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Chromatin Remodelling (chromatin + remodelling)
Selected AbstractsChanges in chromatin structure and methylation of the human interleukin-1, gene during monopoiesisIMMUNOLOGY, Issue 3 2010Inga Wessels Summary Interleukin-1, (IL-1,) induces the expression of a variety of proteins responsible for acute inflammation and chronic inflammatory diseases. However, the molecular regulation of IL-1, expression in myeloid differentiation has not been elucidated. In this study the chromatin structure of the IL-1, promoter and the impact of methylation on IL-1, expression in monocytic development were examined. The results revealed that the IL-1, promoter was inaccessible in undifferentiated promyeloid HL-60 cells but highly accessible in differentiated monocytic cells which additionally acquired the ability to produce IL-1,. Accessibilities of differentiated cells were comparable to those of primary monocytes. Lipopolysaccharide (LPS) stimulation did not affect promoter accessibility in promyeloid and monocytic HL-60 cells, demonstrating that the chromatin remodelling of the IL-1, promoter depends on differentiation and not on the transcriptional status of the cell. Demethylation via 5-aza-2,-deoxycytodine led to the induction of IL-1, expression in undifferentiated and differentiated cells, which could be increased after LPS stimulation. Our data indicate that the IL-1, promoter is reorganized into an open poised conformation during monopoiesis being a privilege of mature monocytes but not of the entire myeloid lineage. As a second mechanism, IL-1, expression is regulated by methylation acting independently of the developmental stage of myeloid cells. [source] Adaptive differences in gene expression associated with heavy metal tolerance in the soil arthropod Orchesella cinctaMOLECULAR ECOLOGY, Issue 15 2009DICK ROELOFS Abstract Field-selected tolerance to heavy metals has been reported for Orchesella cincta (Arthropoda: Collembola) populations occurring at metal-contaminated mining sites. This tolerance correlated with heritable increase in metal excretion efficiency, less pronounced cadmium (Cd)-induced growth reduction and overexpression of the metallothionein gene. We applied transcriptomics to determine differential gene expression caused by this abiotic stress in reference and Cd-tolerant populations. Many cDNAs responded to Cd exposure in the reference population. Significantly fewer clones were Cd responsive in tolerant animals. Analysis of variance revealed transcripts that interact between Cd exposure and population. Hierarchical cluster analysis of these clones identified two major groups. The first one contained cDNAs that were up-regulated by Cd in the reference culture but non-responsive or down-regulated in tolerant animals. This cluster was also characterized by elevated constitutive expression in the tolerant population. Gene ontology analysis revealed that these cDNAs were involved in structural integrity of the cuticle, anti-microbial defence, calcium channel-blocking, sulphur assimilation and chromatin remodelling. The second group consisted of cDNAs down-regulated in reference animals but not responding or slightly up-regulated in tolerant animals. Their functions involved carbohydrate metabolic processes, Ca2+ -dependent stress signalling, redox state, proteolysis and digestion. The reference population showed a strong signature of stress-induced genome-wide perturbation of gene expression, whereas the tolerant animals maintained normal gene expression upon Cd exposure. We confirmed the micro-evolutionary processes occurring in soil arthropod populations and suggest a major contribution of gene regulation to the evolution of a stress-adapted phenotype. [source] H4 acetylation does not replace H3 acetylation in chromatin remodelling and transcription activation of Adr1-dependent genesMOLECULAR MICROBIOLOGY, Issue 5 2006Eleonora Agricola Summary Histone acetylation regulates gene expression. Whether this is caused by a general increase in nucleosome fluidity due to charge neutralization or by a more specific code is still matter of debate. By using a set of glucose-repressed Adr1-dependent genes of Saccharomyces cerevisiae, whose transcription was previously shown to require both Gcn5 and Esa1, we asked how changes of histone acetylation patterns at the promoter nucleosomes regulate chromatin remodelling and activation. When the signal of glucose reduction reaches the cells, H4 acetylation is kept constant while an increase of H3 acetylation occurs, in an Adr1- and Gcn5-dependent manner. In cells lacking Gcn5 activity, the H3 acetylation increase does not occur and an unexpected increase of histone H4 acetylation is observed. Nevertheless, chromatin remodelling and transcription activation are impaired, suggesting that acetylation of H3 and H4 histones plays different roles. [source] Genetics of human iris colour and patternsPIGMENT CELL & MELANOMA RESEARCH, Issue 5 2009Richard A. Sturm Summary The presence of melanin pigment within the iris is responsible for the visual impression of human eye colouration with complex patterns also evident in this tissue, including Fuchs' crypts, nevi, Wolfflin nodules and contraction furrows. The genetic basis underlying the determination and inheritance of these traits has been the subject of debate and research from the very beginning of quantitative trait studies in humans. Although segregation of blue-brown eye colour has been described using a simple Mendelian dominant-recessive gene model this is too simplistic, and a new molecular genetic perspective is needed to fully understand the biological complexities of this process as a polygenic trait. Nevertheless, it has been estimated that 74% of the variance in human eye colour can be explained by one interval on chromosome 15 that contains the OCA2 gene. Fine mapping of this region has identified a single base change rs12913832 T/C within intron 86 of the upstream HERC2 locus that explains almost all of this association with blue-brown eye colour. A model is presented whereby this SNP, serving as a target site for the SWI/SNF family member HLTF, acts as part of a highly evolutionary conserved regulatory element required for OCA2 gene activation through chromatin remodelling. Major candidate genes possibly effecting iris patterns are also discussed, including MITF and PAX6. [source] Arabidopsis transcript and metabolite profiles: ecotype-specific responses to open-air elevated [CO2]PLANT CELL & ENVIRONMENT, Issue 11 2008PINGHUA LI ABSTRACT A Free-Air CO2 Enrichment (FACE) experiment compared the physiological parameters, transcript and metabolite profiles of Arabidopsis thaliana Columbia-0 (Col-0) and Cape Verde Island (Cvi-0) at ambient (,0.375 mg g,1) and elevated (,0.550 mg g,1) CO2 ([CO2]). Photoassimilate pool sizes were enhanced in high [CO2] in an ecotype-specific manner. Short-term growth at elevated [CO2] stimulated carbon gain irrespective of down-regulation of plastid functions and altered expression of genes involved in nitrogen metabolism resembling patterns observed under N-deficiency. The study confirmed well-known characteristics, but the use of a time course, ecotypic genetic differences, metabolite analysis and the focus on clusters of functional categories provided new aspects about responses to elevated [CO2]. Longer-term Cvi-0 responded by down-regulating functions favouring carbon accumulation, and both ecotypes showed altered expression of genes for defence, redox control, transport, signalling, transcription and chromatin remodelling. Overall, carbon fixation with a smaller commitment of resources in elevated [CO2] appeared beneficial, with the extra C only partially utilized possibly due to disturbance of the C : N ratio. To different degrees, both ecotypes perceived elevated [CO2] as a metabolic perturbation that necessitated increased functions consuming or storing photoassimilate, with Cvi-0 emerging as more capable of acclimating. Elevated [CO2] in Arabidopsis favoured adjustments in reactive oxygen species (ROS) homeostasis and signalling that defined genotypic markers. [source] Proteomic analysis of cells in the early stages of herpes simplex virus type-1 infection reveals widespread changes in the host cell proteomePROTEINS: STRUCTURE, FUNCTION AND BIOINFORMATICS, Issue 15 2009Robin Antrobus Abstract During infection by herpes simplex virus type-1 (HSV-1) the host cell undergoes widespread changes in gene expression and morphology in response to viral replication and release. However, relatively little is known about the specific proteome changes that occur during the early stages of HSV-1 replication prior to the global damaging effects of virion maturation and egress. To investigate pathways that may be activated or utilised during the early stages of HSV-1 replication, 2-DE and LC-MS/MS were used to identify cellular proteome changes at 6,h post infection. Comparative analysis of multiple gels representing whole cell extracts from mock- and HSV-1-infected HEp-2 cells revealed a total of 103 protein spot changes. Of these, 63 were up-regulated and 40 down-regulated in response to infection. Changes in selected candidate proteins were verified by Western blot analysis and their respective cellular localisations analysed by confocal microscopy. We have identified differential regulation and modification of proteins with key roles in diverse cellular pathways, including DNA replication, chromatin remodelling, mRNA stability and the ER stress response. This work represents the first global comparative analysis of HSV-1 infected cells and provides an important insight into host cell proteome changes during the early stages of HSV-1 infection. [source] Manipulation of DET1 expression in tomato results in photomorphogenic phenotypes caused by post-transcriptional gene silencingTHE PLANT JOURNAL, Issue 3 2004Ganga Rao Davuluri Summary The tomato HIGH PIGMENT-2 gene encodes an orthologue of the Arabidopsis nuclear protein DE-ETIOLATED 1 (DET1). From genetic analyses it has been proposed that DET1 is a negative regulator of light signal transduction, and recent results indicate that it may control light-regulated gene expression at the level of chromatin remodelling. To gain further understanding about the function of DET1 during plant development, we generated a range of overexpression constructs and introduced them into tomato. Unexpectedly, we only observed phenotypes characteristic of DET1 inactivation, i.e. hyper-responsiveness to light. Molecular analysis indicated in all cases that these phenotypes were a result of suppression of endogenous DET1 expression, due to post-transcriptional gene silencing. DET1 silencing was often lethal when it occurred at relatively early stages of plant development, whereas light hyper-responsive phenotypes were obtained when silencing occurred later on. The appearance of phenotypes correlated with the generation of siRNAs but not DNA hypermethylation, and was most efficient when using constructs with mutations in the DET1 coding sequence or with constructs containing only the 3,-terminal portion of the gene. These results indicate an important function for DET1 throughout plant development and demonstrate that silencing of DET1 in fruits results in increased carotenoids, which may have biotechnological potential. [source] Electron microscopy analysis of histone acetylation and DNA strand breaks in mouse elongating spermatids using a dual labelling approachANDROLOGIA, Issue 5 2010G. Bikond Nkoma Summary Chromatin remodelling steps in mammalian spermatids include post-translational modifications of histones and DNA fragmentation. Histone H4 hyperacetylation (AcH4) establishes a chromatin state that facilitates DNA repair in somatic cells. So we sought to determine whether a similar link exists in spermatids by combining immunogold labelling with detection of DNA strand breaks, making use of gold particles of different sizes. DNA strand breaks were not detected in the vicinity of AcH4 chromatin, suggesting that this modified histone may not be involved in the aetiology of DNA fragmentation and repair in spermatids. The AcH4 reactivity, however, indicates that chromatin remodelling is distributed throughout the nucleus. [source] Cloning, purification, crystallization and preliminary X-ray crystallographic analysis of SET/TAF-I,,N from Homo sapiensACTA CRYSTALLOGRAPHICA SECTION F (ELECTRONIC), Issue 8 2010Zhen Xu The histone chaperone SET encoded by the SET gene, which is also known as template-activating factor I, (TAF-I,), is a multifunctional molecule that is involved in many biological phenomena such as histone binding, nucleosome assembly, chromatin remodelling, replication, transcription and apoptosis. A truncated SET/TAF-I,,N protein that lacked the first 22 residues of the N-terminus but contained the C-terminal acidic domain and an additional His6 tag at the C-terminus was overexpressed in Escherichia coli and crystallized by the hanging-drop vapour-diffusion method using sodium acetate as precipitant at 283,K. The crystals diffracted to 2.7,Å resolution and belonged to space group P43212. [source] Crystallization and preliminary X-ray diffraction analysis of the dimerization domain of the tumour suppressor ING4ACTA CRYSTALLOGRAPHICA SECTION F (ELECTRONIC), Issue 5 2010Simone Culurgioni Inhibitor of growth protein 4 (ING4) belongs to the ING family of tumour suppressors and is involved in chromatin remodelling, in growth arrest and, in cooperation with p53, in senescence and apoptosis. Whereas the structure and histone H3-binding properties of the C-terminal PHD domains of the ING proteins are known, no structural information is available for the N-terminal domains. This domain contains a putative oligomerization site rich in helical structure in the ING2,5 members of the family. The N-terminal domain of ING4 was overexpressed in Escherichia coli and purified to homogeneity. Crystallization experiments yielded crystals that were suitable for high-resolution X-ray diffraction analysis. The crystals belonged to the orthorhombic space group C222, with unit-cell parameters a = 129.7, b = 188.3, c = 62.7,Å. The self-rotation function and the Matthews coefficient suggested the presence of three protein dimers per asymmetric unit. The crystals diffracted to a resolution of 2.3,Å using synchrotron radiation at the Swiss Light Source (SLS) and the European Synchrotron Radiation Facility (ESRF). [source] Crystallization and preliminary X-ray diffraction analysis of inositol 1,3,4,5,6-pentakisphosphate kinase from Arabidopsis thalianaACTA CRYSTALLOGRAPHICA SECTION F (ELECTRONIC), Issue 1 2010Jose Ignacio Baños-Sanz Inositol 1,3,4,5,6-pentakisphosphate kinase (IP5 2-K) is an enzyme involved in inositol metabolism that synthesizes IP6 (inositol 1,2,3,4,5,6-hexakisphosphate) from inositol 1,3,4,5,6-pentakisphosphate (IP5) and ATP. IP6 is the major phosphorus reserve in plants, while in mammals it is involved in multiple cellular events such as DNA editing and chromatin remodelling. In addition, IP6 is the precursor of other highly phosphorylated inositols which also play highly relevant roles. IP5 2-K is the only enzyme that phosphorylates the 2-OH axial position of the inositide and understanding its molecular mechanism of substrate specificity is of great interest in cell biology. IP5 2-K from Arabidopsis thaliana has been expressed in Escherichia coli as two different fusion proteins and purified. Both protein preparations yielded crystals of different quality, always in the presence of IP6. The best crystals obtained for X-ray crystallographic analysis belonged to space group P212121, with unit-cell parameters a = 58.124, b = 113.591, c = 142.478,Å. Several diffraction data sets were collected for the native enzyme and two heavy-atom derivatives using a synchrotron source. [source] A phase I study of vorinostat in combination with idarubicin in relapsed or refractory leukaemiaBRITISH JOURNAL OF HAEMATOLOGY, Issue 1 2010Tapan M. Kadia Summary Histone deacetylase inhibitors (HDACi) affect chromatin remodelling and modulate the expression of aberrantly silenced genes. HDACi have single-agent clinical activity in haematological malignancies and have synergistic anti-leukaemia activity when combined with anthracyclines in vitro. We conducted a two-arm, parallel Phase I trial to investigate two schedules of escalating doses of vorinostat (Schedule A: thrice daily (TID) for 14 d; B: TID for 3 d) in combination with a fixed dose of idarubicin in patients with refractory leukaemia. Of the 41 patients enrolled, 90% had acute myeloid leukaemia, with a median of 3 prior therapies. Seven responses (17%) were documented (two complete response (5%), one complete response without platelet recovery (2·5%), and four marrow responses). The 3-d schedule of vorinostat was better tolerated than the 14-d schedule. The maximum tolerated dose for vorinostat was defined as 400 mg TID for 3 d. The most common grade 3 and 4 toxicities included mucositis, fatigue and diarrhoea. Correlative studies demonstrated histone acetylation in patients on therapy and modulation of CDKN1A and TOP2A (topoisomerase II) gene expression. Pharmacokinetic analysis confirmed a dose-related elevation in plasma vorinostat concentrations. The combination of vorinostat and idarubicin is generally tolerable and active in patients with advanced leukaemia and should be studied in the front-line setting. [source] Listeria monocytogenes infection in the face of innate immunityCELLULAR MICROBIOLOGY, Issue 5 2009Sinead C. Corr Summary Pathogen recognition and induction of immune responses are important for efficient elimination of infection. However, pathogens such as Listeria monocytogenes employ strategies to evade or modulate these defences, thus creating a more favourable environment that ensures their survival and pathogenesis. New insights into these strategies, particularly those targeting innate immunity, have recently emerged. L. monocytogenes is initially detected at the cell surface or in phagosomes by toll-like receptor 2 and in the cytosol by nuclear oligodimerization domain (NOD)-like receptors (NOD1, NOD2) and NALP3 and Ipaf. It carries out N-deacetylation of peptidoglycan to avoid this detection by toll-like receptor 2 and NOD-like receptors. L. monocytogenes modulates transcription of host immunity genes through modification of histones and chromatin remodelling. Furthermore, L. monocytogenes has recently been shown to avoid autophagy and induce apoptosis in immune effector cells. In this review we discuss some of these strategies, which have provided new insights into the interaction between L. monocytogenes and the immune response at a crucial stage of infection. [source] Mutations in PHD-like domain of the ATRX gene correlate with severe psychomotor impairment and severe urogenital abnormalities in patients with ATRX syndromeCLINICAL GENETICS, Issue 1 2006C Badens Mutations in ATRX are associated with a wide and clinically heterogeneous spectrum of X-linked mental retardation syndromes. The ATRX protein, involved in chromatin remodelling, belongs to the family of SWI/SNF DNA helicases and contains a plant homeodomain (PHD)-like domain. To date, more than 60 different mutations have been reported in ATRX. One of them is recurrent and accounts for 20% of all the reported mutations, whereas all others are private. Most mutations are clustered in the two major functional domains, the helicase and the PHD-like domain. So far, no clear genotype,phenotype correlation has been established, with exception to the rare truncating mutations located at the C-terminal part of the protein, which are consistently associated with severe urogenital defects. In this study, we report the molecular analysis performed in 16 families positive for ATRX. Our findings indicate that, in addition to the previously described mutation ,hotspot' in the PHD-like domain, two other protein sections emerge as minor ,hotspots' in the helicase region encoded by exons 18,20 and 26,29, respectively, gathering 33% of all described mutations. Additionally, based on the clinical data collected for 22 patients from the 16 families, we observe that mutations in the PHD-like domain produce severe and permanent psychomotor deficiency, usually preventing patients from walking, as well as constant urogenital abnormalities, while mutations in the helicase domain lead to delayed but correct psychomotor acquisitions together with mild or absent urogenital abnormalities. In summary, mutations in the helicase domain are associated with milder phenotypes than mutations in the PHD-like domain. [source] | ||||||||||||||||