Biology Reference
In-Depth Information
fundamental physical principles that drive the folding of
a chromosomal fiber
[6,8,9]
. With these techniques in
place, it has now become possible to study the global
characteristics and general mechanisms that drive chro-
mosome folding. Thus, an approach combining biochem-
istry, genetics, imaging and biophysics promises to unravel
one of the most fascinating topological phenomena in
molecular biology. Integration of biophysical structures
and dynamic spatial architectures of the genome with
transcription profiles will provide a three-dimensional (3D)
view of the systems biology of gene expression.
This chapter consists of several sections that each
highlight a different, basic aspect of chromosome folding.
First we describe the basic structure and protein composi-
tion of the chromatin fiber that makes up each chromo-
some. Then we discuss how fundamental principles of
polymer physics drive key aspects of chromosome folding.
Next, we consider how the anchoring of specific genomic
loci to fixed nuclear scaffolds may constrain the topology
of interphase chromosomes in relation to gene activity.
Subsequently we discuss the formation of networks of
intra- and inter-chromosomal contacts among linearly
distant sequence elements, and their functional relevance.
Finally, we will describe the three-dimensional architecture
of chromosomes as self-organizing systems in which each
of these processes contributes to build a functional cell
nucleus.
of the histone
DNA interactions. Many others are recog-
nized and bound by specific proteins. These histone
modifications may therefore be regarded as signals that
contribute to the local recruitment of proteins with partic-
ular structural or functional roles.
A rough estimate suggests that for each nucleosome
there may be ~30 other protein molecules that make up
chromatin
[12]
. One may therefore envisage the chromatin
fiber as a nucleosomal array coated by a substantial layer of
other proteins. It is likely that several thousands of distinct
proteins contribute to this layer. Most of these proteins
associate with only certain parts of the genome, their
specificity being determined by direct binding to specific
DNA sequences, by recognition of certain histone modifi-
cations, or by interaction with other proteins.
With dozens of histone modifications and thousands of
proteins contributing to chromatin, it is theoretically possible
that each small segment of the genome is bound by a different
combination of proteins and histone marks. However,
systematic mapping surveys in several multicellular organ-
isms indicate that this is not the case. Rather, chromosomes
appear to be organized into domains of relatively homoge-
neous protein composition, and the number of principal
chromatin types appears to be limited to fewer than 10.
For example, genome-wide mapping of the binding patterns
of more than 50 chromatin proteins in Drosophila cells
identified five major types of chromatin, defined by distinct,
recurrent combinations of proteins
[13]
. Thesefive types form
domains that sometimes extend over more than 100 kb, often
including multiple neighboring genes. Of these chromatin
types, two are linked to gene repression while the other three
appear conducive to transcription. Extensive mapping of
many histone marks in various species also points to a limited
number of chromatin states
[12]
.
In summary, eukaryotic genomes are packaged into
a nucleosomal fiber, which in turn is covered by a layer of
many other proteins. A limited number of combinations of
proteins and histone marks define distinct chromatin states
that divide the genome into segments. How these different
chromatin states may relate to the spatial organization of
chromosomes will be discussed below.
e
THE BASIC MATERIAL: THE CHROMATIN
FIBER
DNA and all associated proteins are collectively referred to
as chromatin. In eukaryotes, most nuclear DNA is associ-
ated with specialized protein discs that consist of an
octamer of histone proteins (two each of histones H2A,
H2B, H3 and H4). About 145 bp of DNA is wrapped twice
around a histone disc to form a nucleosome, and approxi-
mately 20
50 bp of 'linker' DNA separates two nucleo-
somes. This beads-on-a-string configuration, which has
a thickness of about 10 nm, forms the first level of
compaction of DNA. In vitro, without the help of other
proteins, nucleosomal filaments can be induced to combine
into a regularly shaped fiber of 30 nm diameter. Models of
the 30 nm fiber are depicted in most standard molecular
biology textbooks, but recent studies indicate that its
occurrence in vivo may in fact be rare and limited to
specialized cell types, such as sperm from sea urchin and
erythrocytes from chicken
[10,11]
.
Histones not only play a structural role, they also carry
a range of post-translational modifications, such as meth-
ylation, acetylation, phosphorylation, ubiquitylation and
several others. Some of these modifications alter the net
charge of the histone particle, thereby altering the tightness
e
THE POLYMER PHYSICS
OF CHROMOSOMES
The chromatin fibers that make up chromosomes are very
long, flexible polymers, and it is therefore not surprising
that insights from the field of polymer physics have been
instrumental in describing their three-dimensional folding
and dynamics. In order to understand how chromosomes
are organized inside the nucleus it is important to first
outline the basic polymer principles of chromosomes that
determine their conformation and shape in the absence of
