Biol/Chem 473

1. Biol/Chem 473 Schulze lecture 1: Eukaryotic genomes

3. What I do… • Ph.D. in Genetics and Molecular Biology • Ph.D. project: studied heterochromatic genes (active genes located in repressive parts of the genome) in Drosophila, which involved an analysis of chromatin structure • Post-doctoral and present research: study the role nuclear organization plays in regulating genome architecture and gene expression, using Drosophila as a model organism

4. Eukarya Archaea Bacteria US (and this part of the course) THEM (fabulous models) Prokaryotes and Eukaryotes

5. Prokaryotic vs eukaryotic cells

6. Prokaryotic vs. eukaryotic cell size

7. Prokaryotic vs. eukaryotic genomes

8. Bacterial genome is oganized into a single (usually) circular chromosome that is relatively small (~106bp) Eukaryotic genome is arranged in a series of linear chromosomes that vary widely in size Prokaryotic vs. eukaryotic genome organization

9. Prokaryotic genomes are very economically organized!

10. “Lower” eukaryotic genomes tend to be economically organized too. Section of chromosome 16 from S. cerevisiae

11. gene within gene transposable elements 5' -> 3' 3' <- 5' exon intron tRNA cluster single tRNA low gene density high gene density 600,000 bp of Drosophila chromosome 2 “Higher” eukaryotes tend to have very spacious genomes.

12. What is a good definition of a genome? • A haploid organism has one set of chromosome(s). • Example? • A diploid organism has two sets of chromosomes. • Example? • A polyploid organism has several sets of chromosomes. • Example?

13. What is a good definition of a genome? • String all the chromosomes from a representative set together, end to end, and read the sequence of the DNA. • The genome is the information content represented by a single set of chromosomes. • The human genome has 46 pairs of chromosomes. • Humans are diploid, so the genome is split over 23 pairs of chromosomes. • About 3 billion base pairs of DNA.

14. What does the human genome look like?

19. 4 deoxy and 1 dideoxy NTP

20. 4 deoxy and 1 dideoxy NTP

21. 4 deoxy and 1 dideoxy NTP

23. The human genome project was a collaborative effort…

24. ..then it was a race… NOT a code – that was cracked in the 1960’s

25. …that everyone won (sort of).

26. Sequenced Genomes

27. Sequenced Genomes

28. Eukaryotic genome sequence complexity • Eukaryotes have single copy, middle repetitive and highly repetitive DNA • Single copy includes DNA encoding genes (~5% of the human genome) • Middle repetitive sequence includes some coding parasitic sequences (e.g., transposable elements; ~50% of the human genome) • Highly repetitive sequence are low complexity, include satellite sequences

29. Satellite sequences? • Nothing to do with outer space. • Satellite sequences are so called because they tend to be AT rich and thus have a lower density than most other sequences. • So where would you expect to see these sequences on a density gradient? • Hint: what happens to satellites in space?

30. Satellite sequences? • Nothing to do with outer space. • Satellite sequences are so called because they tend to be AT rich and thus have a lower density than most other sequences. • So where would you expect to see these sequences on a density gradient? • Hint: what happens to satellites in space?

31. Eukaryotic genome sequence complexity

32. virus yeast E. coli 100 % single-stranded 0 1 10 0.1 log C0t What is sequence complexity?DNA re-association kinetics

33. highly repetitive 100 middle repetitive % single-stranded single copy 0 0.1 1 10 100 log C0t What is sequence complexity?DNA re-association kinetics

34. What proportion of the genome is single copy (sc)?

35. Species DNA bp (C) Genes % Coding phage l 48,502 67 84 E. coli 4,639,221 4289 85 S. cerevisiae 14,213,386 6241 70 D. melanogaster 180,000,000 15,000 5 H. sapiens 3,000,000,000 35,000 2-5 Newt 19,000,000,000 30,000 1-2 Lungfish 140,000,000,000 30,000 <1 C-value paradox The amount of DNA in the haploid cell of an organism is not related to its evolutionary complexity or number of genes.

36. C-value paradox From: Biol. Rev. (2001) 76:65-101

37. How to resolve the C-value paradox? • Genome size does not reflect organismal complexity. • Genome size does not reflect the number of genes. • Sometimes, even closely related organisms have highly divergent genome sizes! • Obviously, a genome does not serve a purely genetic function. • So, what is the function of all that non-coding DNA? • Genome size correlates positively with cell/nuclear size. • Genome size correlates negatively with cell division rate.

38. Eukaryotes have a BIG packaging problem • How do you fit approximately 2 meters (human diploid nucleus) into a space that averages maybe 5 millionths of a meter wide? • How do you replicate, repair and transcribe tightly packaged DNA?