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compaction remain conjectural. Figure 3.2D-F suggests one model for packing
the 30-nm fiber into the highly condensed form found in metaphase chromo-
somes. Somehow, the length of the chromosomal DNA is reduced by a factor of
10,000 in metaphase chromosomes.
3.8 Structure of the Nucleus
The nucleus contains chromosomes, RNAs, and nuclear proteins in an aqueous
solution. It also seems to have an internal structure that organizes the chromo-
somes and localizes some nuclear functions to specific sites ( Kalhor et al. 2012,
Misteli 2012, Sexton et al. 2012 ). The most obvious organized region is the
nucleolus, the site at which the ribosomal RNA (rRNA) genes are transcribed and
ribosomal subunits are assembled.
Nucleoli are RNA-rich spherical bodies, not surrounded by a membrane, asso-
ciated with specific chromosomal segments called the nucleolus organizer. The
nucleolus contains multiple copies of tandem arrays of rRNA genes. There are four
types of rRNA: 5S, 5.8S, 18S, and 28S. The 5.8S, 18S, and 28S rRNAs are transcribed
as a single unit by RNA polymerase I, yielding a 45S precursor rRNA. The 45S pre-
rRNA is processed into the 18S rRNA of the 40S (small ribosomal subunit) and into
the 5.8S and 28S rRNAs of the 60S (large) ribosomal subunit. Transcription of the
5S rRNA, which is found in the 60S subunit, takes place outside the nucleolus and
is catalyzed by RNA polymerase III. The nucleolus is particularly important during
development, when a large number of rRNA genes are transcribed so that large
numbers of ribosomes can be produced.
Much of the heterochromatin (chromosome regions that remain condensed
during most of the interphase of the cell cycle and seem to contain mostly inac-
tive genes or noncoding DNA) is localized at the edge of the nucleus, appar-
ently because the heterochromatin binds to a protein of the inner nuclear
membrane. Much of the heterochromatin consists of transposable elements.
Heterochromatin is maintained by DNA methylation, histone modifications, and
a cellular defense mechanism called RNAi ( Biemont 2009 ). The presence of het-
erochromatin in centromeric and pericentromeric regions is important in cell
division because it enables pairing of homologous chromosomes.
Active euchromatic DNA is arranged into discrete functional domains that are
important in regulating gene expression. Thus, functional euchromatin is non-
randomly distributed within the interphase nucleus. Apparently, each chromo-
some occupies a discrete region of the nucleus. The chromosomes are closely
associated with the nuclear envelope at many sites, with their centromeres and
telomeres clustered at opposite poles ( Cooper 2000 ).
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