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  1. Article ; Online: Quantitative analysis of cell nucleus organisation.

    Shiels, Carol / Adams, Niall M / Islam, Suhail A / Stephens, David A / Freemont, Paul S

    PLoS computational biology

    2007  Volume 3, Issue 7, Page(s) e138

    Abstract: There are almost 1,300 entries for higher eukaryotes in the Nuclear Protein Database. The proteins' subcellular distribution patterns within interphase nuclei can be complex, ranging from diffuse to punctate or microspeckled, yet they all work together ... ...

    Abstract There are almost 1,300 entries for higher eukaryotes in the Nuclear Protein Database. The proteins' subcellular distribution patterns within interphase nuclei can be complex, ranging from diffuse to punctate or microspeckled, yet they all work together in a coordinated and controlled manner within the three-dimensional confines of the nuclear volume. In this review we describe recent advances in the use of quantitative methods to understand nuclear spatial organisation and discuss some of the practical applications resulting from this work.
    MeSH term(s) Cell Nucleus/metabolism ; Models, Biological ; Nuclear Proteins/metabolism
    Chemical Substances Nuclear Proteins
    Language English
    Publishing date 2007-07
    Publishing country United States
    Document type Journal Article ; Review
    ZDB-ID 2193340-6
    ISSN 1553-7358 ; 1553-734X
    ISSN (online) 1553-7358
    ISSN 1553-734X
    DOI 10.1371/journal.pcbi.0030138
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  2. Article: Promyelocytic leukemia nuclear bodies associate with transcriptionally active genomic regions.

    Wang, Jayson / Shiels, Carol / Sasieni, Peter / Wu, Pei Jun / Islam, Suhail A / Freemont, Paul S / Sheer, Denise

    The Journal of cell biology

    2004  Volume 164, Issue 4, Page(s) 515–526

    Abstract: The promyelocytic leukemia (PML) protein is aggregated into nuclear bodies that are associated with diverse nuclear processes. Here, we report that the distance between a locus and its nearest PML body correlates with the transcriptional activity and ... ...

    Abstract The promyelocytic leukemia (PML) protein is aggregated into nuclear bodies that are associated with diverse nuclear processes. Here, we report that the distance between a locus and its nearest PML body correlates with the transcriptional activity and gene density around the locus. Genes on the active X chromosome are more significantly associated with PML bodies than their silenced homologues on the inactive X chromosome. We also found that a histone-encoding gene cluster, which is transcribed only in S-phase, is more strongly associated with PML bodies in S-phase than in G0/G1 phase of the cell cycle. However, visualization of specific RNA transcripts for several genes showed that PML bodies were not themselves sites of transcription for these genes. Furthermore, knock-down of PML bodies by RNA interference did not preferentially change the expression of genes closely associated with PML bodies. We propose that PML bodies form in nuclear compartments of high transcriptional activity, but they do not directly regulate transcription of genes in these compartments.
    MeSH term(s) ATP-Binding Cassette Transporters ; Cell Cycle/physiology ; Cell Nucleus/metabolism ; Cells, Cultured ; Chromosomes, Human, X ; Collagen Type I/genetics ; Collagen Type I, alpha 1 Chain ; Female ; Fibroblasts/cytology ; Fibroblasts/metabolism ; Gene Expression Regulation ; Histocompatibility Antigens Class I/genetics ; Humans ; In Situ Hybridization, Fluorescence ; Intranuclear Inclusion Bodies/metabolism ; Male ; Multigene Family ; Neoplasm Proteins/genetics ; Neoplasm Proteins/metabolism ; Nuclear Proteins/genetics ; Nuclear Proteins/metabolism ; Promyelocytic Leukemia Protein ; RNA, Small Interfering/genetics ; RNA, Small Interfering/metabolism ; Regression Analysis ; Transcription Factors/genetics ; Transcription Factors/metabolism ; Transcription, Genetic ; Tumor Suppressor Proteins
    Chemical Substances ATP-Binding Cassette Transporters ; Collagen Type I ; Collagen Type I, alpha 1 Chain ; Histocompatibility Antigens Class I ; Neoplasm Proteins ; Nuclear Proteins ; Promyelocytic Leukemia Protein ; RNA, Small Interfering ; Transcription Factors ; Tumor Suppressor Proteins ; transporter associated with antigen processing (TAP) ; PML protein, human (143220-95-5)
    Language English
    Publishing date 2004-02-06
    Publishing country United States
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 218154-x
    ISSN 1540-8140 ; 0021-9525
    ISSN (online) 1540-8140
    ISSN 0021-9525
    DOI 10.1083/jcb.200305142
    Database MEDical Literature Analysis and Retrieval System OnLINE

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