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

Section D: Chromosome Structure 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