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  • CELLS  (6)
  • 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: CANCER ; CELLS ; PROTEINS ; DIFFERENTIATION ; BINDING ; RECOGNITION ; exon-intron structure ; LYSINE 9 ; GENOME-WIDE ; HISTONE H3
    Abstract: The global impact of DNA methylation on alternative splicing is largely unknown. Using a genome-wide approach in wild-type and methylation-deficient embryonic stem cells, we found that DNA methylation can either enhance or silence exon recognition and affects the splicing of more than 20% of alternative exons. These exons are characterized by distinct genetic and epigenetic signatures. Alternative splicing regulation of a subset of these exons can be explained by heterochromatin protein 1 (HP1), which silences or enhances exon recognition in a position-dependent manner. We constructed an experimental system using site-specific targeting of a methylated/unmethylated gene and demonstrate a direct causal relationship between DNA methylation and alternative splicing. HP1 regulates this gene's alternative splicing in a methylation-dependent manner by recruiting splicing factors to its methylated form. Our results demonstrate DNA methylation's significant global influence on mRNA splicing and identify a specific mechanism of splicing regulation mediated by HP1.
    Type of Publication: Journal article published
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  • 3
    Keywords: CANCER ; CELLS ; transcription ; MOUSE ; ORGANIZATION ; SATELLITE REPEATS ; CTCF ; HISTONE ; CCCTC-BINDING FACTOR ; TRIMETHYLATION
    Abstract: Cohesin plays an important role in chromatid cohesion and has additional functions in higher-order chromatin organization and in transcriptional regulation. The binding of cohesin to euchromatic regions is largely mediated by CTCF or the mediator complex. However, it is currently unknown how cohesin is recruited to pericentric heterochromatin in mammalian cells. Here we define the histone methyltransferase Suv4-20h2 as a major structural constituent of heterochromatin that mediates chromatin compaction and cohesin recruitment. Suv4-20h2 stably associates with pericentric heterochromatin through synergistic interactions with multiple heterochromatin protein 1 (HP1) molecules, resulting in compaction of heterochromatic regions. Suv4-20h mutant cells display an overall reduced chromatin compaction and an altered chromocenter organization in interphase referred to as "chromocenter scattering." We found that Suv4-20h-deficient cells display chromosome segregation defects during mitosis that coincide with reduced sister chromatid cohesion. Notably, cohesin subunits interact with Suv4-20h2 both in vitro and in vivo. This interaction is necessary for cohesin binding to heterochromatin, as Suv4-20h mutant cells display substantially reduced cohesin levels at pericentric heterochromatin. This defect is most prominent in G0-phase cells, where cohesin is virtually lost from heterochromatin, suggesting that Suv4-20h2 is involved in the initial loading or maintenance of cohesion subunits. In summary, our data provide the first compelling evidence that Suv4-20h2 plays essential roles in regulating nuclear architecture and ensuring proper chromosome segregation.
    Type of Publication: Journal article published
    PubMed ID: 23599346
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  • 4
    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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  • 5
    Keywords: CELLS ; CELL ; Germany ; IN-VIVO ; MICROSCOPY ; VIVO ; imaging ; INFORMATION ; SYSTEM ; SYSTEMS ; COMPLEX ; BIOLOGY ; MOLECULAR-BIOLOGY ; SIGNAL ; FIELD ; genetics ; LOCALIZATION ; NETHERLANDS ; FLUORESCENCE ; heredity ; ARCHITECTURE ; molecular biology ; molecular ; RE ; FLUORESCENCE MICROSCOPY ; analysis ; NUCLEAR ; 3D ; SIGNATURE ; 2 OBJECTIVE LENSES ; 3D WIDEFIELD MICROSCOPY ; AXIAL RESOLUTION ; TEMPERATURE ; EXCITATION ; ERRORS ; three-dimensional ; live cell imaging ; SECONDS ; STORM ; DATA-ACQUISITION ; 3-DIMENSIONAL SUPERRESOLUTION ; DISTANCE MEASUREMENTS ; FPALM ; localization microscopy ; nanosizing ; NANOSTRUCTURE ; OPTICAL RECONSTRUCTION MICROSCOPY ; PALM ; PALMIRA ; SALM ; SIZE DETERMINATION ; SMI microscopy ; SPDM ; Vertico-SMI microscope
    Abstract: Spatially modulated illumination (SMI) microscopy is a method of wide field fluorescence microscopy featuring interferometric illumination, which delivers structural information about nanoscale architecture in fluorescently labelled cells. The first prototype of the SMI microscope proved its applicability to a wide range of biological questions. For the SMI live cell imaging this system was enhanced in terms of the development of a completely new upright configuration. This so called Vertico-SMI transfers the advantages of SMI nanoscaling to vital biological systems, and is shown to work consistently at different temperatures using both oil- and water-immersion objective lenses. Furthermore, we increased the speed of data acquisition to minimize errors in the detection signal resulting from cellular or object movement. By performing accurate characterization, the present Vertico-SMI now offers a fully-fledged microscope enabling a complete three-dimensional (3D) SMI data stack to be acquired in less than 2 seconds. We have performed live cell measurements of a tet-operator repeat insert in U2OS cells, which provided the first in vivo signatures of subnuclear complexes. Furthermore, we have successfully implemented an optional optical configuration allowing the generation of high-resolution localization microscopy images of a nuclear pore complex distribution
    Type of Publication: Journal article published
    PubMed ID: 18461478
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  • 6
    Keywords: CELLS ; CELL ; Germany ; MICROSCOPY ; IMAGES ; GENOME ; PROTEIN ; PROTEINS ; MOLECULES ; RESOLUTION ; DOMAIN ; MOLECULE ; DISTRIBUTIONS ; US ; LOCALIZATION ; NUCLEUS ; ORGANIZATION ; DOMAINS ; SINGLE ; structure ; PRINCIPLES ; PRECISION ; DIMENSIONS ; localization microscopy ; Application
    Abstract: The dual color localization microscopy (2CLM) presented here is based on the principles of spectral precision distance microscopy (SPDM) with conventional autofluorescent proteins under special physical conditions. This technique allows us to measure the spatial distribution of single fluorescently labeled molecules in entire cells with an effective optical resolution comparable to macromolecular dimensions. Here, we describe the application of the 2CLM approach to the simultaneous nanoimaging of cellular structures using two fluorochrome types distinguished by different fluorescence emission wavelengths. The capabilities of 2CLM for studying the spatial organization of the genome in the mammalian cell nucleus are demonstrated for the relative distributions of two chromosomal proteins labeled with autofluorescent GFP and mRFP1 domains. The 2CLM images revealed quantitative information on their spatial relationships down to length-scales of 30 nm.
    Type of Publication: Journal article published
    PubMed ID: 19548231
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