Molecular Biology of the Cell by Bruce Alberts, Alexander Johnson, Julian Lewis, David Morgan, Martin Raff, Keith Roberts, Peter Walter by by Bruce Alberts, Alexander Johnson, Julian Lewis, David Morg

202 Chapter 4: DNA, Chromosomes, and Genomes
Barrier DNA Sequences Block the Spread of Reader–Writer
Complexes and thereby Separate Neighboring Chromatin
Domains
The above mechanism for spreading chromatin structures raises a potential problem.
Inasmuch as each chromosome contains one continuous, very long DNA
molecule, what prevents a cacophony of confusing cross-talk between adjacent
chromatin domains of different structure and function? Early studies of position
effect variegation had suggested an answer: certain DNA sequences mark the
boundaries of chromatin domains and separate one such domain from another
(see Figure 4–31). Several such barrier sequences have now been identified and
characterized through the use of genetic engineering techniques that allow specific
DNA segments to be deleted from, or inserted in, chromosomes.
For example, in cells that are destined to give rise to red blood cells, a sequence
called HS4 normally separates the active chromatin domain that contains the
human β-globin locus from an adjacent region of silenced, condensed chromatin.
If this sequence is deleted, the β-globin locus is invaded by condensed chromatin.
This chromatin silences the genes it covers, and it spreads to a different extent in
different cells, causing position effect variegation similar to that observed in Drosophila.
As described in Chapter 7, the consequences are dire: the globin genes
are poorly expressed, and individuals who carry such a deletion have a severe
form of anemia.
In genetic engineering experiments, the HS4 sequence is often added to both
ends of a gene that is to be inserted into a mammalian genome, in order to protect
that gene from the silencing caused by spreading heterochromatin. Analysis of
this barrier sequence reveals that it contains a cluster of binding sites for histone
acetylase enzymes. Since the acetylation of a lysine side chain is incompatible
with the methylation of the same side chain, and specific lysine methylations are
required to spread heterochromatin, histone acetylases are logical candidates for
the formation of DNA barriers to spreading (Figure 4–41). However, several other
types of chromatin modifications are known that can also protect genes from
silencing.
(A)
nuclear pore
(B)
(C)
spreading
heterochromatin
euchromatin
barrier protein
barrier protein
barrier protein
Figure 4–41 Some mechanisms of
barrier action. These models are derived
from experimental analyses of barrier
action, and a combination of several of
them may function at any one site.
(A) The tethering of a region of chromatin to
a large fixed site, such as the nuclear pore
complex illustrated here, can form a barrier
that stops the spread of heterochromatin.
(B) The tight binding of barrier proteins to
a group of nucleosomes can make this
chromatin resistant to heterochromatin
spreading. (C) By recruiting a group of
highly active histone-modifying enzymes,
barriers can erase the histone marks that
are required for heterochromatin to spread.
For example, a potent acetylation of lysine
9 on histone H3 will compete with lysine 9
methylation, thereby preventing the binding
of the HP1 protein needed to form a major
form of heterochromatin. (Based on
A.G. West and P. Fraser, Hum. Mol. Genet.
14:R101–R111, 2005. With permission
from Oxford University Press.)