Biology Reference
In-Depth Information
I. Introduction
DNA double-strand breaks (DSBs) are particularly toxic lesions to cells.
Endogenous DSBs, generated through stalling or collapse of replication forks
when they encounter single-strand DNA lesions such as abasic sites and single-
strand breaks, have been calculated to occur at a frequency of
50 per cell
cycle in human cells and
1 per 4-5 cells per cell cycle for
Saccharomyces
cerevisiae
.
1
DSBs can also be formed by exposure to genotoxic agents such as
ionizing radiation (IR). Efficient repair of DSBs is essential in order to maintain
genome stability, as a single unrepaired break can result in lethality. There are
two major pathways for the repair of DSBs, namely nonhomologous end-joining
(NHEJ) and homologous recombination (HR). NHEJ involves processing and
religation of broken ends, and is an inherently error-prone process (reviewed in
Ref.
2
) while HR uses homologous sequences as a template for accurate repair
(reviewed in Ref.
3
).
In eukaryotes, repair of DSBs and other lesions must occur in the context of
chromatin. The basic unit of chromatin is the nucleosome, comprising
approximately 146 bp DNA wrapped nearly two times around a histone
octamer, formed from a tetramer consisting of (H3-H4)
2
and two H2A-H2B
dimers. In the presence of linker histones and other scaffold proteins, this
''beads-on-a-string'' chromatin is able to be packaged into higher-order
chromatin structures such as the 30 nm fiber and chromosome loops. There-
fore, in order to efficiently repair DNA damage within chromatin, remodeling
is necessary to allow repair enzymes to access the lesion, followed by restora-
tion of the original chromatin structure upon completion of repair, termed the
''access-repair-restore'' model.
4
In the past decade, it has become apparent
that chromatin functions not only as a means of packaging DNA, but that it also
plays an active role in signaling during repair, modulating both recruitment and
activity of repair and checkpoint proteins.
Access to chromatin can be regulated in two ways: by covalent posttransla-
tional modification of histone proteins, including phosphorylation, methylation,
acetylation, and ubiquitylation, and by the action of adenosine triphosphate
(ATP)-dependent remodeling enzymes. ATP-dependent remodelers are large
multi-subunit complexes that couple ATP hydrolysis to movement of histones
or nucleosomes. A number of different remodeling activities can be performed
by these complexes, including exchange or incorporation of core histones
or histone variants, eviction of histones or nucleosomes, and repositioning or
sliding of nucleosomes.
5
Each complex contains a catalytic ATPase subunit that is a member of the
Snf2 family of helicases and translocases. Based on conserved motifs within
the catalytic subunit, remodeling complexes can be further divided into 24
subfamilies,
6,7
including SWI/SNF2 types (characterized by bromodomains
