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1.
Adv Protein Chem Struct Biol ; 130: 189-243, 2022.
Artigo em Inglês | MEDLINE | ID: mdl-35534108

RESUMO

Histone modifying enzymes regulate chromatin architecture through covalent modifications and ultimately control multiple aspects of cellular function. Disruption of histone modification leads to changes in gene expression profiles and may lead to disease. Both small molecule inhibitors and intermediary metabolites have been shown to modulate histone modifying enzyme activity although our ability to identify successful drug candidates or novel metabolic regulators of these enzymes has been limited. Using a combination of large scale in silico screens and in vivo phenotypic analysis, we identified several small molecules and intermediary metabolites with distinctive HME activity. Our approach using unsupervised learning identifies the chemical fingerprints of both small molecules and metabolites that facilitate recognition by the enzymes active sites which can be used as a blueprint to design novel inhibitors. Furthermore, this work supports the idea that histone modifying enzymes sense intermediary metabolites integrating genes, environment and cellular physiology.


Assuntos
Cromatina , Histonas , Montagem e Desmontagem da Cromatina , Desenho de Fármacos , Histonas/metabolismo , Processamento de Proteína Pós-Traducional
2.
Nature ; 605(7908): 166-171, 2022 05.
Artigo em Inglês | MEDLINE | ID: mdl-35477757

RESUMO

DNA wraps around the histone octamer to form nucleosomes1, the repeating unit of chromatin, which create barriers for accessing genetic information. Snf2-like chromatin remodellers couple the energy of ATP binding and hydrolysis to reposition and recompose the nucleosome, and have vital roles in various chromatin-based transactions2,3. Here we report the cryo-electron microscopy structure of the 12-subunit human chromatin-remodelling polybromo-associated BRG1-associated factor (PBAF) complex bound to the nucleosome. The motor subunit SMARCA4 engages the nucleosome in the active conformation, which reveals clustering of multiple disease-associated mutations at the interfaces that are essential for chromatin-remodelling activity. SMARCA4 recognizes the H2A-H2B acidic pocket of the nucleosome through three arginine anchors of the Snf2 ATP coupling (SnAc) domain. PBAF shows notable functional modularity, and most of the auxiliary subunits are interwoven into three lobe-like submodules for nucleosome recognition. The PBAF-specific auxiliary subunit ARID2 acts as the structural core for assembly of the DNA-binding lobe, whereas PBRM1, PHF10 and BRD7 are collectively incorporated into the lobe for histone tail binding. Together, our findings provide mechanistic insights into nucleosome recognition by PBAF and a structural basis for understanding SMARCA4-related human diseases.


Assuntos
Histonas , Nucleossomos , Trifosfato de Adenosina/metabolismo , Cromatina/genética , Montagem e Desmontagem da Cromatina , Proteínas Cromossômicas não Histona/metabolismo , Microscopia Crioeletrônica , DNA/metabolismo , DNA Helicases/metabolismo , Histonas/metabolismo , Proteínas de Homeodomínio , Humanos , Modelos Moleculares , Proteínas de Neoplasias , Proteínas Nucleares/metabolismo , Fatores de Transcrição/metabolismo
3.
Front Cell Infect Microbiol ; 12: 860058, 2022.
Artigo em Inglês | MEDLINE | ID: mdl-35433496

RESUMO

Intracellular pathogens manipulate the host cell for their own survival by contributing to modifications of host epigenome, and thus, altering expression of genes involved in the pathogenesis. Both ATP-dependent chromatin remodeling complex and histone modifications has been shown to be involved in the activation of IFNγ responsive genes. Leishmania donovani is an intracellular pathogen that causes visceral leishmaniasis. The strategies employed by Leishmania donovani to modulate the host epigenome in order to overcome the host defense for their persistence has been worked out in this study. We show that L. donovani negatively affects BRG1, a catalytic subunit of mammalian SWI/SNF chromatin remodeling complex, to alter IFNγ induced host responses. We observed that L. donovani infection downregulates BRG1 expression both at transcript and protein levels in cells stimulated with IFNγ. We also observed a significant decrease in IFNγ responsive gene, Class II transactivator (CIITA), as well as its downstream genes, MHC-II (HLA-DR and HLA-DM). Also, the occupancy of BRG1 at CIITA promoters I and IV was disrupted. A reversal in CIITA expression and decreased parasite load was observed with BRG1 overexpression, thus, suggesting BRG1 is a potential negative regulator for the survival of intracellular parasites in an early phase of infection. We also observed a decrease in H3 acetylation at the promoters of CIITA, post parasite infection. Silencing of HDAC1, resulted in increased CIITA expression, and further decreased parasite load. Taken together, we suggest that intracellular parasites in an early phase of infection negatively regulates BRG1 by using host HDAC1 for its survival inside the host.


Assuntos
Leishmania donovani , Fatores de Transcrição , Animais , Cromatina , Montagem e Desmontagem da Cromatina , Humanos , Interferon gama/metabolismo , Leishmania donovani/genética , Mamíferos/genética , Regiões Promotoras Genéticas , Células THP-1 , Fatores de Transcrição/genética , Fatores de Transcrição/metabolismo
4.
Nat Commun ; 13(1): 1807, 2022 Apr 04.
Artigo em Inglês | MEDLINE | ID: mdl-35379786

RESUMO

Enduring behavioral changes upon stress exposure involve changes in gene expression sustained by epigenetic modifications in brain circuits, including the mesocorticolimbic pathway. Brahma (BRM) and Brahma Related Gene 1 (BRG1) are ATPase subunits of the SWI/SNF complexes involved in chromatin remodeling, a process essential to enduring plastic changes in gene expression. Here, we show that in mice, social defeat induces changes in BRG1 nuclear distribution. The inactivation of the Brg1/Smarca4 gene within dopamine-innervated regions or the constitutive inactivation of the Brm/Smarca2 gene leads to resilience to repeated social defeat and decreases the behavioral responses to cocaine without impacting midbrain dopamine neurons activity. Within striatal medium spiny neurons, Brg1 gene inactivation reduces the expression of stress- and cocaine-induced immediate early genes, increases levels of heterochromatin and at a global scale decreases chromatin accessibility. Altogether these data demonstrate the pivotal function of SWI/SNF complexes in behavioral and transcriptional adaptations to salient environmental challenges.


Assuntos
Montagem e Desmontagem da Cromatina , Cromatina , Adenosina Trifosfatases/metabolismo , Animais , Linhagem Celular Tumoral , Camundongos , Recompensa
5.
Nat Commun ; 13(1): 2240, 2022 Apr 26.
Artigo em Inglês | MEDLINE | ID: mdl-35474218

RESUMO

Cognate antigen signal controls CD8+ T cell priming, expansion size and effector versus memory cell fates, but it is not known if and how it modulates the functional features of memory CD8+ T cells. Here we show that the strength of T cell receptor (TCR) signaling controls the requirement for interleukin-2 (IL-2) signals to form a pool of memory CD8+ T cells that competitively re-expand upon secondary antigen encounter. Combining strong TCR and intact IL-2 signaling during priming synergistically induces genome-wide chromatin accessibility in regions targeting a wide breadth of biological processes, consistent with greater T cell functional fitness. Chromatin accessibility in promoters of genes encoding for stem cell, cell cycle and calcium-related proteins correlates with faster intracellular calcium accumulation, initiation of cell cycle and more robust expansion. High-dimensional flow-cytometry analysis of these T cells also highlights higher diversity of T cell subsets and phenotypes with T cells primed with stronger TCR and IL-2 stimulation than those primed with weaker strengths of TCR and/or IL-2 signals. These results formally show that epitope selection in vaccine design impacts memory CD8+ T cell epigenetic programming and function.


Assuntos
Fenômenos Biológicos , Interleucina-2 , Antígenos/metabolismo , Linfócitos T CD8-Positivos , Cálcio/metabolismo , Cromatina/metabolismo , Montagem e Desmontagem da Cromatina , Memória Imunológica , Receptores de Antígenos de Linfócitos T/metabolismo
6.
Biophys J ; 121(9): 1738-1752, 2022 May 03.
Artigo em Inglês | MEDLINE | ID: mdl-35364106

RESUMO

Chromatin remodelers actively target arrays of acetylated nucleosomes at select enhancers and promoters to facilitate or shut down the repeated recruitment of RNA polymerase II during transcriptional bursting. It is poorly understood how chromatin remodelers such as PBAF dynamically target different chromatin states inside a live cell. Our live-cell single-molecule fluorescence microscopy study reveals chromatin hubs throughout the nucleus where PBAF rapidly cycles on and off the genome. Deletion of PBAF's bromodomains impairs targeting and stable engagement of chromatin in hubs. Dual color imaging reveals that PBAF targets both euchromatic and heterochromatic hubs with distinct genome-binding kinetic profiles that mimic chromatin stability. Removal of PBAF's bromodomains stabilizes H3.3 binding within chromatin, indicating that bromodomains may play a direct role in remodeling of the nucleosome. Our data suggests that PBAF's dynamic bromodomain-mediated engagement of a nucleosome may reflect the chromatin-remodeling potential of differentially bound chromatin states.


Assuntos
Cromatina , Nucleossomos , Acetilação , Montagem e Desmontagem da Cromatina , Proteínas de Ligação a DNA/metabolismo , Histonas/metabolismo , Fatores de Transcrição/metabolismo
7.
Nucleic Acids Res ; 50(7): 3892-3910, 2022 04 22.
Artigo em Inglês | MEDLINE | ID: mdl-35380694

RESUMO

Up to seven members of the histone H1 family may contribute to chromatin compaction and its regulation in human somatic cells. In breast cancer cells, knock-down of multiple H1 variants deregulates many genes, promotes the appearance of genome-wide accessibility sites and triggers an interferon response via activation of heterochromatic repeats. However, how these changes in the expression profile relate to the re-distribution of H1 variants as well as to genome conformational changes have not been yet studied. Here, we combined ChIP-seq of five endogenous H1 variants with Chromosome Conformation Capture analysis in wild-type and H1.2/H1.4 knock-down T47D cells. The results indicate that H1 variants coexist in the genome in two large groups depending on the local GC content and that their distribution is robust with respect to H1 depletion. Despite the small changes in H1 variants distribution, knock-down of H1 translated into more isolated but de-compacted chromatin structures at the scale of topologically associating domains (TADs). Such changes in TAD structure correlated with a coordinated gene expression response of their resident genes. This is the first report describing simultaneous profiling of five endogenous H1 variants and giving functional evidence of genome topology alterations upon H1 depletion in human cancer cells.


Assuntos
Cromatina , Histonas , Composição de Bases , Cromatina/genética , Montagem e Desmontagem da Cromatina , Expressão Gênica , Histonas/genética , Histonas/metabolismo , Humanos
8.
Mol Biol (Mosk) ; 56(2): 244-258, 2022.
Artigo em Russo | MEDLINE | ID: mdl-35403618

RESUMO

The process of inflammation is the body's natural defense response to the penetration of foreign substances and molecules from the outside. Many proteins, signaling cascades, and transcription factors are involved in the activation of inflammation genes. Their coordinated activity leads to a change in the expression of proinflammatory genes. The chromatin state of genes responding to the inflammation stimulus is the main factor determining the binding of transcriptional activators to the gene regulatory elements and a key mechanism in the induction of inflammatory genes. The rapid change in the state of chromatin, the creation of an open structure and the removal of the "nucleosome barrier" facilitates the binding of transcription factors and the initiation of transcription. This process is realized by attracting complexes to the gene that modify and remodel chromatin. One of the most important complexes restructuring the chromatin structure during gene activation is the SWI/SNF multisubunit complex. SWI/SNF regulates the expression of inflammation genes through interaction with transcription factors, including factors of the NF-κВ signaling pathway. The variability of the subunits of this complex determines the specificity of its binding to the chromatin and various transcriptional activators. This review considers the role of SWI/SNF in the regulation of inflammation genes, describes its interactions with chromatin, and the molecular mechanisms of its recruitment to the promoters.


Assuntos
Montagem e Desmontagem da Cromatina , Proteínas Nucleares , Cromatina/genética , Expressão Gênica , Regulação da Expressão Gênica , Humanos , Inflamação/genética , Proteínas Nucleares/genética , Fatores de Transcrição/genética , Fatores de Transcrição/metabolismo
9.
Nat Commun ; 13(1): 1731, 2022 04 01.
Artigo em Inglês | MEDLINE | ID: mdl-35365638

RESUMO

Aneuploidy results in decreased cellular fitness in many species and model systems. However, aneuploidy is commonly found in cancer cells and often correlates with aggressive growth, suggesting that the impact of aneuploidy on cellular fitness is context dependent. The BRG1 (SMARCA4) subunit of the SWI/SNF chromatin remodelling complex is frequently lost in cancer. Here, we use a chromosomally stable cell line to test the effect of BRG1 loss on the evolution of aneuploidy. BRG1 deletion leads to an initial loss of fitness in this cell line that improves over time. Notably, we find increased tolerance to aneuploidy immediately upon loss of BRG1, and the fitness recovery over time correlates with chromosome gain. These data show that BRG1 loss creates an environment where karyotype changes can be explored without a fitness penalty. At least in some genetic backgrounds, therefore, BRG1 loss can affect the progression of tumourigenesis through tolerance of aneuploidy.


Assuntos
Aneuploidia , Montagem e Desmontagem da Cromatina , Linhagem Celular , Aberrações Cromossômicas , Cromossomos , DNA Helicases/genética , Humanos , Proteínas Nucleares/genética , Fatores de Transcrição/genética
10.
PLoS Genet ; 18(4): e1009799, 2022 04.
Artigo em Inglês | MEDLINE | ID: mdl-35377871

RESUMO

Centrioles are submicron-scale, barrel-shaped organelles typically found in pairs, and play important roles in ciliogenesis and bipolar spindle assembly. In general, successful execution of centriole-dependent processes is highly reliant on the ability of the cell to stringently control centriole number. This in turn is mainly achieved through the precise duplication of centrioles during each S phase. Aberrations in centriole duplication disrupt spindle assembly and cilia-based signaling and have been linked to cancer, primary microcephaly and a variety of growth disorders. Studies aimed at understanding how centriole duplication is controlled have mainly focused on the post-translational regulation of two key components of this pathway: the master regulatory kinase ZYG-1/Plk4 and the scaffold component SAS-6. In contrast, how transcriptional control mechanisms might contribute to this process have not been well explored. Here we show that the chromatin remodeling protein CHD-1 contributes to the regulation of centriole duplication in the C. elegans embryo. Specifically, we find that loss of CHD-1 or inactivation of its ATPase activity can restore embryonic viability and centriole duplication to a strain expressing insufficient ZYG-1 activity. Interestingly, loss of CHD-1 is associated with increases in the levels of two ZYG-1-binding partners: SPD-2, the centriole receptor for ZYG-1 and SAS-6. Finally, we explore transcriptional regulatory networks governing centriole duplication and find that CHD-1 and a second transcription factor, EFL-1/DPL-1 cooperate to down regulate expression of CDK-2, which in turn promotes SAS-6 protein levels. Disruption of this regulatory network results in the overexpression of SAS-6 and the production of extra centrioles.


Assuntos
Proteínas de Caenorhabditis elegans , Centríolos , Animais , Caenorhabditis elegans/metabolismo , Proteínas de Caenorhabditis elegans/genética , Proteínas de Caenorhabditis elegans/metabolismo , Proteínas de Ciclo Celular/genética , Centríolos/genética , Centríolos/metabolismo , Montagem e Desmontagem da Cromatina/genética , Proteínas Quinases/genética , Fatores de Transcrição/genética , Fatores de Transcrição/metabolismo
11.
Protein Sci ; 31(5): e4294, 2022 05.
Artigo em Inglês | MEDLINE | ID: mdl-35481652

RESUMO

BAF250b and its paralog BAF250a are the DNA-binding central hub proteins present in BAF-B and BAF-A classes of SWI/SNF chromatin-remodeling complexes. BAF250b contains an AT-rich interaction domain (ARID) and C-terminal BAF250_C domain, and it is found mutated in several cancers. ARID is a conserved helix-turn-helix motif-containing DNA-binding domain present in several eukaryotic proteins. The ARID of BAF250b has been proposed to play roles in recruiting SWI/SNF to the target gene promoters for their activation. BAF250b ARID structures had been deposited in the protein data bank by a structural genomics consortium. However, it is not well-studied for its DNA-binding and solution dynamic properties. Here, we report complete backbone NMR resonance assignments of human BAF250b ARID. NMR chemical shifts and the backbone dynamics showed that the solution structure of the protein matched the reported crystal structures. The structure and chemical shift indexing revealed the presence of a short ß-sheet in the DNA-binding region of BAF250b ARID that was absent in the structure of its paralog BAF250a ARID. NMR chemical shift perturbations identified DNA-binding residues and revealed the DNA-binding interface on BAF250b ARID. NMR data-driven HADDOCK models of BAF250b ARID - DNA complexes revealed its plausible mode of DNA-binding. Isothermal titration calorimetry experiments showed that BAF250b ARID interacts with DNA sequences with moderate affinities like BAF250a ARID. However, distinct thermodynamic signatures were observed for binding of BAF250a ARID and BAF250b ARID to AT-rich DNA sequence, suggesting that subtle sequence and structural differences in these two proteins influence their DNA-binding.


Assuntos
Montagem e Desmontagem da Cromatina , DNA , DNA/química , Humanos , Domínios Proteicos , Termodinâmica
12.
Cell Rep ; 39(1): 110637, 2022 04 05.
Artigo em Inglês | MEDLINE | ID: mdl-35385731

RESUMO

ARID2 is the most recurrently mutated SWI/SNF complex member in melanoma; however, its tumor-suppressive mechanisms in the context of the chromatin landscape remain to be elucidated. Here, we model ARID2 deficiency in melanoma cells, which results in defective PBAF complex assembly with a concomitant genomic redistribution of the BAF complex. Upon ARID2 depletion, a subset of PBAF and shared BAF-PBAF-occupied regions displays diminished chromatin accessibility and associated gene expression, while BAF-occupied enhancers gain chromatin accessibility and expression of genes linked to the process of invasion. As a function of altered accessibility, the genomic occupancy of melanoma-relevant transcription factors is affected and significantly correlates with the observed transcriptional changes. We further demonstrate that ARID2-deficient cells acquire the ability to colonize distal organs in multiple animal models. Taken together, our results reveal a role for ARID2 in mediating BAF and PBAF subcomplex chromatin dynamics with consequences for melanoma metastasis.


Assuntos
Proteínas Cromossômicas não Histona , Melanoma , Fatores de Transcrição , Animais , Cromatina , Montagem e Desmontagem da Cromatina , Regulação da Expressão Gênica , Humanos , Melanoma/genética , Fatores de Transcrição/genética , Fatores de Transcrição/metabolismo
13.
Reprod Fertil Dev ; 34(7): 549-559, 2022 Apr.
Artigo em Inglês | MEDLINE | ID: mdl-35296373

RESUMO

CONTEXT: SWI/SNF chromatin remodelling complexes are composed of multiple protein subunits and can be categorised into three sub-families, including the BAF, PBAF, and GBAF complexes. We hypothesised that depletion of SMARCB1 and BRD7, two subunits unique to different SWI/SNF sub-families, would differentially impact porcine embryo development. AIM: The aim of these experiments was to determine the developmental requirements of two SWI/SNF subunits, SMARCB1 and BRD7. METHODS: RNA interference assays were used to determine the developmental requirements of SMARCB1 and BRD7 in porcine embryos. KEY RESULTS: Our findings indicate that knockdown of SMARCB1 dramatically reduces embryo developmental potential, with few embryos developing beyond the pronuclear stage. The knockdown of BRD7 had a less severe impact on developmental potential. CONCLUSIONS: Our findings also demonstrate that knockdown of SMARCB1 alters the expression of NANOG and POU5F1 (also referred to as OCT4 ). IMPLICATIONS: These findings highlight the unique developmental requirements for sub-families of SWI/SNF chromatin remodelling complexes. This new knowledge will enable us to determine how discrete genomic loci are differentially remodelled during key points in embryo development.


Assuntos
Montagem e Desmontagem da Cromatina , Proteínas Cromossômicas não Histona , Animais , Cromatina , Proteínas Cromossômicas não Histona/genética , Proteínas Cromossômicas não Histona/metabolismo , Desenvolvimento Embrionário , Suínos , Fatores de Transcrição/genética , Fatores de Transcrição/metabolismo
14.
Curr Opin Cell Biol ; 75: 102067, 2022 Apr.
Artigo em Inglês | MEDLINE | ID: mdl-35313165

RESUMO

The three-dimensional organisation of the genome modulates biological processes and is, in turn, transformed by the activity in the nucleus. Not surprisingly, understanding how the genome operates requires uncovering the fundamental biophysical and molecular mechanisms that establish and regulate its organisation. Genome organisation starts with the formation of chromatin: a polymer of nucleoprotein complexes, termed nucleosomes, that carry variable chemical signatures according to their biological context. The physicochemical heterogeneity of chromatin, the stochastic organisation it fosters, and the multiscale nature of genome organisation pose great technical challenges. Excitingly, advances in imaging and molecular biology techniques are addressing chromatin organisation at increasing resolutions. In tandem, computer models are testing and postulating hypotheses, interpreting the experimental data, and linking molecular properties of nucleosomes to the mesoscale organisation of chromatin. We discuss how coarse-grained models at varying resolutions are expanding our mechanistic understanding of chromatin organisation, and the challenges still remaining in the field.


Assuntos
Fenômenos Biológicos , Nucleossomos , Núcleo Celular , Cromatina/genética , Montagem e Desmontagem da Cromatina , Nucleossomos/genética
15.
Curr Opin Cell Biol ; 75: 102075, 2022 Apr.
Artigo em Inglês | MEDLINE | ID: mdl-35344802

RESUMO

The sperm genome is tightly packed into a minimal volume of sperm nuclei. Sperm chromatin is highly condensed by protamines (PRMs) after histone-protamine replacement, and the majority of the sperm genome forms a nucleo-protamine structure, namely, the PRM-DNA complex. The outline of sperm chromatin structure was proposed 30 years ago, and the details have been explored by approaches from several independent research fields including male reproduction and infertility, DNA biopolymer, and most recently, genome-wide sequence-based approaches. In this review, the history of research on sperm chromatin structure is briefly described, and the progress of recent related studies is summarized to obtain a more integrated view for the sperm chromatin, an extremely compacted "black box."


Assuntos
Protaminas , Espermatozoides , Cromatina/genética , Montagem e Desmontagem da Cromatina , DNA/genética , Humanos , Masculino , Protaminas/química , Protaminas/genética , Protaminas/metabolismo , Espermatozoides/metabolismo
16.
Sci Rep ; 12(1): 4721, 2022 03 18.
Artigo em Inglês | MEDLINE | ID: mdl-35304523

RESUMO

Layers of genome organization are becoming increasingly better characterized, but less is known about how these structures respond to perturbation or shape changes. Low-salt swelling of isolated chromatin fibers or nuclei has been used for decades to investigate the structural properties of chromatin. But, visible changes in chromatin appearance have not been linked to known building blocks of genome structure or features along the genome sequence. We combine low-salt swelling of isolated nuclei with genome-wide chromosome conformation capture (Hi-C) and imaging approaches to probe the effects of chromatin extension genome-wide. Photoconverted patterns on nuclei during expansion and contraction indicate that global genome structure is preserved after dramatic nuclear volume swelling, suggesting a highly elastic chromosome topology. Hi-C experiments before, during, and after nuclear swelling show changes in average contact probabilities at short length scales, reflecting the extension of the local chromatin fiber. But, surprisingly, during this large increase in nuclear volume, there is a striking maintenance of loops, TADs, active and inactive compartments, and chromosome territories. Subtle differences after expansion are observed, suggesting that the local chromatin state, protein interactions, and location in the nucleus can affect how strongly a given structure is maintained under stress. From these observations, we propose that genome topology is robust to extension of the chromatin fiber and isotropic shape change, and that this elasticity may be beneficial in physiological circumstances of changes in nuclear size and volume.


Assuntos
Cromatina , Cromossomos , Núcleo Celular/metabolismo , Cromatina/metabolismo , Montagem e Desmontagem da Cromatina , Genoma
17.
Cells ; 11(5)2022 02 25.
Artigo em Inglês | MEDLINE | ID: mdl-35269430

RESUMO

Smarca5, an ATPase of the ISWI class of chromatin remodelers, is a key regulator of chromatin structure, cell cycle and DNA repair. Smarca5 is deregulated in leukemia and breast, lung and gastric cancers. However, its role in oncogenesis is not well understood. Chromatin remodelers often play dosage-dependent roles in cancer. We therefore investigated the epigenomic and phenotypic impact of controlled stepwise attenuation of Smarca5 function in the context of primary cell transformation, a process relevant to tumor formation. Upon conditional single- or double-allele Smarca5 deletion, the cells underwent both accelerated growth arrest and senescence entry and displayed gradually increased sensitivity to genotoxic insults. These phenotypic characteristics were explained by specific remodeling of the chromatin structure and the transcriptome in primary cells prior to the immortalization onset. These molecular programs implicated Smarca5 requirement in DNA damage repair, telomere maintenance, cell cycle progression and in restricting apoptosis and cellular senescence. Consistent with the molecular programs, we demonstrate for the first time that Smarca5-deficient primary cells exhibit dramatically decreased capacity to bypass senescence and immortalize, an indispensable step during cell transformation and cancer development. Thus, Smarca5 plays a crucial role in key homeostatic processes and sustains cancer-promoting molecular programs and cellular phenotypes.


Assuntos
Cromatina , Neoplasias , Adenosina Trifosfatases/metabolismo , Montagem e Desmontagem da Cromatina , Dano ao DNA , Reparo do DNA
18.
Yeast ; 39(4): 262-271, 2022 04.
Artigo em Inglês | MEDLINE | ID: mdl-35348238

RESUMO

The nucleosome is the basic structural element of genomic DNA packaging and plays a role in transcription, replication, and recombination. Poly(dA) tracts are considered major sequence determinants of nucleosome positioning, although their role is not well understood. Here, we show that the homopolymeric character and the low GC content of poly(dA)s play different roles in nucleosome formation. We found that the inherent low GC content of poly(dA) alone can account for the deep and anisotropic nucleosome depletion at structurally and functionally important regions of promoters and origins of replication. We also show that the level of nucleosome occupancy at poly(dA) is strongly related to the local nucleotide background and its high frequency of occurrence in Saccharomyces cerevisiae does not appear merely to be associated with its intrinsic nucleosome-excluding properties. In addition, we show that the GC content alone can predict more than 60% of the in vitro nucleosome map, providing further evidence that the intrinsic nucleosome positioning is more greatly determined by GC content than poly(dA) stretches. Our results are consistent with a model in which poly(dA) stretches act at two distinct levels: first, by its low GC content, which intrinsically contributes to hinder nucleosome formation, and second, by its contiguous runs of dA that selectively drive the recruitment of non-histone proteins with structural and functional roles.


Assuntos
Nucleossomos , Saccharomyces cerevisiae , Composição de Bases , Montagem e Desmontagem da Cromatina , Nucleossomos/genética , Nucleossomos/metabolismo , Poli A , Saccharomyces cerevisiae/genética , Saccharomyces cerevisiae/metabolismo
19.
Biochem Soc Trans ; 50(2): 907-919, 2022 Apr 29.
Artigo em Inglês | MEDLINE | ID: mdl-35356970

RESUMO

Structural and biochemical studies have identified a histone surface on each side of the nucleosome disk termed 'the nucleosome acidic patch' that acts as a regulatory hub for the function of numerous nuclear proteins, including ATP-dependent chromatin complexes (remodelers). Four major remodeler subfamilies, SWI/SNF, ISWI, CHD, and INO80, have distinct modes of interaction with one or both nucleosome acidic patches, contributing to their specific remodeling outcomes. Genome-wide sequencing analyses of various human cancers have uncovered high-frequency mutations in histone coding genes, including some that map to the acidic patch. How cancer-related acidic patch histone mutations affect nucleosome remodeling is mainly unknown. Recent advances in in vitro chromatin reconstitution have enabled access to physiologically relevant nucleosomes, including asymmetric nucleosomes that possess both wild-type and acidic patch mutant histone copies. Biochemical investigation of these substrates revealed unexpected remodeling outcomes with far-reaching implications for alteration of chromatin structure. This review summarizes recent findings of how different remodeler families interpret wild-type and mutant acidic patches for their remodeling functions and discusses models for remodeler-mediated changes in chromatin landscapes as a consequence of acidic patch mutations.


Assuntos
Histonas , Nucleossomos , Adenosina Trifosfatases/metabolismo , Cromatina , Montagem e Desmontagem da Cromatina , Histonas/metabolismo , Humanos , Mutação
20.
Genetics ; 221(1)2022 May 05.
Artigo em Inglês | MEDLINE | ID: mdl-35323946

RESUMO

During proteotoxic stress, a pathway known as the heat shock response is induced to maintain protein-folding homeostasis or proteostasis. Previously, we identified the Caenorhabditis elegans GATAD2 ortholog, dcp-66, as a novel regulator of the heat shock response. Here, we extend these findings to show that dcp-66 positively regulates the heat shock response at the cellular, molecular, and organismal levels. As GATAD2 is a subunit of the nucleosome remodeling and deacetylase chromatin remodeling complex, we examined other nucleosome remodeling and deacetylase subunits and found that the let-418 (CHD4) nucleosome repositioning core also regulates the heat shock response. However, let-418 acts as a negative regulator of the heat shock response, in contrast to positive regulation by dcp-66. The divergent effects of these two nucleosome remodeling and deacetylase subunits extend to the regulation of other stress responses including oxidative, genotoxic, and endoplasmic reticulum stress. Furthermore, a transcriptomic approach reveals additional divergently regulated pathways, including innate immunity and embryogenesis. Taken together, this work establishes new insights into the role of nucleosome remodeling and deacetylase subunits in organismal physiology. We incorporate these findings into a molecular model whereby different mechanisms of recruitment to promoters can result in the divergent effects of nucleosome remodeling and deacetylase subunits.


Assuntos
Complexo Mi-2 de Remodelação de Nucleossomo e Desacetilase , Nucleossomos , Animais , Caenorhabditis elegans/genética , Caenorhabditis elegans/metabolismo , Montagem e Desmontagem da Cromatina , Complexo Mi-2 de Remodelação de Nucleossomo e Desacetilase/genética , Nucleossomos/genética , Fatores de Transcrição/genética , Fatores de Transcrição/metabolismo
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