine when compared to iron-normal controls. Mice with iron deficiency also exhibit attenuated T-dependent or T-independent antigen-specific antibody responses. We show that iron is essential for B cell proliferation; both iron deficiency and α-ketoglutarate inhibition could suppress cyclin E1 induction and S phase entry of B cells upon activation. Finally, we demonstrate that three demethylases, KDM2B, KDM3B and KDM4C, are responsible for histone 3 lysine 9 (H3K9) demethylation at the cyclin E1 promoter, cyclin E1 induction and B cell proliferation. Thus, our data reveal a crucial role of H3K9 demethylation in B cell proliferation, and the importance of iron in humoral immunity.


Assuntos
Linfócitos B/imunologia , Proliferação de Células , Histonas/química , Histonas/imunologia , Imunidade Humoral , Lisina/imunologia , Animais , Linfócitos B/química , Linfócitos B/citologia , Ciclo Celular , Células Cultivadas , Ciclina E/genética , Ciclina E/imunologia , Desmetilação , Proteínas F-Box/genética , Proteínas F-Box/imunologia , Histonas/genética , Ferro/metabolismo , Histona Desmetilases com o Domínio Jumonji/genética , Histona Desmetilases com o Domínio Jumonji/imunologia , Ativação Linfocitária , Lisina/genética , Camundongos , Camundongos Endogâmicos C57BL , Proteínas Oncogênicas/genética , Proteínas Oncogênicas/imunologia , Regiões Promotoras Genéticas , Linfócitos T/citologia , Linfócitos T/imunologia
7.
Biophys Chem ; 253: 106225, 2019 10.
Artigo em Inglês | MEDLINE | ID: mdl-31323431

RESUMO

Several in vitro experiments have highlighted that the Polycomb group protein BMI1 plays a pivotal role in determining the biological functions of the Polycomb Repressor Complex 1 (PRC1), including its E3-ligase activity towards the Lys119 of histone H2A to yield ubiquitinated uH2A. The role of BMI1 in the epigenetic activity of PRC1 is particularly relevant in several cancers, particularly Non-Small Cell Lung Cancer (NSCLC). In this study, using indirect immunofluorescence protocols implemented on a confocal microscopy apparatus, we investigated the relationship between BMI1 and uH2A at different resolutions, in cultured (A549) and clinical NSCLC tissues, at the single cell level. In both cases, we observed a linear dependence of uH2A concentration upon BMI1 expression at the single nucleus level, indicating that the association of BMI1 to PRC1, which is needed for E3-ligase activity, occurs linearly in the physiological BMI1 concentration range. Additionally, in the NSCLC cell line model, a minor pool of uH2A may exist in absence of concurrent BMI1 expression, indicating non-exclusive, although predominant, role of BMI1 in the amplification of the E3-ligase activity of PRC1. A pharmacological downregulator of BMI1, PTC-209, was also tested in this context. Finally, the absence of significant colocalization (as measured by the Pearson's coefficient) between BMI1 and uH2A submicron clusters hints to a dynamic model where PRC1 resides transiently at ubiquitination sites. Beside unveiling subtle functional relationships between BMI1 and uH2A, these results also validate the use of uH2A as downstream "reporter" for BMI1 activity at the nuclear level in NSCLC contexts.


Assuntos
Histonas/química , Imagem Óptica , Complexo Repressor Polycomb 1/química , Análise de Célula Única , Ubiquitinas/química , Células A549 , Humanos
8.
J Chem Phys ; 150(21): 215102, 2019 Jun 07.
Artigo em Inglês | MEDLINE | ID: mdl-31176328

RESUMO

A central question in epigenetics is how histone modifications influence the 3D structure of eukaryotic genomes and, ultimately, how this 3D structure is manifested in gene expression. The wide range of length scales that influence the 3D genome structure presents important challenges; epigenetic modifications to histones occur on scales of angstroms, yet the resulting effects of these modifications on genome structure can span micrometers. There is a scarcity of computational tools capable of providing a mechanistic picture of how molecular information from individual histones is propagated up to large regions of the genome. In this work, a new molecular model of chromatin is presented that provides such a picture. This new model, referred to as 1CPN, is structured around a rigorous multiscale approach, whereby free energies from an established and extensively validated model of the nucleosome are mapped onto a reduced coarse-grained topology. As such, 1CPN incorporates detailed physics from the nucleosome, such as histone modifications and DNA sequence, while maintaining the computational efficiency that is required to permit kilobase-scale simulations of genomic DNA. The 1CPN model reproduces the free energies and dynamics of both single nucleosomes and short chromatin fibers, and it is shown to be compatible with recently developed models of the linker histone. It is applied here to examine the effects of the linker DNA on the free energies of chromatin assembly and to demonstrate that these free energies are strongly dependent on the linker DNA length, pitch, and even DNA sequence. The 1CPN model is implemented in the LAMMPS simulation package and is distributed freely for public use.


Assuntos
Cromatina/química , Modelos Químicos , Montagem e Desmontagem da Cromatina , DNA/química , Epigênese Genética , Histonas/química , Conformação de Ácido Nucleico , Nucleossomos/química
9.
J Biochem ; 166(1): 3-6, 2019 Jul 01.
Artigo em Inglês | MEDLINE | ID: mdl-31198932

RESUMO

Heterochromatin is a condensed and transcriptionally silent chromatin structure and that plays important roles in epigenetic regulation of the genome. Two types of heterochromatin exist: constitutive heterochromatin is primarily associated with trimethylation of histone H3 at lysine 9 (H3K9me3), and facultative heterochromatin with trimethylation of H3 at lysine 27 (H3K27me3). The methylated histones are bound by the chromodomain of histone code 'reader' proteins: HP1 family proteins for H3K9me3 and Polycomb family proteins for H3K27me3. Each repressive reader associates with various 'effector' proteins that provide the functional basis of heterochromatin. Heterochromatin regulation is primarily achieved by controlling histone modifications. However, recent studies have revealed that the repressive readers are phosphorylated, like other regulatory proteins, suggesting that phosphorylation also participates in heterochromatin regulation. Detailed studies have shown that phosphorylation of readers affects the binding specificities of chromodomains for methylated histone H3, as well as the binding of effector proteins. Thus, phosphorylation adds another layer to heterochromatin regulation. Interestingly, casein kinase 2, a strong and predominant kinase within the cell, is responsible for phosphorylation of repressive readers. In this commentary, I summarize the regulation of repressive readers by casein kinase 2-dependent phosphorylation and discuss the functional meaning of this modification.


Assuntos
Caseína Quinase II/metabolismo , Heterocromatina/metabolismo , Código das Histonas/fisiologia , Histonas/química , Histonas/metabolismo , Animais , Heterocromatina/química , Heterocromatina/genética , Histonas/genética , Humanos , Fosforilação
10.
Nucleic Acids Res ; 47(11): 5617-5633, 2019 06 20.
Artigo em Inglês | MEDLINE | ID: mdl-31216039

RESUMO

Nucleosomes, the fundamental organizing units of eukaryotic genomes, contain ∼146 base pairs of DNA wrapped around a histone H3-H4 tetramer and two histone H2A-H2B dimers. Converting nucleosomes into hexasomes by removal of a H2A-H2B dimer is an important regulatory event, but its regulation and functional consequences are not well-understood. To investigate the influence of hexasomes on DNA accessibility, we used the property of the Widom-601 Nucleosome Positioning Sequence (NPS) to form homogeneously oriented hexasomes in vitro. We find that DNA accessibility to transcription factors (TF) on the hexasome H2A-H2B distal side is identical to naked DNA, while the accessibility on the H2A-H2B proximal side is reduced by 2-fold, which is due to a 2-fold reduction in hexasome unwrapping probability. We then determined that a 23 bp region of the Widom-601 NPS is responsible for forming homogeneously oriented hexasomes. Analysis of published ChIP-exo data of hexasome containing genes identified two DNA sequence motifs that correlate with hexasome orientation in vivo, while ExoIII mapping studies of these sequences revealed they generate homogeneously oriented hexasomes in vitro. These results indicate that hexasome orientation, which is influenced by the underlying DNA sequence in vivo, is important for modulating DNA accessibility to regulate transcription.


Assuntos
Montagem e Desmontagem da Cromatina , Proteínas de Ligação a DNA/química , DNA/química , Histonas/química , Nucleossomos/química , Fatores de Transcrição/química , DNA/genética , Regulação da Expressão Gênica , Nucleossomos/genética , Ligação Proteica , Multimerização Proteica , Transcrição Genética
11.
Artif Cells Nanomed Biotechnol ; 47(1): 2343-2351, 2019 Dec.
Artigo em Inglês | MEDLINE | ID: mdl-31184227

RESUMO

Recent papers suggest that oncogenic Ras participate in regulating tumour cells proliferation and metastasis. This work linked Ras with H1.4 modification in non-small-cell lung carcinoma (NSCLC), to better understand the oncogenic effects of Ras. A plasmid for expressing Ras mutated at G13D and T35S was transfected into NCI-H2126 and A549 cells. Phosphorylation of H1.4S36 was determined by immunoblotting. Effects of phosphorylation of H1.4 at serine (S) 36 (H1.4S36ph) on NCI-H2126 and A549 cells were tested by MTT assay, soft-agar colony formation assay, flow cytometry and transwell assay. Chromatin-immunoprecipitation (ChIP) and RT-qPCR were conducted to measure the effects of H1.4S36ph on Ras downstream genes. The catalyzing enzymes participate in H1.4S36 phosphorylation were further studied. We found that Ras-ERK signalling repressed the phosphorylation of H1.4 at S36. H1.4S36ph functioned as a tumour suppressor, as its overexpression repressed NCI-H2126 and A549 cells viability, colony formation, S-phase arrest, migration and invasion. H1.4S36ph was able to mediate the transcription of Ras downstream genes. Ras-ERK signalling repressed H1.4S36ph through degradation of PKA, and the degradation was mediated by MDM2. In conclusion, Ras-ERK signalling repressed H1.4 phosphorylation at S36 to participate in NSCLC cells growth, migration and invasion. Ras-ERK signalling repressed H1.4S36ph through MDM2-dependent degradation of PKA. This study provides a novel explanation for Ras-ERK's tumour-promoting function. Highlights: H1.4S36 phosphorylation is repressed by Ras-ERK activation; H1.4S36ph inhibits the phenotype of NSCLC cells; H1.4S36ph regulates the transcription of Ras downstream genes; Ras-ERK represses H1.4S36ph by MDM2-dependent degradation of PKA.


Assuntos
Carcinoma Pulmonar de Células não Pequenas/patologia , Movimento Celular , MAP Quinases Reguladas por Sinal Extracelular/metabolismo , Histonas/metabolismo , Neoplasias Pulmonares/patologia , Transdução de Sinais , Proteínas ras/metabolismo , Células A549 , Carcinoma Pulmonar de Células não Pequenas/genética , Carcinoma Pulmonar de Células não Pequenas/metabolismo , Proliferação de Células , Proteínas Quinases Dependentes de AMP Cíclico/metabolismo , Regulação Neoplásica da Expressão Gênica , Histonas/química , Humanos , Neoplasias Pulmonares/genética , Neoplasias Pulmonares/metabolismo , Fenótipo , Fosforilação , Proteólise , Serina/metabolismo
12.
Fish Shellfish Immunol ; 92: 667-679, 2019 Sep.
Artigo em Inglês | MEDLINE | ID: mdl-31252047

RESUMO

Antimicrobial peptides (AMPs) derived from histone proteins form an important category of peptide antibiotics. Present study deals with the molecular and functional characterization of a 27-amino acid histone H2A derived AMP from the Indian White shrimp, Fenneropenaeus indicus designated as Fi-Histin. This peptide displayed distinctive features of AMPs such as amphiphilic alpha helical structure and a net charge of +6. The synthetic peptide exhibited significant antimicrobial activity against Gram-negative and Gram-positive bacteria especially against V. vulnificus, P. aeruginosa, V. parahaemolyticus, V. cholera and S. aureus. Disruption of cell membrane and cell content leakage were observed in peptide treated V. vulnificus using scanning electron microscopy. The synthetic peptide Fi-His1-21 exhibited DNA binding activity and found to be non-haemolytic at the tested concentrations. Peptide was also found to possess anticancer activity against NCI-H460 and HEp-2 cell lines with an IC50 of 22.670 ±â€¯13.939 µM and 31.274 ±â€¯24.531 µM respectively. This is the first report of a histone H2A derived peptide from F. indicus with a specific antimicrobial activity and anticancer activity, which could be a new candidate for future applications in aquaculture and medicine.


Assuntos
Peptídeos Catiônicos Antimicrobianos/farmacologia , Antineoplásicos/farmacologia , Histonas/genética , Histonas/imunologia , Penaeidae/genética , Penaeidae/imunologia , Sequência de Aminoácidos , Animais , Peptídeos Catiônicos Antimicrobianos/química , Peptídeos Catiônicos Antimicrobianos/genética , Proteínas de Artrópodes/química , Proteínas de Artrópodes/genética , Proteínas de Artrópodes/imunologia , Sequência de Bases , Linhagem Celular Tumoral , Bactérias Gram-Negativas/efeitos dos fármacos , Bactérias Gram-Positivas/efeitos dos fármacos , Histonas/química , Humanos , Filogenia , Alinhamento de Sequência
13.
J Chem Phys ; 150(18): 185103, 2019 May 14.
Artigo em Inglês | MEDLINE | ID: mdl-31091895

RESUMO

The nucleosome is the fundamental packaging unit for the genome. It must remain tightly wound to ensure genome stability while simultaneously being flexible enough to keep the DNA molecule accessible for genome function. The set of physicochemical interactions responsible for the delicate balance between these naturally opposed processes have not been determined due to challenges in resolving partially unwound nucleosome configurations at atomic resolution. Using a near atomistic protein-DNA model and advanced sampling techniques, we calculate the free energy cost of nucleosome DNA unwinding. Our simulations identify a large energetic barrier that decouples the outer and the inner DNA unwinding into two separate processes, occurring on different time scales. This dynamical decoupling allows the exposure of outer DNA at a modest cost to ensure accessibility while keeping the inner DNA and the histone core intact to maintain stability. We also reveal that this energetic barrier arises from a delayed loss of contacts between disordered histone tails and the DNA and is, surprisingly, largely offset by an entropic contribution from these tails. Implications of this enthalpy entropy compensation for the regulation of nucleosome stability and genome function are discussed.


Assuntos
DNA/química , Entropia , Histonas/química , Nucleossomos/química , Modelos Químicos , Modelos Moleculares , Conformação de Ácido Nucleico , Conformação Proteica
14.
J Dairy Sci ; 102(7): 6047-6055, 2019 Jul.
Artigo em Inglês | MEDLINE | ID: mdl-31103295

RESUMO

The rapid and sensitive detection of foodborne pathogens is one of the most important issues in food safety control. In this work, we developed a novel fluorescence immunoassay method for the sensitive detection of Salmonella choleraesuis. The method uses the fluorescent signals of histone-ds-poly(AT)-templated copper nanoparticles (His-pAT CuNP) as signal transducers and glucose oxidase as an alternative for horseradish peroxidase for the generation of hydrogen peroxide (H2O2) through the catalysis of glucose. The H2O2 is then further converted into hydroxyl radical (·OH) by Fenton reagents. Owing to the ultrahigh sensitivity of His-pAT CuNP synthesis toward ·OH, the proposed fluorescence immunoassay method exhibited excellent sensitivity for S. choleraesuis, with a limit of detection of 8.04 × 101 cfu/mL, which is 3 orders of magnitude lower than that of the tetramethylbenzidine-based traditional immunoassay. The reliability of the proposed method was evaluated by using spiked milk samples with S. choleraesuis concentration ranging from 8.8 × 101 to 8.8 × 104 cfu/mL. The average recoveries for the intra- and inter-assay ranged from 73.52 to 96.59% and from 66.99 to 98.24% with a coefficient of variation from 6.85 to 31.26% and 5.46 to 17.99%, respectively. These results indicated that the proposed fluorescence immunoassay possesses a great potential for ultra-sensitive detection of foodborne pathogens in food safety control.


Assuntos
Fluorimunoensaio/veterinária , Histonas/química , Nanopartículas Metálicas , Leite/microbiologia , Salmonella enterica/isolamento & purificação , Animais , Bovinos , Cobre , Fluorimunoensaio/métodos , Glucose Oxidase/metabolismo , Peróxido de Hidrogênio/química , Ferro , Nanopartículas Metálicas/química , Reprodutibilidade dos Testes
15.
Nature ; 571(7763): 79-84, 2019 07.
Artigo em Inglês | MEDLINE | ID: mdl-31142837

RESUMO

Access to DNA packaged in nucleosomes is critical for gene regulation, DNA replication and DNA repair. In humans, the UV-damaged DNA-binding protein (UV-DDB) complex detects UV-light-induced pyrimidine dimers throughout the genome; however, it remains unknown how these lesions are recognized in chromatin, in which nucleosomes restrict access to DNA. Here we report cryo-electron microscopy structures of UV-DDB bound to nucleosomes bearing a 6-4 pyrimidine-pyrimidone dimer or a DNA-damage mimic in various positions. We find that UV-DDB binds UV-damaged nucleosomes at lesions located in the solvent-facing minor groove without affecting the overall nucleosome architecture. In the case of buried lesions that face the histone core, UV-DDB changes the predominant translational register of the nucleosome and selectively binds the lesion in an accessible, exposed position. Our findings explain how UV-DDB detects occluded lesions in strongly positioned nucleosomes, and identify slide-assisted site exposure as a mechanism by which high-affinity DNA-binding proteins can access otherwise occluded sites in nucleosomal DNA.


Assuntos
Dano ao DNA , Proteínas de Ligação a DNA/metabolismo , DNA/metabolismo , DNA/ultraestrutura , Nucleossomos/metabolismo , Nucleossomos/ultraestrutura , Dímeros de Pirimidina/análise , Microscopia Crioeletrônica , DNA/química , DNA/efeitos da radiação , Proteínas de Ligação a DNA/química , Proteínas de Ligação a DNA/genética , Proteínas de Ligação a DNA/ultraestrutura , Histonas/química , Histonas/metabolismo , Histonas/ultraestrutura , Humanos , Modelos Moleculares , Nucleossomos/genética , Nucleossomos/efeitos da radiação , Dímeros de Pirimidina/química , Dímeros de Pirimidina/genética , Termodinâmica , Raios Ultravioleta/efeitos adversos
16.
Nat Commun ; 10(1): 2314, 2019 05 24.
Artigo em Inglês | MEDLINE | ID: mdl-31127101

RESUMO

Histone methyltransferase MLL4 is centrally involved in transcriptional regulation and is often mutated in human diseases, including cancer and developmental disorders. MLL4 contains a catalytic SET domain that mono-methylates histone H3K4 and seven PHD fingers of unclear function. Here, we identify the PHD6 finger of MLL4 (MLL4-PHD6) as a selective reader of the epigenetic modification H4K16ac. The solution NMR structure of MLL4-PHD6 in complex with a H4K16ac peptide along with binding and mutational analyses reveal unique mechanistic features underlying recognition of H4K16ac. Genomic studies show that one third of MLL4 chromatin binding sites overlap with H4K16ac-enriched regions in vivo and that MLL4 occupancy in a set of genomic targets depends on the acetyltransferase activity of MOF, a H4K16ac-specific acetyltransferase. The recognition of H4K16ac is conserved in the PHD7 finger of paralogous MLL3. Together, our findings reveal a previously uncharacterized acetyllysine reader and suggest that selective targeting of H4K16ac by MLL4 provides a direct functional link between MLL4, MOF and H4K16 acetylation.


Assuntos
Proteínas de Ligação a DNA/metabolismo , Histona Acetiltransferases/metabolismo , Histona-Lisina N-Metiltransferase/metabolismo , Histonas/metabolismo , Dedos de Zinco PHD/fisiologia , Acetilação , Animais , Sítios de Ligação , Cromatina/metabolismo , Proteínas de Ligação a DNA/química , Proteínas de Ligação a DNA/genética , Proteínas de Ligação a DNA/isolamento & purificação , Técnicas de Inativação de Genes , Células HEK293 , Histona Acetiltransferases/genética , Histona-Lisina N-Metiltransferase/química , Histonas/química , Humanos , Camundongos Transgênicos , Modelos Moleculares , Mutagênese Sítio-Dirigida , Ressonância Magnética Nuclear Biomolecular , Processamento de Proteína Pós-Traducional/fisiologia , Proteínas Recombinantes/química , Proteínas Recombinantes/genética , Proteínas Recombinantes/isolamento & purificação , Proteínas Recombinantes/metabolismo
17.
Mol Biol (Mosk) ; 53(2): 268-273, 2019.
Artigo em Russo | MEDLINE | ID: mdl-31099776

RESUMO

Many human genes that control human embryonic development and differentiation of human cells form chromosomal contact with rRNA gene clusters, which are involved in the epigenetic regulation of many genes. The sites of rRNA gene contact often fall on extended (up to 50 kb) regions containing a chromatin mark, H3K27ac histone, typical for superenhancers, as well as on pericentromeric and subtelomeric regions of chromosomes. We found that the DUX4 genes located in the subtelomeric region of human chromosome 4 are surrounded by regions that are often in contact with the rRNA genes. The 25 kb region of this chromosome, presented in version hg19 of the sequenced human genome, contains several copies of the DUX4 gene. The sites of rRNA gene contacts located around this region contain methylation sites as well as CTCF binding sites. It is assumed that the rRNA gene contacts are important in silencing these DUX4 gene copies.


Assuntos
DNA Ribossômico/genética , Desenvolvimento Embrionário/genética , Proteínas de Homeodomínio/genética , Família Multigênica/genética , Fator de Ligação a CCCTC/metabolismo , Cromatina/genética , Cromatina/metabolismo , Cromossomos Humanos Par 4/genética , Epigênese Genética , Histonas/química , Histonas/metabolismo , Humanos , Telômero/genética , Telômero/metabolismo
18.
Mol Biol (Mosk) ; 53(2): 339-348, 2019.
Artigo em Russo | MEDLINE | ID: mdl-31099784

RESUMO

Cortexin is a clinically approved cerebral cortex polypeptide complex in calves. The mechanism of cortexin action is not understood well. Two cortexin derivatives, short peptides EDR and DS with neuroprotective activity, were synthesized. According to the data of molecular modeling, these peptides are able to bind to the histone H1.3 protein. This can affect the conformation of histone H1.3, which leads to a change in the chromatin structure in the loci of some genes, in particular Fkbp1b encoding the FK506-binding protein. Electrophysiological processes associated with the Ca^(2+) exchange are disturbed in the pyramidal neurons of the hippocampus during aging of the brain. The Fkbp1b gene encodes peptidyl-prolyl cis-trans isomerase, regulating the release of calcium ions from the sarcoplasmic and endoplasmic reticulum of neurons. The activation of the Fkbp1b gene transcription under treatment with short peptides can promote the synthesis of its protein product and the activation of the Ca^(2+) release from organelles of the sarcoplasmic and endoplasmic reticulum of neurons, which, in turn, can lead to an increase in the functional activity of neurons.


Assuntos
Epigênese Genética , Neuroproteção , Peptídeos/metabolismo , Proteínas de Ligação a Tacrolimo/genética , Proteínas de Ligação a Tacrolimo/metabolismo , Adulto , Idoso , Sequência de Aminoácidos , Animais , Histonas/química , Histonas/metabolismo , Humanos , Pessoa de Meia-Idade , Modelos Moleculares , Neuroproteção/genética , Neuroproteção/fisiologia , Peptídeos/química , Ligação Proteica , Células Piramidais/metabolismo , Proteínas de Ligação a Tacrolimo/química
19.
Nat Commun ; 10(1): 1751, 2019 04 15.
Artigo em Inglês | MEDLINE | ID: mdl-30988309

RESUMO

Ubiquitination of chromatin by modification of histone H2A is a critical step in both regulation of DNA repair and regulation of cell fate. These very different outcomes depend on the selective modification of distinct lysine residues in H2A, each by a specific E3 ligase. While polycomb PRC1 complexes modify K119, resulting in gene silencing, the E3 ligase RNF168 modifies K13/15, which is a key event in the response to DNA double-strand breaks. The molecular origin of ubiquitination site specificity by these related E3 enzymes is one of the open questions in the field. Using a combination of NMR spectroscopy, crosslinking mass-spectrometry, mutagenesis and data-driven modelling, here we show that RNF168 binds the acidic patch on the nucleosome surface, directing the E2 to the target lysine. The structural model highlights the role of E3 and nucleosome in promoting ubiquitination and provides a basis for understanding and engineering of chromatin ubiquitination specificity.


Assuntos
Histonas/química , Ubiquitina-Proteína Ligases/química , Diferenciação Celular , Reparo do DNA , Histonas/metabolismo , Humanos , Modelos Moleculares , Domínios Proteicos , Ubiquitina-Proteína Ligases/metabolismo , Ubiquitina-Proteína Ligases/fisiologia , Ubiquitinação
20.
Nat Commun ; 10(1): 1705, 2019 04 12.
Artigo em Inglês | MEDLINE | ID: mdl-30979870

RESUMO

Enhancers are critical for developmental stage-specific gene expression, but their dynamic regulation in plants remains poorly understood. Here we compare genome-wide localization of H3K27ac, chromatin accessibility and transcriptomic changes during flower development in Arabidopsis. H3K27ac prevalently marks promoter-proximal regions, suggesting that H3K27ac is not a hallmark for enhancers in Arabidopsis. We provide computational and experimental evidence to confirm that distal DNase І hypersensitive sites are predictive of enhancers. The predicted enhancers are highly stage-specific across flower development, significantly associated with SNPs for flowering-related phenotypes, and conserved across crucifer species. Through the integration of genome-wide transcription factor (TF) binding datasets, we find that floral master regulators and stage-specific TFs are largely enriched at developmentally dynamic enhancers. Finally, we show that enhancer clusters and intronic enhancers significantly associate with stage-specific gene regulation by floral master TFs. Our study provides insights into the functional flexibility of enhancers during plant development, as well as hints to annotate plant enhancers.


Assuntos
Arabidopsis/genética , Arabidopsis/fisiologia , Elementos Facilitadores Genéticos , Flores/fisiologia , Imunoprecipitação da Cromatina , Genes de Plantas , Estudo de Associação Genômica Ampla , Histonas/química , Fenótipo , Polimorfismo de Nucleotídeo Único , Análise de Sequência de RNA
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