Chromosomes and chromatin
Chromosomes organize and
package genes inside cells
• Bind packaging proteins to DNA to make it
more compact.
– Histones +DNA = chromatin in eukaryotes
– Virion proteins in viruses
– HU (?) or other proteins in bacteria
• Loop chromatin and attach it to a matrix in
nuclei
Bands and specialized regions of
human chromosomes
TEL
15 .5
15 .4
.3
15 .2 15
15 .1
short arm (p)
Centromere = CEN
p1 5
p1 4
p1 3
p1 2
p1 1
HRAS
HBB
PTH
MYOD
long arm (q)
Geimsa dark band
ATA=ataxia
telangiectasia
Geimsa light band
Telomere = TEL
(CCCTAA) n
or
(AGGGTT) n
Human
chromosome 11:
125 Mb, 180 cM
Human chromosomes, ideograms
Mitotic
chromosomes
are spread and
stained with
Geimsa. Those
that stain are
shown in
black.
G-bands (more
A+T rich).
Human chromosomes, spectral karyotype
Reagents
specific to each
chromosome.
Chromosome
painting.
Identifying translocations
http://www.ncbi.nlm.nih.gov/disease/
Distinctive and common features of
chromosomes
• Distinctive proteins and DNA sequences
have been used to develop chromosome
painting reagents.
• Genomic DNA in vertebrates has long
(megabase) stretches of G+C rich DNA, and
other long stretches of A+T rich DNA
– Called isochores
• Virtually all this DNA is organized into
chromatin, which has a common
fundamental structure.
Chromatin Structure
Principal proteins in chromatin are
histones
H3 and H4 : Arg rich, mostly conserved sequence
H2A and H2B : Slightly Lys rich, fairly conserved
H1 : very Lys rich, most variable in sequence
between species
Histone structure and function
Histone structure and function
"Minimal" structure for a core histone, e.g. H4. Others have one additional alpha helix.

N
K5 K8 K12 K16
Highly charged
N-terminal tail.
L1

L2

C
Globular, hydrophobic domain for histone-histone
interactions and for histone-DNA interactions.
Histone interactions via the histone fold
The alpha-helical regions of the core histones mediate dimerization.
N
L2
L1


L2

C
C
C
L1
L1
N
The histone fold flanked
by N and C terminal tails.
L2
N
Dimer of histones joined by interactions at the
histone fold.
Nucleosomes are the subunits of the
chromatin fiber
• Experimental evidence:
– Beads on a string in EM
– Micrococcal nuclease digestion
General model for the nucleosomal
core
A string of nucleosomes
Detailed structure of the nucleosomal
core
Higher order chromatin structure
Histone H1 associates
with the linker DNA,
and may play a role in
forming higher order
structures.
Alterations to chromatin structure are
key steps in regulation
Phosphorylation of histones
Serines in histones can be modified by phosphorylation
O
-O
protein kinase
ATP
OH
O
CH 2
... NH CH C NH CH C ...
2
Gly
Ser
O
phosphate
H 2O
protein phosphatase
OH
O
ADP
O
P
O
CH 2
... NH CH C NH CH C ...
2
Gly
Ser
Negative charge on
phosphoserine
mammalian chromatin asssembly factor 1 (CAF1)
Ac
Ac
Acetylation
and Deacetylation of
K5 K8 K12 K16
lysines in proteins
+
NH 3
CH 2
CH 2
AcCoA
O
CH 2 O
CH 2
... NH CH C NH CH C ...
2
Gly
Lys
Ac
Positive charge on amino group
CH 3
O C
NH
CH 2
CH 2
CoA
O
CH 2 O
CH 2
... NH CH C NH CH C ...
2
No charge on amide group
Acetylation and Deacetylation of
Histone acetylation and deacetylation are key processes in
chromatin assembly
and regulation
histones
E.g., Histone H4
Ac
Ac
K5 K8 K12 K16
Histone
deacetylases, e.g.
yeast Rpd3p and
mammalian HD1
Nuclear histone acetyl transferase (HAT A), e.g.
yeast Gcn5p and its mammalian homolog PCAF

N
L1

L2

C
K5 K8 K12 K16
Histone
deacetylases
Cytoplasmic HAT B, e.g. yeast Hat1p + Hat2p and
mammalian chromatin asssembly factor 1 (CAF1)
Ac
Ac
K5 K8 K12 K16
+
NH 3
O
CH 3
C
Effects of histone modifications
• Highly acetylated histones are associated
with actively transcribed chromatin
– Acetylation of histone N-terminal tails may affect
the ability of nucleosomes to associate in
higher-order structures
– The acetylated chromatin appears to be more
“open”, and accessible to transcription factors
and polymerases
– HATs are implicated as co-activators of genes in
chromatin, and HDACs are implicated as corepressors
Matrix and scaffold
The mitotic scaffold and nuclear matrix provide attachment sites for nuclear DNA
Matrix
Scaffold
loops
of duplex
DNA
Nucleus
Mitotic chromosomes,
with
some DNA released
In interphase
chromosomes, at least
some DNA is attached to a
matrix
Chromosome localization in interphase
In interphase, chromosomes appear
to be localized to a sub-region of the
nucleus.
Gene activation and location in the nucleus
• Condensed chromatin tends to localize
close to the centromeres
– Pericentromeric heterochromatin
• Movement of genes during activation and
silencing
– High resolution in situ hybridization
– Active genes found away from pericentromeric
heterochromatin
– Silenced genes found associated with
pericentromeric heterochromatin