Chromosomes, Chromatin, and the Nucleosome

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Chromosomes, Chromatin, and the Nucleosome
Chromosomes DNA associated with proteins

• The chromosome is a compact form of the DNA that
  readily fits inside
• the cell.
• Packaging the DNA into chromosomes serves to
  protect the DNA from
• damage.
• Only DNA packaged into a chromosome can be
  transmitted efficient to
• daughter cells.

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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.
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Table 2. Comparison of the gene density in
different organisms genomes
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Comparison of the chromosomal gene density for
different organisms
65kb region
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The organization and content of the human genome
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Pseudogenes arise from the action of an enzyme
called reverse transcriptase
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The majority of human intergenic sequences
are Composed of repetitive DNA
(dinucleotide repeats)
( greater 100bp, mostly transposable element)
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Table 7-3 Contribution of introns and repeated
sequences to different genomes
introns (p. 135)
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Chromosome duplication and segregation
Eukaryotic chromosomes require Centromeres,
Telomeres, and Original of Replication to be
maintained during cell division
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More or less than one centromere leads to
chromosome loss or breakage
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Centromere size and composition varies
dramatically
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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.
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The eukaryotic mitotic cell cycle
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Each chromosome of the duplicated pair is called
a chromatid, the two chromatids of a given pair
are called sister chromatids.
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The events of mitosis
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Changes in chromatin structure-DNA condensation
and decondensation
Chromosomes are maximally condensed in M phase
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• Sister Chromatid cohension and Chromosome
  condensation are mediated by SMC ((structural
  maintenance of
• chromosome) proteins

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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
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Mitosis maintains the parental chromosome Number
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Meiosis reduces the parental chromosome number
cohesion is lost
Formation of chiasma
Homologous recombination
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Formation of chromatin structure
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nucleosome- building blocks of chromosomes
Histones are small, positively-charged proteins
H2A red H2B yellow H3 purple H4 green
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The assembly of a nucleosome
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The N-terminal tails are accessible to protease
trypsin (specifically cleaves protein
positively-charged amino acids)
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The nucleosome has an approximate twofold axis of
symmetry
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Interactions of the histones with nucleosomal DNA
H2A.H2B dimer
H3.H4 tertramer
Each associate with about 30 bp of DNA on either
side of the central 60 bp
central 60bp region and two ends
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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
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Higher-order chromatin structure
H binds to linker DNA at one end of The
nucleosome and the central DNA helix
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The addition of H1 leads to more compact
nucleosomal DNA
Without H1
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Histone H1 induces tighter DNA wrapping around
the nucleosome
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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,
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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
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Higher compaction of DNA involves large loops
of nucleosomal DNA
Nuclear scaffold (Topo II, SMC)
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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
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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
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Nucleosome movement by nucleosome remodeling
complexes
restructure
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ATP-dependent chromatin remodeling complex
SWI/SNF 8-11 subunits
Bromodomain
ISWI 2-4 subunits
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Mi2/NuRD 8-10 subunits
chromodomain
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Nucleosome Positioning by DNA-binding proteins
exclusion
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Nucleosome Positioning by DNA-binding proteins
Inducing assembly
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Modifications of the histone N-terminal tails
alters the function of chromatin
Acetylation transcription activation
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Effects of histone tail modification
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Nucleosome modifying enzymes
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Chromatin remodeling complex and histone
modifying enzymes work together to alter
chromatin structure
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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.
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Inheritance of parental H3.H4 tetramers
facilitate the inheritance of chromatin state
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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 histones bound

CAF-1
H3. H4
RCAF
H3. H4
NAP-1
H2A.H2B
(negatively-charged protein)
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How histones chaperones facilitate the assembly
of nucleosome during DNA replication
(sliding clamp)