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Section D
Prokaryotic and Eukaryotic
Chromosome Structure
D1 Prokaryotic Chromosome Structure
D2 Chromatin Structure
D3 Eukaryotic Chromosome Structure
D4 Genome Complexity
D5 Central Dogma
Section D: Chromosome Structure
Yang Xu, College of Life Sciences
D1 Prokaryotic Chromosome Structure
If the DNA of E. coli is
isolated free of most
attached proteins.
Supercoiling
(Lk/Lk = -0.06).
50~100kb
Domain
broken in one strand
Section D: Chromosome Structure
Yang Xu, College of Life Sciences
The Escherichia coli Chromosome
• Prokaryotic genomes are exemplified by the E. coli
chromosome.
• The DNA in E. coli cells consists of:
– a single closed-circular DNA molecule
– it is of length 4.6 million base pairs.
• The DNA is packaged into nucleoid region:
– this region has a very high DNA concentration, perhaps
30-50 mg/ml, (a fairly high DNA concentration in the test
tube would be 1 mg/ml).
– this region contains all the proteins associated with DNA,
such as: polymerases, repressers.
• In normal growth, the DNA is being replicated continuously.
Section D: Chromosome Structure
Yang Xu, College of Life Sciences
D2 Chromatin Structure
•
•
•
•
•
•
•
Chromatin: Nucleoprotein complex
Histones: H2A, H2B, H3 and H4 + H1
Nucleosome: Nucleosome/core
The role of H1: Stabilize
Linker DNA: 55 bp
30 nm fiber: Six per turn/left-handed helix
Higher order structure
30nm
nuclear
matrix
Section D: Chromosome Structure
DNA
core 146bp
H1
300 nm loops
Nucleosome
166bp
Yang Xu, College of Life Sciences
D2 Chromatin Structure
•
•
•
•
•
•
Chromatin : Nucleoprotein complex
Nucleosome : Nucleosome/core
Histones: Histone octamer + H1
Linker DNA: 55 bp
30 nm fiber: Six per turn/left-handed helix
Higher order structure
Section D: Chromosome Structure
Yang Xu, College of Life Sciences
Core histones: H2A, H2B, H3 and H4+146 bp of DNA
Nucleosome core
H1+ 20 bp of DNA
Chromatosome
55 bp of linker DNA
200 bp Nucleosomal repeat unit
30 nm fiber
300nm loops
1000nm chromosome section
Section D: Chromosome Structure
Yang Xu, College of Life Sciences
D3 Eukaryotic Chromosome Structure
• The mitotic chromosome
• The centromere
centromere
• Telomeres
Telomeres
1mm
300nm
• Interphase chromosomes
– being transcribed
– cannot be visualized
• Heterochromatin
– transcriptionally inactive region
• Euchromatin
– transcriptionally active region
Section D: Chromosome Structure
30nm
Yang Xu, College of Life Sciences
DNase I hypersensitivity
DNase I is an enzyme that cuts the
backbone of DNA unless the DNA
is protected by protein.
DNase I hypersensitivity has been
used to map the regions of transcriptionally active chromatin:
• Short regions: the naked DNA can
be attacked by DNase I.
• Longer regions: where
transcription is taking place.
These regions vary between different
cell types and different phases
during cell development.
Section D: Chromosome Structure
Short
regions
Longer
regions
Loop
Yang Xu, College of Life Sciences
CpG methylation
• Definition: It is the methylation of
C-5 in the cytosine base of 5'-CG-3'
sequences in mammalian cells.
• Function: It is an important
chemical modification which is
involved in keeping the appropriate
level of chromosomal packing at
the sites of expressed genes.
Section D: Chromosome Structure
Yang Xu, College of Life Sciences
CpG methylation mutation
• CpG methylation mutation:
CpG sites are ① normally methylated and are ② relatively
scarce throughout most of the genome, because
5-methylcytosine can spontaneously deaminate to thymine and
this error is not always repaired.
Section D: Chromosome Structure
Yang Xu, College of Life Sciences
CpG island
Short
Longer
• CpG island: where the proportion of
regions
regions
Loop
CG dinucleotides is much higher than on average
– The CpG there is unmethylated,
– These islands are commonly around 2000 bp long, and
may be largely free of nucleosomes,
– and are coincident with regions of particular sensitivity to
DNase I.
• Function of CpG island: The CpG islands surround the
promoter regions of housekeeping genes
CpG island
housekeeping genes
methylated
Section D: Chromosome Structure
2 kb
Yang Xu, College of Life Sciences
D4 Genome Complexity
E. coli
1.0
F of
ssDNA
(1)
• Non-coding DNA
interspersed repeated DNA
tandemly repeated DNA
• Reassociation kinetics
(Cot)
Step 1: broken by sonication into same size
Step 2: DNA fragments are thermally denatured
Step 3: re-anneal at a low concentration
Step4: by spectroscopic analysis
• Satellite DNA: are found in phase (1)
• Dispersed repetitive DNA: Alu, L1 (2)
• Tandem gene clusters: rDNA and histone genes (2)
• Unique sequence DNA is found in (3)
Section D: Chromosome Structure
(2)
(3)
Yang Xu, College of Life Sciences
D5 Central Dogma
Section D: Chromosome Structure
Yang Xu, College of Life Sciences
That’s all for Section D
Section D: Chromosome Structure
Yang Xu, College of Life Sciences