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Today

Today. Building a genome Nucleotides, GC content and isochores Gene structure and expression; introns Evolution of noncoding RNAs Evolution of transcription Transcription & Translation Recoding and RNA editing Evolution of the genetic code. The four nucleotides of DNA.

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Today

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  1. Today • Building a genome • Nucleotides, GC content and isochores • Gene structure and expression; introns • Evolution of noncoding RNAs • Evolution of transcription • Transcription & Translation • Recoding and RNA editing • Evolution of the genetic code

  2. The four nucleotides of DNA

  3. Watson & Crick actually got it wrong …

  4. GC content versus optimal growth temperature Ribosomal RNAs Genome-wide

  5. Environmental signature on GC content

  6. Structure of human isochores

  7. Lack of isochores in lizards

  8. GC-content correlates with recombination rate

  9. Anatomy of a eukaryotic gene A Influences gene from afar…. C D { { { AAAAAA F G E B I G H I A._______________ B. _______________ C. _______________ D. _______________ E. _______________ F. _______________ G. _______________ H. _______________ I. _______________

  10. Introns cleaved out by the spliceosome

  11. Phylogenetic distribution of introns implies recent origin

  12. Intron phase and size

  13. Intronic regions adjacent to exons are often conserved Figure 3 Human-mouse alignment of the KCND3 gene, corresponding to RefSeq NM_004980 (from VISTA browser, http://pipeline.lbl.gov/vistabrowser/) Rotem Sorek et al. Genome Res. 2003; 13: 1631-1637

  14. 2005: Widespread transcription in the human genomerevealed by microarray analysis

  15. Fast forward 2010: Expression tracks known genes closely

  16. Number of regulatory genes (R) vs. total number of genes (G) Mycoplasma genitalium Bradyrhizobium japonicum Circles - Bacteria; triangles - Archaea R = 0.00002G2

  17. Does ‘noncoding DNA’ increase genomic complexity?

  18. Was eukaryotic complexity released by noncoding RNAs?

  19. MicroRNAs - a new class of small RNAs with big roles in development and evolution

  20. Translational repression by microRNAs

  21. microRNAs as cladistic characters

  22. Explosive diversity of cichlid fish

  23. Rapid evolution of microRNA targets – a link with speciation?

  24. The ‘universal’ genetic code

  25. Translation

  26. Structure of vertebrate mitochondrial DNA (~17,000 bp) Glu noncoding NADH6 Pro Phe 12s rRNA Val Control Region 16s rRNA Thr Cyt b NADH1 Leu Ile Gln Met NADH5 NADH2 Leu Trp rRNA genes Ser Ala tRNA genes His Asn COI NADH4 Cys ATP synthase genes Ser Asp NADH3 NADH4L Tyr Cytochrome Oxidase COII Lys Gly ATP6 ATP8 Arg COIII Cytochrome bc1 complex NADH:Ubiquinone Oxidoreductase

  27. Four ways to change the coding of amino acids from RNA

  28. Wobble rules in various organismsbase modifications in tRNAs can increase decoding breadth

  29. A code that minimizes polarity changes better than the universal code

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