chromosomes and chromatin. chromosomes organize and package genes inside cells bind packaging...
TRANSCRIPT
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
p15
Geimsa dark band
Geimsa light band
Centromere = CEN
Telomere = TEL
long arm (q)
short arm (p)
n
TEL
(CCCTAA) or (AGGGTT)n
p11p12
p14p13
15.115.2 15.315.4 15.5
ATA=ataxia telangiectasia
HRASHBBPTHMYOD
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).
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.
Principal proteins in chromatin are histones
H3 and H4 : Arg rich, mostly conserved sequenceH2A and H2B : Slightly Lys rich, fairly conserved
H1 : very Lys rich, most variable in sequence between species
Histone structure and function
K5 K8 K12 K16
α1 α2 α31L 2L
CN
Highly charged
- . N terminal tail
Histone structure and function
, - Globular hydrophobic domain for histone histone
- .interactions and for histone DNA interactions
" " , . . 4. .Minimal structure for a core histone e g H Others have one additional alpha helix
Histone interactions via the histone fold
α1
L1
α2
L2
α3
C
N
The histone fold flanked
by N and C terminal tails.
Dimer of histones joined by interactions at the
histone fold.
The alpha-helical regions of the core histones mediate dimerization.
L1
L2
C
N
L1
L2
C
N
Nucleosomes are the subunits of the chromatin fiber
• Experimental evidence:– Beads on a string in EM– Micrococcal nuclease digestion
Higher order chromatin structure
Histone H1 associates with the linker DNA, and may play a role in forming higher order structures.
Phosphorylation of histones
C
O
CHNHCH
2
C
O
NH......
CH
2
Gly Ser
OH
ATP ADP
phosphate
protein kinase
protein phosphatase
H O2
C
O
CHNHCH
2
C
O
NH......
CH
2
Gly Ser
OHP
O
O
O
-
Negative charge on
phosphoserine
Serines in histones can be modified by phosphorylation
Acetylation and Deacetylation of lysines in proteins
AcCoA
C
O
CHNHCH
2
C
O
NH... ...
CH
2
CH
2
CH
2
CH
2
NH3
+
C
O
CHNHCH
2
C
O
NH... ...
CH
2
CH2
CH
2
CH
2
NH
Gly Lys
C
CH3
O
CoA
Ac
Positive charge on amino group No charge on amide group
Acetylation and Deacetylation of histones
K5 K8 K12 K16
α1 α2 α31L 2L
CN
5K 8K 12K 16K
5K 8K 12K 16K
Ac Ac
( ), . . Nuclear histone acetyl transferase HAT A e g
5 yeast Gcn p and its mammalian homolog PCAF
. ., 4E g Histone H
, . . 1 + 2 Cytoplasmic HAT B e g yeast Hat p Hat p and
1 ( 1)mammalian chromatin asssembly factor CAF
Ac Ac
Histone
, . . deacetylases e g
3 yeast Rpd p and
1mammalian HD
Histone
deacetylases
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 co-repressors
Matrix and scaffold
Scaffold
loops
of duplex
DNA
Matrix
Nucleus
Mitotic chromosomes, withsome DNA released
In interphase chromosomes, at least some DNA is attached to a matrix
Chromosome localization in interphase
In interphase, chromosomes appearto be localized to a sub-region of thenucleus.
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