340 C h ro m a t i n
involve different pairs of nonsister chromatids and is
manifested as a paucity of 2-chromatid double cross-
overs. When chromatid interference is reported, it is
usually weak and negative.
See also: Coincidence, Coefficient of;
Interference, Genetic; Negative Interference;
Tetrad Analysis
Chromatin
J Y Lee and T L Orr-Weaver
Copyright ß 2001 Academic Press
doi: 10.1006/rwgn.2001.0199
Composition and Structure
Chromatin is composed of a cell's DNA and asso-
ciated proteins. Histone proteins and DNA are
found in approximately equal mass in eukaryotic
chromatin, and nonhistone proteins are also in great
abundance. The basic unit of organization of chro-
matin is the nucleosome, a structure of DNA and
histone proteins that repeats itself throughout an
organism's genetic material.
Histones are highly conserved basic proteins,
whose positively charged character helps them to
bind the negatively charged phosphate backbone of
DNA. There are five histone proteins in the family:
H1, H2A, H2B, H3, and H4. Two H3 and two H4
proteins form a tetramer, which combines with two
H2A/H2B dimers to form the disk-shaped histone
core. Approximately 150 bp of DNA wrap around
this protein structure almost twice to make a nucleo-
some core particle. With linker histone (e.g., histone
H1) and linker DNA, this is called the nucleosome.
The linker DNA can vary in length, usually be-
tween 10 and 90 bp, depending on the species,
gene activity, developmental stage, and other factors.
The nucleosome repeats approximately every 200 bp
and is close to 10 nm in diameter. The X-ray crystal
structure of the nucleosome core particle was derived
in 1997. The core histones each have a central fold,
which lies within the DNA, and an unstructured N-
terminal tail, which protrudes outside the core. The
tail extensions of histone H3 in particular are very
long and are held in place by nucleosome±nucleosome
interactions.
The nucleosome is the most basic unit of structure
of chromatin, but the chromatin is even further organ-
ized by folding into a higher-order structure. Early
evidence for this came from the observation that
in vitro, when chromatin is treated with salt, the over-
all chromatin structure falls apart and the nucleosomes
resemble `beads on a string.' In addition, in solutions
of salt with concentrations comparable with physio-
logical conditions, chromatin is usually seen in a
thicker structure (30 nm fiber) than would be expected
by a string of nucleosomes. In the `solenoid' model of
chromatin folding, each nucleosome associates with
one H1 protein and a group of six nucleosomes is
turned into a spiral shape (see Figure 1). The structure
of the nucleosome predicts that interactions between
histone tails and nucleosomes may also play a role in
the coiling of chromatin fibers. During cell division,
further compaction of DNA occurs when the chro-
matin is condensed into chromosomes in prophase. As
it is very difficult to organize and move large amounts
of chromatin fiber, this condensation is necessary for
the cell to be able to properly segregate chromosomes
in mitosis and meiosis. Though all of the proteins
necessary for this process have not been identified,
the condensin complex is a group of proteins that is
essential for the proper condensation of chromo-
somes. It is thought that compaction may involve
the 30-nm chromatin, forming loops extending from
a proteinaceous scaffold composed of nonhistone pro-
teins, though there may be even more complex mech-
anisms of condensation (see Figure 1 for a model).
Function
Chromatin structure plays an important role in con-
trolling gene expression and replication. The packaging
of DNA into nucleosomes forms a `closed' structure
that is not very accessible to enzymes that perform
replication, transcription, and DNA repair. This struc-
ture is generally transcriptionally repressive, allowing
only a basal level of gene expression. In a disrupted,
`open' nucleosome structure, the DNA is more acces-
sible to replication and transcription factors.
In transcription, some activators and repressors
interact with RNA polymerases to change the chro-
matin structure and modulate gene activity. Activators
can help to disrupt nucleosome structure and thereby
stimulate the assembly of RNA polymerase and tran-
scription factors at the promoter. For replication,
a similar modulation of chromatin structure must
occur to allow the replication machinery to be pos-
itioned at the origins of replication.
The structure of chromatin can also have long-
range effects on gene expression. In a phenomenon
termed `position effect variegation,' genes located
near silent heterochromatic regions can also be made
transcriptionally inactive. Genes as far as 1000 kb
away can be silenced. Because the exact areas that are
repressed vary from cell to cell, this is an epigenetic
phenomenon that produces variegation in phenotype.
It is generally thought that the highly condensed

Short region of 2 nm
DNA double helix
‘Beads-on-a-string’ 11 nm
form of chromatin
30-nm chromatin
fiber of 30 nm
packed nucleosomes
Section of
chromosome in an
extended form 300 nm
Condensed section
of metaphase
chromosome 700 nm
Entire
metaphase
1400 nm
chromosome
Figure 1 Model of chromatin packing into higher-
order structures. DNA is assembled into the `beads-on-
a-string' conformation by wrapping around histones to
form nucleosomes, which can then be packed into a 30-
nm fiber. The fibers coil to form a chromosome. In
metaphase, the chromosomes condense even more
extensively. Reproduced from Alberts, Bruce et al.
(1994) Molecular Biology of the Cell, 3rd edn. New York:
Garland Publishing. (Permission from Elsevier Science).
nature of heterochromatin prevents access by tran-
scription factors, but how this can affect neighboring,
nonheterochromatic regions is not fully understood.
While it is accepted that proteins found in the hetero-
chromatin can `spread' to adjoining regions and im-
pact a similar repressive effect, another possibility
is that the heterochromatin may be grouped into com-
partments of the nucleus that are inaccessible to tran-
scription factors.
Chromatin structure can also affect DNA replica-
tion on a global level. For example, heterochromatin
and other silent areas of the genome replicate late in
S-phase, but the reason that these late-replicating
regions are silent is unknown. One possibility is a
specific repressive chromatin structure that can be
overcome to allow origin firing late in S-phase.
Chromatin 341
Modification
Both protein complexes and small organic molecules
modulate the state of chromatin in the cell. Large
chromatin-remodeling complexes use the energy
from ATP hydrolysis to destabilize and reposition
nucleosomes. These complexes are highly conserved
in many eukaryotic organisms (see Table 1). They
all include a helicase-like subunit that has a DNA-
dependent ATPase activity. The SWI/SNF family of
chromatin-remodeling complexes are very large pro-
tein complexes with many subunits. They are thought
to help activate transcription by disrupting the
nucleosome structure, by displacing the histone octa-
mer to neighboring DNA. The ISWI family of remod-
eling complexes are smaller in mass and generally
have fewer subunits. Unlike the SWI/SNF complexes,
they are thought to promote gene expression by slid-
ing the nucleosomes along the DNA, opening up a
local area.
Another example of a chromatin-remodeling com-
plex is the polycomb (Pc) group in Drosophila. This
complex is a negative regulator of transcription, acting
to repress homeotic genes during development. The
Pc complex is believed to cause a tightening of chro-
matin structure, inducing a heterochromatin-like
state, or to coat the chromatin, thus preventing access
by transcription factors. The Pc group is also needed
for position effect variegation.
Posttranslational modifications also exert signifi-
cant effects on chromatin activity (see Figure 2).
Acetylation of the N-terminal tails of core histones
is the best-studied histone modification. The addition
and removal of acetyl groups has considerable influ-
ence on gene regulation. This connection was made
by several observations. First, some transcriptional
activators are histone acetyl transferases (HAT), while-
some transcriptional repressors are or recruit histone
deacetylases (HDAC). Second, in Saccharomyces
cerevisiae, regions with hyperacetylated histones (in
particular, H3 and H4) tend to be transcriptionally
active, while areas with hypoacetylated histones are
mostly silent. In mammals, the inactive X chromo-
some has little acetylation of histone H4.
The addition of an acetyl group on a lysine residue
will reduce the positive charge of the histone, thereby
causing a weaker interaction between the histone and
the DNA. This loss of stability in the nucleosome
probably facilitates access to the DNA by transcrip-
tion factors. By the crystal structure of the nucleo-
some, the N-terminal tails of histones were shown
to mediate nucleosome±nucleosome interaction, and
acetylation of these tails is predicted to disrupt these
interactions and thereby open the chromatin struc-
ture. Since multiple lysine residues are often modified,
342 C h ro m a t i n

Table 1 Chromatin-remodeling complexes.

Complex Organism ATPase Mass No. of
(MDa) Subunits
SWI/SNF family
SWI/SNF S. cerevisiae Swi2/Snf2 2 11
RSC S. cerevisiae Sth1 1 15
Brahma D. melanogaster brahma 2 nd
h SWI/SNF H. sapiens hBRM 2 *10
h SWI/SNF H. sapiens BRG1 2 *10
NRD H. sapiens CHD4 1.5 18
ISWI family
I SWI1 S. cerevisiae ISWI1 0.4 4
I SWI2 S. cerevisiae ISWI2 0.3 2
NURF D. melanogaster ISWI 0.5 4
CHRAC D. melanogaster ISWI 0.7 5
ACF D. melanogaster ISWI 0.2 4
RSF H. sapiens hISWI 0.5 2
(Reprinted from Kornberg and Lorch, 1999. Twenty-five years of the nucleosome, fundamental particle of the eukaryote
chromosome. Cell 98: 285±294; with permission from Elsevier Science.)

Me
Me P Ac N
Ac P Ac
N Me K
KS
Ac A
c Ac Me c Ac K S 9
K A P c A K 41
0
9 10 K
14 18 K c P A K 8 1
23 2 KS SK 23 1
7 28 27
H3 H3 28
C
C
20 H4 H4
1 5 8 12 16 K 20 16
12 1
S K K K K Me K K K 8 5 S
K K
Ac Ac Me Ac Ac
P Ac Ac Ac Ac P

Ac Ac
1 K Ac Ac Ac
S H2A H2B K K K K N
5 5
P 119 120 20 15 12
K K C
C Ub
Ub
Ub
Ub

Figure 2 Schematic of modification of chromatin histones (H2A, H2B, H3, H4). The sites of acetylation (Ac),
phosphorylation (P), methylation (Me), and ubiquitination (Ub) of the core histones are diagrammed. Acetylation,
methylation, and phosphorylation occur on the N-terminal tails of the histones. With the exception of
phosphorylation of serine residues (S), modifications are of lysine residues (K). (Adapted from Spencer VA and
Davie JR (1999) Role of covalent modifications of histones in regulating gene expression. Gene 240: 1±12; with
permission from Elsevier Science.)

it is suspected that these hyperacetylated histones
could affect global chromatin structure, e.g., by desta-
bilizing the 30-nm fiber structure.
Phosphorylation is another modification seen on
histone tails. In particular, the phosphorylation level
of N-terminal serines of H1 and H3 changes with
mitotic and meiotic stages, appearing late in G2,
reaching its peak in metaphase, and disappearing at
anaphase. This correlates with the timing of chromo-
some condensation, and phosphorylation of histone
H3 is required for proper chromosome condensation
and segregation.
Methylation occurs on histone lysines, beginning
after nucleosome assembly and peaking in mitosis.
Recent work has shown that methylation at a particu-
lar lysine in H3 is required for proper cell division.

Also, ADP ribosylation and ubiquitination on his-
tones have been observed, but their effects are not as
yet well understood.
Modification of the DNA itself has profound
effects on chromatin structure and gene expression.
In most eukaryotes, methyl groups are often added to
the cytosine residue in a CG doublet. Silent genes are
often methylated, while active genes are usually not
methylated. Since methylation is found frequently
at the 50 ends of genes, this modification probably
induces some sort of silent chromatin state that pre-
vents access by RNA polymerase. One example of
genes silenced by methylation is the globin gene
cluster in adult chicken erythroid cells. In mammals,
the inactive X chromosome in females is silenced
by methylation. Studies on methylated genes have
shown that the methylation patterns are heritable,
and models have been proposed as to how such a
state would be propagated.
Replication
The exact mechanism of how chromatin is replicated
is not yet clear, but important observations have been
made on certain aspects of this process. Most of chro-
matin assembly occurs during S-phase, so the nucleo-
some is assembled soon after DNA replication. Only
a very small area of DNA is perturbed at a time as
replication occurs: only two nucleosomes in front of
the replication fork are disturbed, and less than 300 bp
behind the fork are without nucleosomes. The first
nucleosome behind the fork is almost complete (lack-
ing only H1), but, 450±650 bp behind the fork, fully
assembled nucleosomes are found. As the replication
fork approaches, the histone octamers disassemble
into H2A/H2B dimers and (H3, H4)2 tetramers. The
formation of the new nucleosome occurs in several
stages. The tetramer of histones H3 and H4 is deposited
onto the newly replicated DNA first with the help
of chromatin assembly factor-1 (CAF-1). This is
dependent on replication. Interestingly, H3 and H4
are acetylated on specific lysines when they are first
deposited, and are deacetylated to another form after
they are incorporated. The H2A/H2B dimers are
then deposited in a replication-independent process
that may involve NAP-1 (nucleosome assembly
protein-1). H1 is the last protein added, and the new
nucleosome is made up of both old and new histone
proteins.
The overall state of the chromatin is preserved after
replication. For instance, regions that are silent because
of position effect variegation are maintained. It has
been hypothesized that the modification state of the
chromatin can be the epigenetic mark that is passed
onto new chromatin. During cell division in females,
Chromomeres 343
the same X chromosome is inactivated faithfully
through its methylation state. More work is needed
on whether the modification state of histones may
also be a carrier of gene-expression information after
replication.
Further Reading
Krude T (1999) Chromatin assembly during DNA replication in
somatic cells. European Journal of Biochemistry 263: 1±5.
Strahl BD and Allis CD (2000) The language of covalent histone
modifications. Nature 403: 41± 45.
Vignali M, Hassan AH, Neely KE and Workman JL (2000) ATP-
dependent chromatin-remodeling complexes. Molecular and
Cellular Biology 20: 1899±1910.
Wolffe A (1998) Chromatin: Structure and Function, 3rd edn. San
Diego, CA: Academic Press.
References
Kornberg RD and Lorch Y (1999) Twenty-five years of the
nucleosome, fundamental particle of the eukaryote chromo-
some. Cell 98: 285±294.
See also: Euchromatin; Heterochromatin;
X-Chromosome Inactivation
Chromomeres
M HulteÂn and C Tease
Copyright ß 2001 Academic Press
doi: 10.1006/rwgn.2001.0200
At prophase of mitosis and meiosis in plants and
animals, condensing chromosomes display a beaded,
granular appearance. These beads are termed chromo-
meres. Chromomeres can also be seen in polytene
interphase chromosomes of dipteran insects.
Chromomeres vary considerably in size, but pro-
vide a constant pattern on any given chromosome.
The term chromomere has been applied inconsistently
in different organisms to include chromatin of variable
composition. In mammals, the pattern of chromomeres
at pachytene of meiosis is very similar to that of the
dark bands on somatic chromosomes obtained by
staining with Giemsa following trypsin treatment.
Such dark G-bands tend to be AT-rich and also gene-
poor regions of the genome. This implies that the
chromomeres visible at meiosis have a similar consti-
tution. Somewhat in contrast, chromomeres are pres-
ent at the bases of transcription loops of lampbrush
chromosomes of urodeles. This would indicate that
in these organisms, chromomeres form in chromatin
segments that are gene-rich. The significance of
chromomeres, in terms of chromosome structure and
function, remains a matter of debate.