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The genetic material is
compacted to a limited volume
Condensing viral
genomes into their coats
The bacterial genome is negatively supercoiled
• with ~100 independently negatively supercoiled indipendent
domains
• an average density of supercoiling of ~1 turn/100 bp.
Domain of a chromosome may
refer either to
•a discrete structural entity
defined as a region within
which supercoiling is
independent of other domains;
• an extensive region including
an expressed gene that has
heightened sensitivity to
degradation by the enzyme
DNAase I.
eukaryotic DNA
DNA of interphase chromatin is negatively supercoiled into
independent domains of ~85 kb.
Nuclear matrix is a network of fibers surrounding and
penetrating the nucleus.
Metaphase chromosomes have a protein scaffold to which the
loops of supercoiled DNA are attached.
Scaffold of a chromosome is a proteinaceous structure in the
shape of a sister chromatid pair, generated when
chromosomes are depleted of histones.
Metaphase chromosomes
have a protein scaffold to
which the loops of
supercoiled DNA are
attached.
Histone-depleted
chromosomes consist of a
protein scaffold to which
loops of DNA are
anchored. Photograph
kindly provided by
Ulrich K. Laemmli.
MAR (matrix attachment site;
also known as SAR for scaffold
attachment site) is a region of
DNA that attaches to the
nuclear matrix.
DNA is attached to the nuclear
matrix at specific sequences
called MARs or SARs.
The MARs are A·T-rich but do
not have any specific consensus
sequence.
Centromeres have short DNA sequences in S. cerevisiae
CEN elements are identified in S. cerevisiae by the ability
to allow a plasmid to segregate accurately at mitosis.
CEN elements consists of short conserved sequences
CDE-I and CDE-III that flank the A·T-rich region CDE-II.
The CBF3 protein complex that binds to CDE-III is
essential for centromeric function.
Centromeres in higher eukaryotic chromosomes contain
large amounts of repetitious DNA.
Telomere is the natural end of a chromosomeis required for
the stability of the chromosome end
Its DNA sequence consists of a simple repeating unit with a
protruding single-stranded end that may fold into a hairpin.
The protein TRF2 catalyzes a reaction in which the 3
repeating unit of the G+T-rich strand forms a loop by
displacing its homologue in an upstream region of the
telomere
A nucleosome contains ~200
bp of DNA, 2 copies of each
core histone (H2A, H2B, H3,
H4), and 1 copy of H1.
DNA is wrapped around the
outside surface of the protein
octamer.
Micrococcal nuclease is an endonuclease that cleaves DNA; in
chromatin, DNA is cleaved preferentially between nucleosomes.
Micrococcal nuclease releases individual nucleosomes from
chromatin as 11S particles.
>95% of the DNA is recovered in nucleosomes or
multimers when micrococcal nuclease cleaves DNA of
chromatin.
The length of DNA per nucleosome varies for individual
tissues in a range from 154-260 bp.
Linking number paradox
describes the discrepancy
between the existence of -2
supercoils in the path of DNA
on the nucleosome compared
with the measurement of -1
supercoil released when
histones are removed.
The histone octamer has a kernel of
a H32·H42 tetramer associated with
two H2A·H2B dimers.
Each histone is extensively
interdigitated with its partner.
All core histones have the
structural motif of the histone
fold. N-terminal tails extend out
of the nucleosome.
Hypersensitive site is a short region of chromatin detected by
its extreme sensitivity to cleavage by DNAase I and other
nucleases; comprises an area from which nucleosomes are
excluded.
A domain containing a
transcribed gene is defined by
increased sensitivity to
degradation by DNAase I.
Euchromatin are chromosome regions less packed
occupies most nuclear regions and represents the active
structure
Heterochromatin is nucleated at a specific sequence and
the inactive structure propagates along the chromatin fiber.
Genes within regions of heterochromatin are inactivated.
Because the length of the inactive region varies from cell to
cell, inactivation of genes in this vicinity causes position
effect variegation.
Similar spreading effects occur at telomeres and at the silent
cassettes in yeast mating type.
RAP1 initiates formation of
heterochromatin in yeast by
binding to specific target
sequences in DNA.
The targets of RAP1 include
telomeric repeats and silencers
at HML and HMR.
RAP1 recruits SIR3/SIR4, which
interact with the N-terminal tails
of H3 and H4.
In eukariotes DNA can be modified although
with important differences with respect
to procariotes
Hemi-methylated site is a palindromic
sequence that is methylated on only
one strand of
DNA.
Maintenance methylase adds a
methyl group to a target site that is
already hemimethylated.
Methylase is an enzyme that adds a
methyl group to a substrate, which
can be a small molecule, a protein, or
a nucleic acid.
De novo methylase adds a
methyl group to an unmethylated
target sequence on DNA.
Fully methylated site is a
palindromic sequence that is
methylated on both strands of
DNA.
Imprinting describes a
change in a gene that occurs
during passage through the
sperm or egg with the result
that the paternal and
maternal alleles have
different properties in the
very early
embryo. May be caused by
methylation of DNA.
Chromatine structure controls gene expression
in eukariotes
The pre-emptive model for
transcription of chromatin
proposes that if nucleosomes
form at a promoter,
transcription factors
(and RNA polymerase) cannot
bind.
If transcription factors (and
RNA
polymerase) bind to the
promoter to establish a stable
complex for initiation, histones
are excluded.
Chromatin remodeling describes the energy-dependent displacement
or reorganization of nucleosomes that occurs in conjunction with
activation of genes for transcription.
There are several chromatin remodeling complexes that use energy
provided by hydrolysis of ATP.
The SWI/SNF, RSC, and NURF complexes all are very large; there
are some common subunits.
A remodeling complex does not itself have specificity for any
particular target site, but must be recruited by a component of the
transcription apparatus.
Hormone receptor and NF1
cannot bind simultaneously
to the MMTV promoter in
the form of linear DNA,
but can bind when the
DNA is presented on a
nucleosomal surface.
HAT (histone acetyltransferase) enzymes
modify histones by addition of acetyl groups;
some transcriptional coactivators have HAT
activity.
HDAC (histone deacetyltransferase) enzymes
remove acetyl groups from histones; they may
be associated with repressors of transcription.
Coactivators may have HAT activities that
acetylate the tails of nucleosomal
histones.
Histone acetylation is associated with activation of
gene expression. Deacetylated chromatin may have a
more condensed structure.
A repressor complex
contains three components:
• a DNA binding subunit,
• a corepressor,
• a histone deacetylase.
Polycomb and trithorax are
antagonisticnrepressors and activators
Polycomb group proteins (Pc-G)
perpetuate a state of repression
through cell divisions.
The PRE is a DNA sequence that is
required for the action of Pc-G.
The PRE provides a nucleation center
from which Pc-G proteins propagate to
maintain an inactive structure.
No individual Pc-G protein has yet
been found that can bind the PRE.
Trithorax group proteins antagonize
the actions of the Pc-G.
LCR is the locus control region that is required for
the expression of several genes in a domain.
An LCR is located at the 5 end of the domain and
consists of several hypersensitive sites.
Insulators block enhancer actions. Insulator between two sites will
prevent an activating or inactivating effect passing from one to the
other.
Special structures, called scs and scs (specialized
chromatin structures, are found at the ends of the
bands.
insulator between two sites will prevent an activating
or inactivating effect passing from one to the other.
LCR is the locus control region that is required for
the expression of several genes in a domain.
MAR (matrix attachment site; also known as SAR for
scaffold attachment site) is a region of DNA that
attaches to the nuclear matrix.
Gene expression is associated with
demethylation