Det humane genom

1. Det humane genom Menneskekroppen har 100 billioner celler, hver med 46 kromosomer. Samlet lengde av DNA: 2 meter/celle

2. …er ganske stort

3. Andre genomer som kan lære oss mye om det humane genom

4. Antall kromosomer i forskjellige organismer

5. K-value paradox: Complexity does not correlate with chromosome number. Homo sapiens Lysandra atlantica Ophioglossum reticulatum 46 250 1260

6. Størrelse av genomer

7. C-value paradox: Complexity does not correlate with genome size.

8. Det humane genom

9. The human genome is disappointing: • It is small • It is empty • It is unoriginal • It is repetitive

10. En oversikt over det humane genom

11. Hvor mange gener i genomet?

12. Genomstørrelser – hvor mange gener?

13. N-value paradox: Complexity does not correlate with gene number. ~31,000 genes ~26,000 genes ~50,000 genes

14. Sammensetning av genomet

15. 1.5% Exons Introns (junk) Intergenic regions (junk) The genome is empty.

16. Den molekylære funksjonen til 26383 humane gener

17. Funksjonelle kategorier i eukaryote proteomer

18. Flere proteiner fra samme gen (alternativ spleising) • Menneske: 60 % av genene koder for mer enn ett protein • Orm: 22 % av genene koder for mer enn ett protein

19. Forskjeller i geninhold • Fibroblastvekstfaktor – menneske 30, bananflue og orm 2 hver • Transformerende vekstfaktor β – menneske 42, bananflue 9, orm 6 • Gener som koder for proteiner med immunglobulindomener – menneske 765, bananflue 140, orm 64 • ”Sinkfinger”-proteiner – menneske dobbelt så mange som bananflue og 5 ganger flere enn orm

21. CpG-frekvens og CpG-øyer The typical density of CpG doublets in mammalian DNA is ~1/100 bp, as seen for a -globin gene. In a CpG-rich island, the density is increased to >10 doublets/100 bp. The island in the APRT gene starts ~100 bp upstream of the promoter and extends ~400 bp into the gene. Each vertical line represents a CpG doublet.

22. CpG-øyer

23. Vedlikeholdsmetylering Ved maintenance-metylering induserer metyleringsmønsteret i en parental DNA-tråd det tilsvarende metyleringsmønster i den komplementære tråden. Slik kan et stabilt metyleringsmønster opprettholdes i en cellelinje

24. CpG – underrepresentert i genomet The CpG doublet occurs in vertebrate DNA at only ~20% of the frequency that would be expected from the proportion of G·C base pairs. (this is because CpG doublets are methylated on C, and spontaneous deamination of methyl-C converts it to T, introducing a mutation that removes the doublet.) In certain regions, however, the density of CpG doublets reaches the predicted value; in fact, it is increased by 10× relative to the rest of the genome. The CpG doublets in these regions are unmethylated

25. Cytosin, metylcytosin og tymin T me

26. Repetitive DNA Alus are like that! interspersed in tandem I

27. Repeterte sekvenser skaper problemer

28. Klasser av intersperserte repetisjoner i det humane genom

29. Elementer i det humane genom som kan transposeres på en RNA-formidlet måte

30. SINEs og utledning av fylogenetiske forhold • En SINE er enten der eller ikke • SINEs innsettes på tilfeldig måte i ikke-kodende områder. Samme plassering i to arter tyder på at innsettingen foregitt i en felles stamfar • Innsetting av en SINE er irreversibel, fravær er derfor et ancestralt trekk

31. Alu elements • Length = ~300 bp • Repetitive: > 1,000,000 times in the human genome • Constitute >10% of the human genome • Found mostly in intergenic regions and introns • Propagate in the genome through retroposition (RNA intermediates).

32. Evolution of Alu elements

33. Alu elements can be divided into subfamilies The subfamilies are distinguished by ~16 diagnostic positions.

34. Sekvenssammenstilling av Alu-familier 14 Alu-familier hos mennesket, hvorav 1 ikke hos andre primater. 2000 Alu-insersjoner spesifikke for mennesket. J, S, Y

35. Evolusjon av Alu-elementer

36. Transposisjonering av et typisk humant Alu-element

37. Alu-elementer hos primater

38. Translation Splicing Eukaryotic genes (exons & introns)

39. Alternative Splicing Mature splice variant I Mature splice variant II Alternative splicing: One gene, several proteins!

40. Types of alternative splicing

41. Cassette exon or internal-exon skipping

42. Donor site Branch point Acceptor site 1 2 CAG GTRAGT A YYYYYYYYYNCAG G 1 2 -OH A A 1 2 Signals of splicing Pyrimidine tract Lariat

43. Because mRNAs and Alus are frequently reversetranscribed and incorporated into the genome, pyrimidinetractsareubiquitous The complementary strand of polyA is polyT = pyrimidine tract.

44. The minus strand of Alu elements contains “near” splice sites • The minus strand of Alu contains ~3 sites that resemble the acceptor recognition site: Consensus acceptor site:YYYYYYNCAG/R Alu-J: (127-114) :TTTTTTGtAG/A • The minus strand of Alu contains ~9 sites thatresemble the consensus donor site: Consensus donor site: CAG/GTRAGT Alu-J: (25-17) : CAG/GTGtGA

45. Our findings • Out of 1,182 alternatively spliced cassette exons, 62 have a significant hit to an Alu sequence. • Out of 4,151 constitutively spliced exons, none has a significant hit to an Alu sequence.  all Alu-containing exons are alternatively spliced.

46. Retention Ratio • Retention ratio = number of mRNA molecules containing the alternatively spliced exon divided by total number of mRNA molecules. • Retention ratio for Alu-containing exons was ~10%. • Retention ratio for alternatively spliced exons that do not contain Alu was ~45%.

47. Exon Exon Proposed model for Alu exonization

48. Hvordan studere genomet? http://www.genome.ucsc.edu/cgi-bin/hgGateway?org=human http://www.ensembl.org/ Men NCBI har også en genombrowser: MapView!