Connecting nuclear architecture and genomic function

Abstract

Research in our laboratory employs a dual approach to correlating genomic function and regulation with nuclear architecture. In one series of projects we are identifying, cloning, and studying the molecular, genetic, and functional properties of the nuclear matrix proteins which comprise the three-dimensional nuclear architecture. In a second series, we are using molecular labeling, microscopic, and computer imaging approaches to visualize in three dimensions sites of genomic organization and function within the in situ nuclear architecture and to obtain precise structural and spatio-temporal information about the individual sites where genomic function and regulation occurs. Additionally, our group is investigating the possible arrangement of the functional sites into higher-order domains and their relationship to the overall architecture and regulation in the cell nucleus. Nuclear Matrix Proteins as a Basis for Cenomic Organization, Function, and RegulationWhile a plethora of functional properties are associated with the isolated nuclear matrix [Berezney, 1991; Berezney et al., 19951, our knowledge of the proteins which compose the nuclear matrix is still in its infancy. Comprehensive analysis of the individual proteins is, therefore, critical as a basis for correlating higher order structural organization in the nucleus with the associated genomic functions.Studies in our laboratory are emphasizing the major proteins of the nuclear matrix (termed nuclear matrins) which are common among mammalian cells [Nakayasu and Berezney, 1991; Belgrader et al., 1991al. Microsequencing, molecular suggested that a significant portion of the major nuclear matrix proteins correspond to known pre-mRNP proteins, transcriptional or RNA splicing factors [Mattern et al., 1996; S. Kim, X. Wei, and R. Berezney, unpublished findings].Additional proteins are involved in other regulatory properties or are newly identified proteins whose function remains to be resolved. Our research group is currently concentrating its efforts on three nuclear matrix-associated proteins termed matrin 3, matrin cyp, and matrin p250.Matrin 3 is an acidic nuclear matrix protein (125 kDa). Antibodies to this protein decorate the nuclear interior with a fibrogranular pattern typical of the nuclear matrins [Nakayasu and Berezney, 1991; Belgrader et al., 1991bl. The analysis of matrin 3 human and rat cDNA sequences indicates a high degree of conservation among mammals [Belgrader et al., 1991bl. The lack of homologies with other proteins or functional motifs gives few clues to possible function, although the presence of over 40 potential phosphorylation sites suggests the role of protein phosphorylation. As a prelude to studying matrin 3 function, we are investigating the genomic organization of the matrin 3 gene in the rat. Preliminary results suggest the presence of at least two closely related genes and the possibility of alternatively spliced transcripts [Mortillaro et al., 1993; Somanathan et al., 19951. Matrin cyp is a 106 kDa protein that is localize...

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