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  • CHROMATIN  (15)
  • 1
    Keywords: APOPTOSIS ; CANCER ; CELLS ; EXPRESSION ; CELL ; Germany ; IN-VIVO ; VIVO ; PROTEIN ; cell line ; DIFFERENTIATION ; DNA ; DOMAIN ; image analysis ; FLOW ; cell cycle ; CELL-CYCLE ; CYCLE ; SPECTROSCOPY ; IDENTIFICATION ; PROGRESSION ; CHROMATIN ; INDUCED APOPTOSIS ; CYCLE PROGRESSION ; CELL-LINE ; LINE ; acetylation ; REGION ; REGIONS ; MAMMALIAN-CELLS ; LENGTH ; REORGANIZATION ; STRUCTURAL-CHANGES ; HISTONE DEACETYLASE ; FLOW-CYTOMETRY ; INTERPHASE ; CHROMATIN STRUCTURE ; S-PHASE ; DOMAINS ; TRICHOSTATIN-A ; CORRELATION SPECTROSCOPY ; ARREST ; ACETYLTRANSFERASE ; SCALE ; DEPENDENCE ; fractal dimension ; DEACETYLASE INHIBITORS ; GENE-CONTROL ; HYPERACETYLATION ; image correlation ; NUCLEOSOME CORE ; TSA
    Abstract: The effect of trichostatin A (TSA)-induced histone acetylation on the interphase chromatin structure was visualized in vivo with a HeLa cell line stably expressing histone H2A, which was fused to enhanced yellow fluorescent protein. The globally increased histone acetylation caused a reversible decondensation of dense chromatin regions and led to a more homogeneous distribution. These structural changes were quantified by image correlation spectroscopy and by spatially resolved scaling analysis. The image analysis revealed that a chromatin reorganization on a length scale from 200 nm to 〉1 mum was induced consistent with the opening of condensed chromatin domains containing several Mb of DNA. The observed conformation changes could be assigned to the folding of chromatin during G1 phase by characterizing the effect of TSA on cell cycle progression and developing a protocol that allowed the identification of G1 phase cells on microscope coverslips. An analysis by flow cytometry showed that the addition of TSA led to a significant arrest of cells in S phase and induced apoptosis. The concentration dependence of both processes was studied
    Type of Publication: Journal article published
    PubMed ID: 15292402
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  • 2
    Keywords: ENERGIES ; EXPRESSION ; Germany ; GENE ; GENE-EXPRESSION ; PROTEIN ; PROTEINS ; DNA ; IMPACT ; SIMULATION ; BINDING ; CHROMATIN ; gene expression ; ENERGY ; EXCHANGE ; ANGSTROM RESOLUTION ; MONTE-CARLO ; ORDER ; CHAIN ; higher-order structure ; LINKER HISTONE ; nucleosomes ; PROTOCOL ; interaction ; NUCLEOSOME ; MONTE-CARLO-SIMULATION ; USA ; CHROMATIN FIBER ; COMPUTER-SIMULATION ; SCANNING FORCE MICROSCOPY ; computer simulations ; CORE PARTICLE ; SHAPE ; COOPERATIVE BINDING ; NUCLEOSOME REPEAT LENGTH
    Abstract: The folding of the nucleosome chain into a chromatin fiber modulates DNA accessibility and is therefore an important factor for the control of gene expression. The fiber conformation depends crucially on the interaction between individual nucleosomes. However, this parameter has not been accurately determined experimentally, and it is affected by posttranslational histone modi. cations and binding of chromosomal proteins. Here, the effect of different internucleosomal interaction strengths on the fiber conformation was investigated by Monte Carlo computer simulations. The fiber geometry was modeled to fit that of chicken erythrocyte chromatin, which has been examined in numerous experimental studies. In the Monte Carlo simulation, the nucleosome shape was described as an oblate spherocylinder, and a replica exchange protocol was developed to reach thermal equilibrium for a broad range of internucleosomal interaction energies. The simulations revealed the large impact of the nucleosome geometry and the nucleosome repeat length on the compaction of the chromatin fiber. At high internucleosomal interaction energies, a lateral self-association of distant fiber parts and an interdigitation of nucleosomes were apparent. These results identify key factors for the control of the compaction and higher order folding of the chromatin fiber
    Type of Publication: Journal article published
    PubMed ID: 18658212
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  • 3
    Keywords: recombination ; CHROMATIN ; CANCER-CELLS ; MAMMALIAN-CELLS ; EPSTEIN-BARR-VIRUS ; ATAXIA-TELANGIECTASIA ; RNA INTERFERENCE ; HP1 PROTEINS ; HUMAN-CELLS ; LEUKEMIA NUCLEAR-BODIES
    Abstract: The alternative lengthening of telomeres (ALT) mechanism allows cancer cells to escape senescence and apoptosis in the absence of active telomerase. A characteristic feature of this pathway is the assembly of ALT-associated promyelocytic leukemia (PML) nuclear bodies (APBs) at telomeres. Here, we dissected the role of APBs in a human ALT cell line by performing an RNA interference screen using an automated 3D fluorescence microscopy platform and advanced 3D image analysis. We identified 29 proteins that affected APB formation, which included proteins involved in telomere and chromatin organization, protein sumoylation and DNA repair. By integrating and extending these findings, we found that APB formation induced clustering of telomere repeats, telomere compaction and concomitant depletion of the shelterin protein TRF2 (also known as TERF2). These APB-dependent changes correlated with the induction of a DNA damage response at telomeres in APBs as evident by a strong enrichment of the phosphorylated form of the ataxia telangiectasia mutated (ATM) kinase. Accordingly, we propose that APBs promote telomere maintenance by inducing a DNA damage response in ALT-positive tumor cells through changing the telomeric chromatin state to trigger ATM phosphorylation.
    Type of Publication: Journal article published
    PubMed ID: 25908860
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  • 4
    Keywords: EXPRESSION ; Germany ; DISTINCT ; PROTEIN ; SACCHAROMYCES-CEREVISIAE ; COMPLEX ; COMPLEXES ; DNA ; BINDING ; SEQUENCE ; SEQUENCES ; LINKAGE ; ELEMENT ; PATTERNS ; CHROMATIN ; Drosophila ; PROMOTER ; REGION ; PRODUCT ; REGIONS ; TRANSLOCATION ; CHROMATIN STRUCTURE ; REGULATOR ; AFFINITY ; TRANSCRIPTIONAL REGULATION ; DNA-SEQUENCE ; FEATURES ; PATTERN ; END ; GENE-TRANSCRIPTION ; ISWI ; USA ; nucleosome positioning ; comparison ; ACCESSIBILITY ; HISTONE OCTAMER ; nucleosome remodeling ; ACF ; SWI-SNF ; YEAST ALPHA-2 REPRESSOR
    Abstract: Chromatin-remodeling complexes can translocate nucleosomes along the DNA in an ATP-coupled reaction. This process is an important regulator of all DNA-dependent processes because it determines whether certain DNA sequences are found in regions between nucleosomes with increased accessibility for other factors or wrapped around the histone octamer complex. In a comparison of seven different chromatin-remodeling machines (ACF, ISWI, Snf2H, Chd1, Mi-2, Brg1, and NURF), it is demonstrated that these complexes can read out DNA sequence features to establish specific nucleosome-positioning patterns. For one of the remodelers, ACF, we identified a 40-bp DNA sequence element that directs nucleosome positioning. Furthermore, we show that nucleosome positioning by the remodelers ACF and Chd1 is determined by a reduced affinity to the end product of the translocation reaction. The results suggest that the linkage of differential remodeling activities with the intrinsic binding preferences of nucleosomes can result in establishing distinct chromatin structures that depend on the DNA sequence and define the DNA accessibility for other protein factors
    Type of Publication: Journal article published
    PubMed ID: 17893337
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  • 5
    Keywords: ENVIRONMENT ; CELL ; Germany ; MODEL ; DISTINCT ; GENE-EXPRESSION ; GENOME ; PROTEINS ; COMPONENTS ; mechanisms ; BIOLOGY ; FORM ; CHROMATIN ; genetics ; COMPONENT ; NUCLEUS ; DNA-REPLICATION ; CHROMOSOME TERRITORIES ; ORGANIZATION ; heredity ; LAYER ; BODIES ; review ; assembly ; interaction ; PRINCIPLES ; NUCLEAR ; BIOLOGICAL-ACTIVITY ; function ; OCCURS ; modification ; MITOTIC CHROMOSOMES
    Abstract: The dynamic organization of the cell nucleus into subcompartments with distinct biological activities represents an important regulatory layer for cell function. Recent studies provide new insights into the principles, by which nuclear organelles form. This process frequently occurs in a self-organizing manner leading to the assembly of stable but plastic structures from multiple relatively weak interaction forces. These can rearrange into different functional states in response to specific modifications of the constituting components or changes in the nuclear environment
    Type of Publication: Journal article published
    PubMed ID: 17913491
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  • 6
    Keywords: CELLS ; GENOME ; CHROMATIN ; ORGANIZATION ; HIGH-RESOLUTION
    Abstract: MOTIVATION: Recent experimental advancements allow determining positions of nucleosomes for complete genomes. However, the resulting nucleosome occupancy maps are averages of heterogeneous cell populations. Accordingly, they represent a snapshot of a dynamic ensemble at a single time point with an overlay of many configurations from different cells. To study the organization of nucleosomes along the genome and to understand the mechanisms of nucleosome translocation, it is necessary to retrieve features of specific conformations from the population average. RESULTS: Here, we present a method for identifying non-overlapping nucleosome configurations that combines binary-variable analysis and a Monte Carlo approach with a simulated annealing scheme. In this manner, we obtain specific nucleosome configurations and optimized solutions for the complex positioning patterns from experimental data. We apply the method to compare nucleosome positioning at transcription factor binding sites in different mouse cell types. Our method can model nucleosome translocations at regulatory genomic elements and generate configurations for simulations of the spatial folding of the nucleosome chain. AVAILABILITY: Source code, precompiled binaries, test data and a web-based test installation are freely available at http://bioinformatics.fh-stralsund.de/nucpos/ CONTACT: gero.wedemann@fh-stralsund.de SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.
    Type of Publication: Journal article published
    PubMed ID: 23846748
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  • 7
    Keywords: GENE ; GENOME ; PATTERNS ; CHROMATIN ; leukemia ; INSTABILITY ; ORGANIZATION ; ORIGIN ; DEFECTS ; MUTATION-RATE
    Abstract: Mutation is a fundamental process in tumorigenesis. However, the degree to which the rate of somatic mutation varies across the human genome and the mechanistic basis underlying this variation remain to be fully elucidated. Here, we performed a cross-cancer comparison of 402 whole genomes comprising a diverse set of childhood and adult tumors, including both solid and hematopoietic malignancies. Surprisingly, we found that the inactive X chromosome of many female cancer genomes accumulates on average twice and up to four times as many somatic mutations per megabase, as compared to the individual autosomes. Whole-genome sequencing of clonally expanded hematopoietic stem/progenitor cells (HSPCs) from healthy individuals and a premalignant myelodysplastic syndrome (MDS) sample revealed no X chromosome hypermutation. Our data suggest that hypermutation of the inactive X chromosome is an early and frequent feature of tumorigenesis resulting from DNA replication stress in aberrantly proliferating cells.
    Type of Publication: Journal article published
    PubMed ID: 24139898
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  • 8
    Keywords: GENE-EXPRESSION ; GENOME ; CHROMATIN ; MAMMALIAN-CELLS ; REVEALS ; NUCLEAR ; POLYMERASE ; LONG NONCODING RNAS ; NUCLEOTIDE RESOLUTION ; REGULATORY FUNCTIONS
    Abstract: While mapping total and poly-adenylated human transcriptomes has now become routine, characterizing nascent transcripts remains challenging, largely because nascent RNAs have such short half-lives. Here, we describe a simple, fast and cost-effective method to isolate RNA associated with transcription factories, the sites responsible for the majority of nuclear transcription. Following stimulation of human endothelial cells with the pro-inflammatory cytokine TNFalpha, we isolate and analyse the RNA content of factories by sequencing. Comparison with total, poly(A)(+) and chromatin RNA fractions reveals that sequencing of purified factory RNA maps the complete nascent transcriptome; it is rich in intronic unprocessed transcript, as well as long intergenic non-coding (lincRNAs) and enhancer-associated RNAs (eRNAs), micro-RNA precursors and repeat-derived RNAs. Hence, we verify that transcription factories produce most nascent RNA and confer a regulatory role via their association with a set of specifically-retained non-coding transcripts.
    Type of Publication: Journal article published
    PubMed ID: 25897132
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  • 9
    Keywords: SIMULATIONS ; SIMULATION ; SPECTROSCOPY ; CHROMATIN ; FIBER ; ENERGETICS ; MONTE-CARLO ; CHROMATIN FIBER
    Type of Publication: Journal article published
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  • 10
    Keywords: SIMULATIONS ; MODEL ; transcription ; DYNAMICS ; CHROMATIN ; REVEALS ; CHROMATIN STRUCTURE ; PROTEIN INTERACTIONS ; higher-order structure ; LINKER HISTONE ; NUCLEOSOME ; Monte Carlo simulation ; COMPUTER-SIMULATION ; DNA TARGET SITES ; force spectroscopy ; NUCLEOSOME REPEAT LENGTH ; H4-K16 ACETYLATION
    Abstract: The folding of the nucleosome chain into a chromatin fiber is a central factor for controlling the DNA access of protein factors involved in transcription, DNA replication and repair. Force spectroscopy experiments with chromatin fibers are ideally suited to dissect the interactions that drive this process, and to probe the underlying fiber conformation. However, the interpretation of the experimental data is fraught with difficulties due to the complex interplay of the nucleosome geometry and the different energy terms involved. Here, we apply a Monte Carlo simulation approach to derive virtual chromatin fiber force spectroscopy curves. In the simulations, the effect of the nucleosome geometry, repeat length, nucleosome-nucleosome interaction potential, and the unwrapping of the DNA from the histone protein core on the shape of the force-extension curves was investigated. These simulations provide a framework for the evaluation of experimental data sets. We demonstrate how the relative contributions of DNA bending and twisting, nucleosome unstacking and unwrapping the nucleosomal DNA from the histone octamer can be dissected for a given fiber geometry
    Type of Publication: Journal article published
    PubMed ID: 21294108
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