1. Section D: Chromosome StructureYang Xu, College of Life Sciences Section D Prokaryotic and Eukaryotic Chromosome Structure D1 Prokaryotic Chromosome Structure D2 Chromatin Structure D3 Eukaryotic Chromosome Structure D4 Genome Complexity D5 Central Dogma

2. Section D: Chromosome StructureYang 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

3. Section D: Chromosome StructureYang 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.

4. Section D: Chromosome StructureYang 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 146bp H1 Nucleosome 166bp 300 nm loops 30nm nuclear matrix

5. Section D: Chromosome StructureYang 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

6. Section D: Chromosome StructureYang 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 fiber300nm loops 1000nm chromosome section

7. Section D: Chromosome StructureYang Xu, College of Life Sciences D3 Eukaryotic Chromosome Structure The mitotic chromosome The centromere Telomeres centromere 30nm 1  m 300nm Interphase chromosomes –being transcribed –cannot be visualized Heterochromatin –transcriptionally inactive region Euchromatin –transcriptionally active region

8. Section D: Chromosome StructureYang 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. Short regions Longer regions Loop

9. Section D: Chromosome StructureYang 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.

10. Section D: Chromosome StructureYang 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.

11. Section D: Chromosome StructureYang 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 Short regions Longer regions Loop

12. Section D: Chromosome StructureYang Xu, College of Life Sciences D4 Genome Complexity Non-coding DNA interspersed repeated DNA tandemly repeated DNA Reassociation kinetics 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) F of ssDNA 1.0 (C o t) (1) (2) (3) E. coli

13. Section D: Chromosome StructureYang Xu, College of Life Sciences D5 Central Dogma

14. Section D: Chromosome StructureYang Xu, College of Life Sciences That’s all for Section D