422
Cell Nucleus Biogenesis, Structure and Function
chromatin organization that dictate how
chromatin is packaged
in vivo
.Animpor
-
tant consideration here is the way genes
might be organized into chromatin do-
mains – these are usually conceptualized
as DNA loops – that might be regarded as
the structural units of gene expression.
Evidence for the existence of discrete
chromatin domains comes from a num-
ber of sources. Nucleases sensitivity is
the classical indicator of chromatin struc-
tures that correlates with gene expression;
general nuclease sensitivity of active loci
will often spread throughout domains that
cover many kbp up- and downstream of
an expressed gene. Chromatin immuno-
precipitation experiments – using antibod-
ies to histone variants found in active
chromatin – conFrm this. Moreover, clear
transitions from active to inactive chro-
matin suggest that chromatin domains are
demarcated by elements that determine
the boundaries of functional genetic units.
As an example, consider a high-resolution
analysis of acetylation across three genes
in the vicinity of the chicken
β
-globin lo-
cus. This chromosomal region contains a
folate receptor gene, a 16-kbp condensed
chromatin region, the
β
-globin gene do-
main and an adjacent olfactory receptor
gene. The condensed chromatin maintains
very low levels of histone acetylation at all
developmental stages, with similar levels
maintained in inactive genes. Much higher
levels of acetylation are seen through-
out the transcribed gene domains, while
chromatin in the vicinity of upstream reg-
ulatory sites maintain the highest levels
of acetylation. Most signiFcantly, a very
strong constitutive focus of hyperacetyla-
tion corresponds with an insulator element
that appears to deFne the globin and
adjacent folate receptor domains. These
observations show how epigenetic modiF-
cations influence the chromatin domain
structure and also imply that different
classes of histone acetyl transferase with
different chromatin targets are involved in
the control of gene expression.
Various genetic elements have been de-
scribed that together deFne the structure
of chromatin domains and regulate gene
expression. These include: promoter el-
ements, enhancers, LCRs, S/MARs and
insulators. Enhancers and LCRs generally
contain arrays of transcription factor bind-
ing sites that bind appropriate factors to
augment levels of gene expression, by di-
rectly upregulating rates of transcription.
These components contribute to the main-
tenance of a gene’s expressional status
and are responsible for establishing a pro-
ductive spatial conFguration in chromatin
and perhaps for targeting chromatin to
speciFc nuclear sites. In some cases, LCRs
are required to establish natural levels of
gene expression from ectopic (unnatural)
chromosomal sites.
The nuclear matrix and related scaf-
fold are believed to play important roles
in different aspects of chromatin func-
tion. S/MARs are DNA elements that
clearly augment transcription and may
achieve this using AT-rich sequences to
modulate superhelical stress that arises
during transcription. The importance of
these elements in gene regulation is con-
Frmed by the fact that a classical MAR
element is known to play a critical role
in orchestrating the temporal and spatial
expression of many genes during T-cell
development. In addition to this, efFcient
MAR elements have been shown to sup-
port long-term gene expression from ec-
topic chromosomal sites, suggesting that
these elements might play a role in tar-
geting gene domains to speciFc nuclear
sites, such as matrix-associated transcrip-
tion centers, prior to gene expression.
These elements are probably distinct from
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