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