Chromatin is a complex of macromolecules found in cells, consisting of
DNA, protein, and RNA. The primary functions of chromatin are 1) to
DNA into a more compact, denser shape, 2) to reinforce the DNA
macromolecule to allow mitosis, 3) to prevent
DNA damage, and 4) to
control gene expression and
DNA replication. The primary protein
components of chromatin are histones that compact the DNA. Chromatin
is only found in eukaryotic cells (cells with defined nuclei).
Prokaryotic cells have a different organization of their
prokaryotic chromosome equivalent is called genophore and is localized
within the nucleoid region).
Chromatin's structure is currently poorly understood despite being
subjected to intense investigation. Its structure depends on several
factors. The overall structure depends on the stage of the cell cycle.
During interphase, the chromatin is structurally loose to allow access
DNA polymerases that transcribe and replicate the DNA. The
local structure of chromatin during interphase depends on the genes
present on the DNA. That
DNA which codes genes that are actively
transcribed ("turned on") is more loosely packaged and associated with
RNA polymerases (referred to as euchromatin) while that
codes inactive genes ("turned off") is more condensed and associated
with structural proteins (heterochromatin).
modification of the structural proteins in chromatin also alters the
local chromatin structure, in particular chemical modifications of
histone proteins by methylation and acetylation. As the cell prepares
to divide, i.e. enters mitosis or meiosis, the chromatin packages more
tightly to facilitate segregation of the chromosomes during anaphase.
During this stage of the cell cycle this makes the individual
chromosomes in many cells visible by optical microscope.
In general terms, there are three levels of chromatin organization:
DNA wraps around histone proteins forming nucleosomes; the "beads on a
string" structure (euchromatin).
Multiple histones wrap into a 30 nm fibre consisting of nucleosome
arrays in their most compact form (heterochromatin). (Definitively
established to exist in vitro, the 30-nanometer fibre was not seen in
recent X-ray studies of human mitotic chromosomes.)
DNA packaging of the 30 nm fibre into the metaphase
chromosome (during mitosis and meiosis).
There are, however, many cells that do not follow this organisation.
For example, spermatozoa and avian red blood cells have more tightly
packed chromatin than most eukaryotic cells, and trypanosomatid
protozoa do not condense their chromatin into visible chromosomes for
1 Dynamic chromatin structure and hierarchy
1.2 Nucleosomes and beads-on-a-string
1.3 30 nanometer chromatin fibre
1.4 Spatial organization of chromatin in the cell nucleus
1.5 Cell-cycle dependent structural organization
Chromatin and bursts of transcription
2.1 Alternative chromatin organizations
4 Methods to investigate chromatin
5 Chromatin: alternative definitions
6 Nobel Prizes
7 See also
9 Other references
10 External links
Dynamic chromatin structure and hierarchy
Chromatin undergoes various structural changes during a cell cycle.
Histone proteins are the basic packer and arranger of chromatin and
can be modified by various post-translational modifications to alter
chromatin packing (
Histone modification). Most of the modifications
occur on the histone tail. The consequences in terms of chromatin
accessibility and compaction depend both on the amino-acid that is
modified and the type of modification. For example, Histone
acetylation results in loosening and increased accessibility of
chromatin for replication and transcription. Lysine tri-methylation
can either be correlated with transcriptional activity
(tri-methylation of histone H3 Lysine 4) or transcriptional repression
and chromatin compaction (tri-methylation of histone H3 Lysine 9 or
27). Several studies suggested that different modifications could
occur simultaneously. For example, it was proposed that a bivalent
structure (with tri-methylation of both Lysine 4 and 27 on histone H3)
was involved in mammalian early development.
Polycomb-group proteins play a role in regulating genes through
modulation of chromatin structure.
For additional information, see
Histone modifications in chromatin
RNA polymerase control by chromatin structure.
The structures of A-, B-, and Z-DNA.
Main articles: Mechanical properties of
DNA and Z-DNA
DNA can form three structures, A-, B-, and Z-DNA. A- and
DNA are very similar, forming right-handed helices, whereas Z-
a left-handed helix with a zig-zag phosphate backbone. Z-
thought to play a specific role in chromatin structure and
transcription because of the properties of the junction between B- and
At the junction of B- and Z-DNA, one pair of bases is flipped out from
normal bonding. These play a dual role of a site of recognition by
many proteins and as a sink for torsional stress from
or nucleosome binding.
Nucleosomes and beads-on-a-string
Main articles: Nucleosome,
Chromatosome and Histone
A cartoon representation of the nucleosome structure. From PDB:
The basic repeat element of chromatin is the nucleosome,
interconnected by sections of linker DNA, a far shorter arrangement
DNA in solution.
In addition to the core histones, there is the linker histone, H1,
which contacts the exit/entry of the
DNA strand on the nucleosome. The
nucleosome core particle, together with histone H1, is known as a
chromatosome. Nucleosomes, with about 20 to 60 base pairs of linker
DNA, can form, under non-physiological conditions, an approximately
10 nm "beads-on-a-string" fibre. (Fig. 1-2). .
The nucleosomes bind
DNA non-specifically, as required by their
function in general
DNA packaging. There are, however, large DNA
sequence preferences that govern nucleosome positioning. This is due
primarily to the varying physical properties of different DNA
sequences: For instance, adenine and thymine are more favorably
compressed into the inner minor grooves. This means nucleosomes can
bind preferentially at one position approximately every 10 base pairs
(the helical repeat of DNA)- where the
DNA is rotated to maximise the
number of A and T bases that will lie in the inner minor groove. (See
mechanical properties of DNA.)
30 nanometer chromatin fibre
Two proposed structures of the 30nm chromatin filament.
Left: 1 start helix "solenoid" structure.
Right: 2 start loose helix structure.
Note: the histones are omitted in this diagram - only the
With addition of H1, the beads-on-a-string structure in turn coils
into a 30 nm diameter helical structure known as the 30 nm
fibre or filament. The precise structure of the chromatin fibre in the
cell is not known in detail, and there is still some debate over
This level of chromatin structure is thought to be the form of
heterochromatin, which contains mostly transcriptionally silent genes.
EM studies have demonstrated that the 30 nm fibre is highly
dynamic such that it unfolds into a 10 nm fiber
("beads-on-a-string") structure when transversed by an
engaged in transcription.
Four proposed structures of the 30 nm chromatin filament for DNA
repeat length per nucleosomes ranging from 177 to 207 bp.
DNA in yellow and nucleosomal
DNA in pink.
The existing models commonly accept that the nucleosomes lie
perpendicular to the axis of the fibre, with linker histones arranged
internally. A stable 30 nm fibre relies on the regular
positioning of nucleosomes along DNA. Linker
DNA is relatively
resistant to bending and rotation. This makes the length of linker DNA
critical to the stability of the fibre, requiring nucleosomes to be
separated by lengths that permit rotation and folding into the
required orientation without excessive stress to the DNA. In this
view, different lengths of the linker
DNA should produce different
folding topologies of the chromatin fiber. Recent theoretical work,
based on electron-microscopy images of reconstituted fibers
supports this view.
Spatial organization of chromatin in the cell nucleus
The spatial arrangement of the chromatin within the nucleus is not
random - specific regions of the chromatin can be found in certain
territories. Territories are, for example, the lamina-associated
domains (LADs), and the topological association domains (TADs), which
are bound together by protein complexes. Currently, polymer models
such as the Strings & Binders Switch (SBS) model and the
Dynamic Loop (DL) model are used to describe the folding of
chromatin within the nucleus.
Cell-cycle dependent structural organization
Interphase: The structure of chromatin during interphase of mitosis is
optimized to allow simple access of transcription and
factors to the
DNA while compacting the
DNA into the nucleus. The
structure varies depending on the access required to the DNA. Genes
that require regular access by
RNA polymerase require the looser
structure provided by euchromatin.
Karyogram of human male using
Giemsa staining, showing the classic
metaphase chromatin structure.
Metaphase: The metaphase structure of chromatin differs vastly to that
of interphase. It is optimised for physical strength
and manageability, forming the classic chromosome structure seen in
karyotypes. The structure of the condensed chromatin is thought to be
loops of 30 nm fibre to a central scaffold of proteins. It is,
however, not well-characterised.The physical strength of chromatin is
vital for this stage of division to prevent shear damage to the
the daughter chromosomes are separated. To maximise strength the
composition of the chromatin changes as it approaches the centromere,
primarily through alternative histone H1 analogues.It should also be
noted that, during mitosis, while most of the chromatin is tightly
compacted, there are small regions that are not as tightly compacted.
These regions often correspond to promoter regions of genes that were
active in that cell type prior to entry into chromatosis. The lack of
compaction of these regions is called bookmarking, which is an
epigenetic mechanism believed to be important for transmitting to
daughter cells the "memory" of which genes were active prior to entry
into mitosis. This bookmarking mechanism is needed to help
transmit this memory because transcription ceases during mitosis.
Chromatin and bursts of transcription
Chromatin and its interaction with enzymes has been researched, and a
conclusion being made is that it is relevant and an important factor
in gene expression. Vincent G. Allfrey, a professor at Rockefeller
University, stated that
RNA synthesis is related to histone
acetylation. The lysine amino acid attached to the end of the
histones is positively charged. The acetylation of these tails would
make the chromatin ends neutral, allowing for
When the chromatin decondenses, the
DNA is open to entry of molecular
machinery. Fluctuations between open and closed chromatin may
contribute to the discontinuity of transcription, or transcriptional
bursting. Other factors are probably involved, such as the association
and dissociation of transcription factor complexes with chromatin. The
phenomenon, as opposed to simple probabilistic models of
transcription, can account for the high variability in gene expression
occurring between cells in isogenic populations
Alternative chromatin organizations
During metazoan spermiogenesis, the spermatid's chromatin is remodeled
into a more spaced-packaged, widened, almost crystal-like structure.
This process is associated with the cessation of transcription and
involves nuclear protein exchange. The histones are mostly displaced,
and replaced by protamines (small, arginine-rich proteins). It is
proposed that in yeast, regions devoid of histones become very fragile
after transcription; HMO1 an HMGB protein helps in stabilizing
The packaging of eukaryotic
DNA into chromatin presents a barrier to
all DNA-based processes that require recruitment of enzymes to their
sites of action. To allow the critical cellular process of
the chromatin must be remodeled. In eukaryotes, ATP dependent
chromatin remodeling complexes and histone-modifying enzymes are two
predominant factors employed to accomplish this remodeling
Chromatin relaxation occurs rapidly at the site of a
This process is initiated by
PARP1 protein that starts to appear at
DNA damage in less than a second, with half maximum accumulation
within 1.6 seconds after the damage occurs. Next the chromatin
remodeler Alc1 quickly attaches to the product of PARP1, and completes
arrival at the
DNA damage within 10 seconds of the damage. About
half of the maximum chromatin relaxation, presumably due to action of
Alc1, occurs by 10 seconds. This then allows recruitment of the
DNA repair enzyme MRE11, to initiate
DNA repair, within 13
γH2AX, the phosphorylated form of H2AX is also involved in the early
steps leading to chromatin decondensation after
DNA damage occurrence.
The histone variant H2AX constitutes about 10% of the H2A histones in
human chromatin. γH2AX (H2AX phosphorylated on serine 139) can be
detected as soon as 20 seconds after irradiation of cells (with DNA
double-strand break formation), and half maximum accumulation of
γH2AX occurs in one minute. The extent of chromatin with
phosphorylated γH2AX is about two million base pairs at the site of a
DNA double-strand break. γH2AX does not, itself, cause chromatin
decondensation, but within 30 seconds of irradiation,
RNF8 protein can
be detected in association with γH2AX.
RNF8 mediates extensive
chromatin decondensation, through its subsequent interaction with
CHD4, a component of the nucleosome remodeling and deacetylase
After undergoing relaxation subsequent to
DNA damage, followed by DNA
repair, chromatin recovers to a compaction state close to its
pre-damage level after about 20 min.
Methods to investigate chromatin
Chromatin immunoprecipitation sequencing), aimed against
different histone modifications, can be used to identify chromatin
states throughout the genome. Different modifications have been linked
to various states of chromatin.
DNase I hypersensitive sites Sequencing) uses the
sensitivity of accessible regions in the genome to the
DNase I enzyme
to map open or accessible regions in the genome.
FAIRE-seq (Formaldehyde-Assisted Isolation of Regulatory Elements
sequencing) uses the chemical properties of protein-bound
DNA in a
two-phase separation method to extract nucleosome depleted regions
from the genome.
ATAC-seq (Assay for Transposable Accessible
Chromatin sequencing) uses
the Tn5 transposase to integrate (synthetic) transposons into
accessible regions of the genome consequentially highlighting the
localisation of nucleosomes and transcription factors across the
DNA footprinting is a method aimed at identifying protein-bound DNA.
It uses labeling and fragmentation coupled to gel electrophoresis to
identify areas of the genome that have been bound by proteins.
MNase-seq (Micrococcal Nuclease sequencing) uses the micrococcal
nuclease enzyme to identify nucleosome positioning throughout the
Chromosome conformation capture determines the spatial organization of
chromatin in the nucleus, by inferring genomic locations that
MACC profiling (
Micrococcal nuclease ACCessibility profiling) uses
titration series of chromatin digests with micrococcal nuclease to
identify chromatin accessibility as well as to map nucleosomes and
non-histone DNA-binding proteins in both open and closed regions of
Chromatin: alternative definitions
The term, introduced by Walther Flemming, has multiple meanings:
Simple and concise definition:
Chromatin is a macromolecular complex
DNA macromolecule and protein macromolecules (and RNA). The
proteins package and arrange the
DNA and control its functions within
the cell nucleus.
A biochemists’ operational definition:
Chromatin is the
RNA complex extracted from eukaryotic lysed interphase
nuclei. Just which of the multitudinous substances present in a
nucleus will constitute a part of the extracted material partly
depends on the technique each researcher uses. Furthermore, the
composition and properties of chromatin vary from one cell type to the
another, during development of a specific cell type, and at different
stages in the cell cycle.
DNA + histone = chromatin definition: The
DNA double helix in the
cell nucleus is packaged by special proteins termed histones. The
DNA complex is called chromatin. The basic structural
unit of chromatin is the nucleosome.
The following scientists were recognized for their contributions to
chromatin research with Nobel Prizes:
Albrecht Kossel (University of Heidelberg)
Nobel Prize in Physiology or Medicine for his discovery of the five
nuclear bases: adenine, cytosine, guanine, thymine, and uracil.
Thomas Hunt Morgan
Thomas Hunt Morgan (California Institute of Technology)
Nobel Prize in Physiology or Medicine for his discoveries of the role
played by the gene and chromosome in heredity, based on his studies of
the white-eyed mutation in the fruit fly Drosophila.
Francis Crick, James Watson and
Maurice Wilkins (MRC Laboratory of
Molecular Biology, Harvard University and London University
Nobel Prize in Physiology or Medicine for their discoveries of the
double helix structure of
DNA and its significance for information
transfer in living material.
Aaron Klug (MRC Laboratory of Molecular Biology)
Nobel Prize in Chemistry "for his development of crystallographic
electron microscopy and his structural elucidation of biologically
important nucleic acid-protein complexes"
Richard J. Roberts
Richard J. Roberts and Phillip A. Sharp
Nobel Prize in Physiology "for their independent discoveries of split
genes," in which
DNA sections called exons express proteins, and are
DNA sections called introns, which do not express
Roger Kornberg (Stanford University)
Nobel Prize in Chemistry for his discovery of the mechanism by which
DNA is transcribed into messenger RNA.
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Chromatin, Histones & Cathepsin; PMAP The Proteolysis
[ Recent chromatin publications and news]
Protocol for in vitro
ENCODE threads Explorer
Chromatin patterns at transcription factor
binding sites. Nature (journal)
Autosome/Sex chromosome (or allosome or heterosome)
Circular chromosome/Linear chromosome
Extra chromosome (or accessory chromosome)
A chromosome/B chromosome
Telomere-binding protein (TINF2)
List of organisms by chromosome count
List of chromosome lengths for various organisms
List of sequenced genomes
International System for Human Cytogenetic Nomenclature
Structures of the cell nucleus / nuclear protein
Cajal (coiled) body
Dot (PML body)
Transition nuclear protein:
Nuclear matrix (Nucleoskeleton)
see also transcription factors and intracellular receptors
see also nucleus diseases