chromosome structure
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Chromosome StructureTRANSCRIPT
Section D: Chromosome Structure Yang Xu, College of Life Sciences
Section DProkaryotic and Eukaryotic
Chromosome Structure
D1 Prokaryotic Chromosome StructureD2 Chromatin StructureD3 Eukaryotic Chromosome StructureD4 Genome ComplexityD5 Central Dogma
Section D: Chromosome Structure Yang Xu, College of Life Sciences
If the DNA of E. coli is isolated free of most attached proteins.
D1 Prokaryotic Chromosome Structure
(Lk/Lk = -0.06).
Supercoiling
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
DNA
core 146bpH1
Nucleosome 166bp
300 nm loops30nm
nuclear matrix
Section D: Chromosome Structure 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
• Telomeres
Telomeres
centromere
30nm
1 m
300nm
• Interphase chromosomes
– being transcribed
– cannot be visualized
• Heterochromatin
– transcriptionally inactive region
• Euchromatin
– transcriptionally active region
Section D: Chromosome Structure 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 trans-criptionally 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.
Shortregions
Longerregions
Loop
Section D: Chromosome Structure 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 normally methylated and are relatively ① ②scarce 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
• CpG island: where the proportion of 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
2 kb
CpG island
housekeeping genes
methylated
Shortregions
Longerregions
Loop
Section D: Chromosome Structure Yang Xu, College of Life Sciences
D4 Genome Complexity
• Non-coding DNAinterspersed repeated DNAtandemly repeated DNA
• Reassociation kineticsStep 1: broken by sonication into same size Step 2: DNA fragments are thermally denaturedStep 3: re-anneal at a low concentrationStep4: 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)
F of ssDNA
1.0
(Cot)
(1)
(2)
(3)
E. coli