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  1. Artikel: Advances and challenges in CRISPR-based real-time imaging of dynamic genome organization.

    Thuma, Jenna / Chung, Yu-Chieh / Tu, Li-Chun

    Frontiers in molecular biosciences

    2023  Band 10, Seite(n) 1173545

    Abstract: Nuclear chromosome compaction is non-random and dynamic. The spatial distance among genomic elements instantly modulates transcription. Visualization of the genome organization in the cell nucleus is essential to understand nuclear function. In addition ... ...

    Abstract Nuclear chromosome compaction is non-random and dynamic. The spatial distance among genomic elements instantly modulates transcription. Visualization of the genome organization in the cell nucleus is essential to understand nuclear function. In addition to cell type-dependent organization, high-resolution 3D imaging shows heterogeneous compaction of chromatin organization among the same cell type. Questions remain to be answered if these structural variations were the snapshots of dynamic organization at different time points and if they are functionally different. Live-cell imaging has provided unique insights into dynamic genome organization at short (milliseconds) and long (hours) time scales. The recent development of CRISPR-based imaging opened windows for studying dynamic chromatin organization in single cells in real time. Here we highlight these CRISPR-based imaging techniques and discuss their advances and challenges as a powerful live-cell imaging method that poses high potential to generate paradigm-shifting discoveries and reveal functional implications of dynamic chromatin organization.
    Sprache Englisch
    Erscheinungsdatum 2023-03-31
    Erscheinungsland Switzerland
    Dokumenttyp Journal Article ; Review
    ZDB-ID 2814330-9
    ISSN 2296-889X
    ISSN 2296-889X
    DOI 10.3389/fmolb.2023.1173545
    Datenquelle MEDical Literature Analysis and Retrieval System OnLINE

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  2. Artikel ; Online: Mouse Models of Cardiomyopathies Caused by Mutations in Troponin C.

    Tikunova, Svetlana B / Thuma, Jenna / Davis, Jonathan P

    International journal of molecular sciences

    2023  Band 24, Heft 15

    Abstract: Cardiac muscle contraction is regulated via ... ...

    Abstract Cardiac muscle contraction is regulated via Ca
    Mesh-Begriff(e) Mice ; Humans ; Animals ; Troponin C/genetics ; Troponin C/chemistry ; Troponin C/metabolism ; Cardiomyopathies/genetics ; Cardiomyopathies/metabolism ; Mutation ; Cardiomyopathy, Dilated/genetics ; Cardiomyopathy, Dilated/metabolism ; Myocardial Contraction ; Calcium/metabolism
    Chemische Substanzen Troponin C ; Calcium (SY7Q814VUP)
    Sprache Englisch
    Erscheinungsdatum 2023-08-02
    Erscheinungsland Switzerland
    Dokumenttyp Journal Article ; Review
    ZDB-ID 2019364-6
    ISSN 1422-0067 ; 1422-0067 ; 1661-6596
    ISSN (online) 1422-0067
    ISSN 1422-0067 ; 1661-6596
    DOI 10.3390/ijms241512349
    Datenquelle MEDical Literature Analysis and Retrieval System OnLINE

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  3. Artikel ; Online: Single-chromosome dynamics reveals locus-dependent dynamics and chromosome territory orientation.

    Chung, Yu-Chieh / Bisht, Madhoolika / Thuma, Jenna / Tu, Li-Chun

    Journal of cell science

    2023  Band 136, Heft 4

    Abstract: Dynamic chromatin organization instantly influences DNA accessibility through modulating local macromolecular density and interactions, driving changes in transcription activities. Chromatin dynamics have been reported to be locally confined but ... ...

    Abstract Dynamic chromatin organization instantly influences DNA accessibility through modulating local macromolecular density and interactions, driving changes in transcription activities. Chromatin dynamics have been reported to be locally confined but contribute to coherent chromatin motion across the entire nucleus. However, the regulation of dynamics, nuclear orientation and compaction of subregions along a single chromosome are not well-understood. We used CRISPR-based real-time single-particle tracking and polymer models to characterize the dynamics of specific genomic loci and determine compaction levels of large human chromosomal domains. Our studies showed that chromosome compaction changed during interphase and that compactions of two arms on chromosome 19 were different. The dynamics of genomic loci were subdiffusive and dependent on chromosome regions and transcription states. Surprisingly, the correlation between locus-dependent nuclear localization and mobility was negligible. Strong tethering interactions detected at the pericentromeric region implies local condensation or associations with organelles within local nuclear microenvironments, such as chromatin-nuclear body association. Based on our findings, we propose a 'guided radial model' for the nuclear orientation of the long arm of chromosome 19.
    Mesh-Begriff(e) Humans ; Chromatin ; Cell Nucleus/physiology ; Chromosomes, Human ; Interphase
    Chemische Substanzen Chromatin
    Sprache Englisch
    Erscheinungsdatum 2023-02-27
    Erscheinungsland England
    Dokumenttyp Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't
    ZDB-ID 2993-2
    ISSN 1477-9137 ; 0021-9533
    ISSN (online) 1477-9137
    ISSN 0021-9533
    DOI 10.1242/jcs.260137
    Datenquelle MEDical Literature Analysis and Retrieval System OnLINE

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  4. Artikel: H1.0 C Terminal Domain Is Integral for Altering Transcription Factor Binding within Nucleosomes

    Burge, Nathaniel L. / Thuma, Jenna L. / Hong, Ziyong Z. / Jamison, Kevin B. / Ottesen, Jennifer J. / Poirier, Michael G.

    Biochemistry. 2022 Apr. 04, v. 61, no. 8

    2022  

    Abstract: The linker histone H1 is a highly prevalent protein that compacts chromatin and regulates DNA accessibility and transcription. However, the mechanisms behind H1 regulation of transcription factor (TF) binding within nucleosomes are not well understood. ... ...

    Abstract The linker histone H1 is a highly prevalent protein that compacts chromatin and regulates DNA accessibility and transcription. However, the mechanisms behind H1 regulation of transcription factor (TF) binding within nucleosomes are not well understood. Using in vitro fluorescence assays, we positioned fluorophores throughout human H1 and the nucleosome, then monitored the distance changes between H1 and the histone octamer, H1 and nucleosomal DNA, or nucleosomal DNA and the histone octamer to monitor the H1 movement during TF binding. We found that H1 remains bound to the nucleosome dyad, while the C terminal domain (CTD) releases the linker DNA during nucleosome partial unwrapping and TF binding. In addition, mutational studies revealed that a small 16 amino acid region at the beginning of the H1 CTD is largely responsible for altering nucleosome wrapping and regulating TF binding within nucleosomes. We then investigated physiologically relevant post-translational modifications (PTMs) in human H1 by preparing fully synthetic H1 using convergent hybrid phase native chemical ligation. Both individual PTMs and combinations of phosphorylation and citrullination of H1 had no detectable influence on nucleosome binding and nucleosome wrapping, and had only a minor impact on H1 regulation of TF occupancy within nucleosomes. This suggests that these H1 PTMs function by other mechanisms. Our results highlight the importance of the H1 CTD, in particular, the first 16 amino acids, in regulating nucleosome linker DNA dynamics and TF binding within the nucleosome.
    Schlagwörter DNA ; amino acids ; fluorescence ; fluorescent dyes ; histones ; humans ; nucleosomes ; phosphorylation ; transcription factors
    Sprache Englisch
    Erscheinungsverlauf 2022-0404
    Umfang p. 625-638.
    Erscheinungsort American Chemical Society
    Dokumenttyp Artikel
    ZDB-ID 1108-3
    ISSN 1520-4995 ; 0006-2960
    ISSN (online) 1520-4995
    ISSN 0006-2960
    DOI 10.1021/acs.biochem.2c00001
    Datenquelle NAL Katalog (AGRICOLA)

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  5. Artikel ; Online: H1.0 C Terminal Domain Is Integral for Altering Transcription Factor Binding within Nucleosomes.

    Burge, Nathaniel L / Thuma, Jenna L / Hong, Ziyong Z / Jamison, Kevin B / Ottesen, Jennifer J / Poirier, Michael G

    Biochemistry

    2022  Band 61, Heft 8, Seite(n) 625–638

    Abstract: The linker histone H1 is a highly prevalent protein that compacts chromatin and regulates DNA accessibility and transcription. However, the mechanisms behind H1 regulation of transcription factor (TF) binding within nucleosomes are not well understood. ... ...

    Abstract The linker histone H1 is a highly prevalent protein that compacts chromatin and regulates DNA accessibility and transcription. However, the mechanisms behind H1 regulation of transcription factor (TF) binding within nucleosomes are not well understood. Using
    Mesh-Begriff(e) Chromatin ; DNA/chemistry ; Histones/metabolism ; Humans ; Nucleosomes ; Protein Binding ; Transcription Factors/genetics ; Transcription Factors/metabolism
    Chemische Substanzen Chromatin ; Histones ; Nucleosomes ; Transcription Factors ; DNA (9007-49-2)
    Sprache Englisch
    Erscheinungsdatum 2022-04-04
    Erscheinungsland United States
    Dokumenttyp Journal Article ; Research Support, N.I.H., Extramural ; Research Support, U.S. Gov't, Non-P.H.S.
    ZDB-ID 1108-3
    ISSN 1520-4995 ; 0006-2960
    ISSN (online) 1520-4995
    ISSN 0006-2960
    DOI 10.1021/acs.biochem.2c00001
    Datenquelle MEDical Literature Analysis and Retrieval System OnLINE

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