Biomedical Engineering Reference
In-Depth Information
picometers to meters) makes experiments and their complex interpretation difficult.
Therefore, while the biochemistry of DSB repair is largely understood, the spatio-
temporal organization of DSB repair is less clear.
20.4.1
Chromatin structure, function and dynamics
in interphase nuclei
In previous chapters, the temporal order of interactions between damaged DNA and
the proteins involved in DDR were described. Nevertheless, in eukaryotes, DNA
exists as chromatin, a complex of DNA, histones, RNA, and non-histone proteins
[
136
-
138
]. These interactions, in turn, result to formation of hierarchical higher-
order chromatin structures and nonrandom organization of chromatin in the cell
nucleus. At the lowest level, DNA wraps around histone octamers and forms nucle-
osomes, the basic units of chromatin [
139
,
140
]. Consequently, nucleosomes form
the nucleohistone fibre that is hierarchically wrapped to yield mitotic chromosomes
with the maximum DNA compaction [
141
-
143
]. Such extreme compaction allows
DNA (about 2-3 m long in humans [
144
,
145
]) to fit into a cell nucleus of about
10
m in diameter and is necessary to allow cell division; however, it precludes
“physiological” functions of DNA such as transcription, replication, and DNA repair
[reviewed in
146
-
148
]. In interphase nuclei, therefore, DNA must adopt a less
compact conformation that lies between the above mentioned extremes [
142
,
143
].
This decondensation of individual mitotic chromosomes results in formation of
spatially separated “chromosomal territories” (CHT) [review
149
] that exhibit
some intermingling [
150
-
152
] and, in some aspects, a specific nuclear localization
[
153
-
155
, and many others]. This organization has been described as “order in ran-
domness” [
153
], since it seems to be more probabilistic than deterministic; however,
this notion continues to be under dispute [
114
,
115
,
156
-
158
, etc.]. For instance,
there is no unequivocal opinion on the level of mutual positioning of individual
CHTs and transmission of this order to daughter cells. On the other hand, it is well
proofed that highly expressed CHTs [
159
,
160
] are preferentially localized closer to
the nuclear center in spherical cycling cells than less expressed chromosomes that
usually appear closer to the nuclear membrane [reviewed,
e.g
., in
153
,
161
,
162
]. In
flat cells (e.g. normal human fibroblasts), however, CHTs might be distributed
according to their size [review
156
,
162
,
163
] and this positioning of individual CHTs
can change as the cells enter quiescence, senescence, or as found in some diseases
[
164
-
168
]. Nuclear organization of CHTs therefore seems to be plastic, depending
on the organism, cell type, cell cycle, level of development, and degree of differ-
entiation [
164
-
168
]. This variability complicates our recognition to the problem in
its whole complexity, which is reflected in a broad spectrum of models that were
suggested to (solely) highlight different aspects of chromatin organization in CHTs
and cell nuclei [
153
-
158
,
161
,
162
,
169
-
172
,
etc
.]. Important questions in the context
of DSB repair therefore are, how can chromatin organization and its dynamics
