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Chromosomes, Chromatin, and the
Nucleosome
Chromosomes: DNA associated with proteins
1. The chromosome is a compact form of the DNA that readily fits inside
the cell.
2. Packaging the DNA into chromosomes serves to protect the DNA from
damage.
3. Only DNA packaged into a chromosome can be transmitted efficient to
daughter cells.
Table I: variation in chromosome makeup in different organisms
The traditional view is that prokaryotic cells have a single, circular chromosome,
and eukaryotic cells have multiple, linear chromosomes.
Table 2. Comparison of the gene
density in different organisms’ genomes
Comparison of the chromosomal gene density for different organisms
65kb region
The organization and content of the human genome
Pseudogenes arise from the action of an enzyme called reverse transcriptase
The majority of human intergenic sequences are
Composed of repetitive DNA
(dinucleotide repeats)
( greater 100bp, mostly transposable
element)
Table 7-3
Contribution of introns and repeated sequences to
different genomes
introns (p. 135)
Chromosome duplication and segregation
Eukaryotic chromosomes require Centromeres, Telomeres,
and Original of Replication to be maintained during cell
division
More or less than one centromere leads to chromosome loss or breakage
Centromere size and composition varies dramatically
Telomeres
1. Telomeres are bound by a number of proteins. These proteins distinguish
the natural ends of the chromosome form sites of chromosome breakage and
other DNA breaks in the cell.
DNA ends are the sites of frequent recombination and DNA degradation. The
Proteins at telomeres form a structure that is resistant to both events.
2. Telomeres act as a specialized origin of replication that allows the cell to
replicate the ends of the chromosomes.
The eukaryotic mitotic cell cycle
Each chromosome of the duplicated pair is called a
chromatid, the two chromatids of a given pair are called
sister chromatids.
The events of mitosis
Changes in chromatin structure-DNA condensation and
decondensation
Chromosomes are maximally condensed in M phase
• Sister Chromatid cohension and
Chromosome condensation are mediated
by SMC ((structural maintenance of
chromosome) proteins
Models for the structure of cohesins and condensins
The structural of cohesin is a large ring
composed of two SMC proteins and a
third non-SMC protein. SMC (structural
maintenance of
chromosome) proteins
Mitosis maintains the parental chromosome Number
Meiosis reduces the parental chromosome number
cohesion is lost
Formation of chiasma
Homologous recombination
Formation of chromatin structure
nucleosome- building blocks of chromosomes
Histones are small, positively-charged proteins
H2A: red
H2B: yellow
H3: purple
H4: green
The assembly of a nucleosome
The N-terminal tails are
accessible to protease
trypsin (specifically
cleaves protein positivelycharged amino acids)
The nucleosome has an approximate twofold axis of symmetry
Interactions of the histones with nucleosomal DNA
H3.H4 tertramer
central 60bp region and two ends
H2A.H2B dimer
Each associate with about 30 bp of
DNA on either side of the central 60
bp
Histones contact the minor groove of the DNA by forming
a large number of hydrogen bonds
The large number of the hydrogen bonds provide the driving force to bend the DNA
Higher-order chromatin structure
H binds to linker DNA at one end of
The nucleosome and the central DNA helix
The addition of H1 leads to more compact nucleosomal DNA
Without H1
Histone H1 induces tighter DNA wrapping around the nucleosome
30-nm fiber
Superhelix, 6 nucleosome per turn, supported by EM and X-ray studies
Based on zigzag pattern upon H1 addition, requires linker DNA to pass through
central axis,
The core Histone N-terminal tails are required for the
formation of the 30-nm fiber
The tail of H2A, H3 and H4 interact with adjacent nucleosome
Higher compaction of DNA involves large loops of
nucleosomal DNA
Nuclear scaffold (Topo II, SMC)
Histone variants alter nucleosome function
1. H2A.z histone inhibits nucleosome from forming repressive
chromatin structures, creating regions of easily accessible chromatin
that are more compatible with transcription
2. CENP-A replace H3, is associated with nucleosomes that include centromeric DNA
Regulation of chromatin structure
The interaction of DNA with histone octamer is dynamic
Unwrapping of the DNA from nucleosome is responsible for the accessibility of the DNA
Nucleosome movement by nucleosome remodeling complexes
restructure
ATP-dependent chromatin remodeling complex
SWI/SNF
8-11 subunits
Bromodomain
ISWI
2-4 subunits
No
Mi2/NuRD
8-10 subunits
chromodomain
Nucleosome Positioning by DNA-binding proteins
exclusion
Nucleosome Positioning by DNA-binding proteins
Inducing assembly
Modifications of the histone N-terminal tails alters
the function of chromatin
Acetylation: transcription activation
Effects of histone tail modification
Nucleosome modifying enzymes
Chromatin remodeling complex and histone modifying enzymes
work together to alter chromatin structure
Nucleosome Assembly
The inheritance of histones after DNA replication
The old histones are present on both of the daughter chromosome
H3.H4 tetramers
remain bound to one
of the two daughter
duplexe at random
but H2A.H2B dimers
are released and
enter the local pool
for new nucleosome
assembly.
Inheritance of parental H3.H4 tetramers
facilitate the inheritance of chromatin
state
Nucleosome Assembly
The assembly of nucleosomes is not a spontaneous process,
it requires high salt condition in-vitro.
Proteins required to direct the assembly of histones to
DNA are histone chaperones.
Name
CAF-1
histones bound
H3. H4
RCAF
H3. H4
NAP-1
H2A.H2B
(negatively-charged protein)
How histones chaperones facilitate the assembly of nucleosome
during DNA replication
(sliding clamp)