Graduate Thesis Or Dissertation
 

Structure and function of chromatin : studies at the nucleosome and nuclear matrix levels

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  • Several levels of eukaryotic chromatin structure have been observed: the nucleosome, the 10 nm and 30 nm fibers and loop domains, apparently attached to the nuclear matrix. In this research, the structure and function of chromatin at two of these levels was investigated, with studies on both nucleosome positioning and chromatin interaction with the nuclear matrix. In some instances, it seems that nucleosome positioning on genes is not random. Although no simple, definitive "nucleosome binding" sequences can be found which explicitly determine nucleosome positions, it is of interest to note that periodicity of some degenerate groupings of dinucleotides and of maximum bendability are correlated in nucleosomal DNA sequences. This research supports the proposition that nucleosome positioning on DNA may depend on the existence of periodic regularities in DNA bendability. It also indicates that information contained within local sequences, determine properties which affect the differential propensity for positioning of nucleosomes. Bendability seems to represent at least one of the major sequence-directed structural constraints on the ability of any particular stretch of DNA to form nucleosomes. Studies of the nucleosome spacing in the 5' flanking region of the chicken beta globin gene and coding sequence of the chicken thymidine kinase gene in chicken erythrocyte cells and chicken embryo myoblast cells demonstrate that the nucleosome spacing in these regions is most likely cell type-dependent, rather than gene dependent; and probably reflects a general effect of the special histone, H5, carried in erythrocyte cells. DNA loops are proposed to be anchored to the nuclear matrix, which may be involved in DNA replication and repair, RNA transcription and processing, hormone action, virus infection, and carcinogenesis. Studies of the relationship between gene activity and nuclear matrix association, have given both positive and negative results with the chicken thymidine kinase gene, the beta-globin gene and the mouse dihydrofolate reductase gene. There appears to be no simple correlation between nuclear matrix association and gene transcriptional activity. The working hypothesis developed here is that the apparent association of specific genes with the nuclear matrix is mainly caused by specific DNA binding proteins which partition in the nuclear matrix fraction. Adenovirus was used as a model to investigate the role which the nuclear matrix may play in virus infection and viral DNA replication. The origins of replication of adenovirus DNA are found to be strongly associated with the nuclear matrix. One of the nuclear matrix proteins, of mass 140 KD, has been found from a UV cross-linking experiment to be able to bind specifically with the origins of replication of adenovirus. However, whether these proteins are in vivo components of the nuclear matrix or that their association is an artifact of the isolation, could not be determined with certainty.
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