Genome Organisation II

1. Genome Organisation II • Eukaryotic genomes are completely different in their organisation compared to prokaryotic, and also much bigger • Their genes are mostly “split” into exons and introns • It is not certain which came first in evolution - genes with introns/exons or genes without • Exons may allow evolution of proteins in a “modular” way

2. Eukaryotic chromosomes • In metaphase of mitosis, chromosomes can be seen under microscope - they have a compact rod-like structure • The ends of chromosome are called telomeres, function is to protect the ends of the DNA • Near the middle is the centromere, function is to attach to spindles during cell division and ensure correct segregation • Telomeres and centromeres contain special DNA sequences and associated proteins • Telomeres are replicated differently from the rest of the genome - see figure 26.37 in Lehninger • Different regions of the chromosome can be stained with dyes (e.g. Giemsa) giving a characteristic banding pattern

3. Eukaryotic chromosome structure Genes, repeated sequences, replication origins (mostly euchromatin) Centromere (heterochromatin) Telomeres (heterochromatin) (Figure 24-3 Lehninger)

4. The problem of telomere replication

5. Telomere replication

6. Centromeres • The centromere is essential for correct segregation of chromosomes during cell division, by attachment to spindles • Centromere consists of a small, core DNA sequence (AT rich) and specific proteins • In many species (e.g. humans) this is flanked by 100s of copies of a tandemly-repeated sequence

7. Unique and repeated DNA • If eukaryotic DNA is melted and allowed to re-anneal, it does so in 3 distinct phases • The explanation is that there is highly repetitive DNA (which re-anneals quickly), moderately repetitive DNA (intermediate) and unique or single copy DNA (re-anneals slowly)

8. DNA melting

9. Classes of DNA • Mammalian DNA contains 3 main classes of DNA sequence, as measured by Cot curves: • Highly repeated DNA (up to 1 million copies) • Moderately repeated DNA (up to 100,000 copies) • Unique sequence DNA (strictly speaking 1 copy, but in practice this also includes sequences with only a few copies)

10. Origins and function of DNA classes • Highly repetitive: • Bits of old virus genomes • Simple sequence repeats e.g. CACACA…. • Special sequences such as centromeres • Moderately repetitive: • Other old virus genomes • Multi-gene families, e.g. ribosomal RNA • Single-copy: • Most “normal” genes

11. Types of repeated DNA

12. Ribosomal RNA genes

13. DNA fingerprinting • An application of repeated DNA sequences found in mammalian genomes • Highly variable between individuals • No 2 people are the same, except identical twins

14. Disease caused by a repeat DNA sequence • Mutations in the low-density lipoprotein receptor gene (LDLR) are a common genetic cause of heart disease due to hypercholesterolemia. • The LDLR gene is 45kb long with Alu (highly-repetitive class) repeats in its introns. Recombination between 2 of these leads to a truncated gene and defective protein.

15. Vertebrate DNA has not much …CG… because it is mostly methylated and mutates to …TG... But there are short (1-3kb) stretches rich in C, G, …CG… without methylation 5-methyl-cytosine Thymine CpG islands

16. CpG islands • CpG islands are found at 5’ ends of many genes • Unlike rest of genome they do not bind the MeCP2 protein • MeCP2 acts as a general repressor of transcription