8. It’s in the way that you use it: same genes, different animals .

1. Genome Evolution 8. It’s in the way that you use it: same genes, different animals. Martin Lercher Bioinformatics Itai Yanai Biology

2. Outline • The importance of gene regulation • King and Wilson’s hypothesis • FOXP2 • Evolution of gene expression patterns • Regulation in Bacteria • The Lac operon • Network motifs • Regulatory changes in bacterial evolution • Overlapping codes • Core promoter and enhancers • Nucleosome code • Genetic code • Codon usage - amelioration

3. Human-Chimp differences Picture: AP Photo/Boris Hege

4. King and Wilson propose in 1975 that the small genetic differences between chimps and humans could not account for the anatomical or behavioral differences. King and Wilson. Science 1975

5. The chimpanzee and bonobos are our closest living relatives • Single-nucleotide substitutions affect 1.23% of nucleotides. • Orthologous proteins in human and chimpanzee are extremely similar: • 29% are identical • the typical ortholog differs by only two amino acids (one per lineage). autosomes Y X chimp bonobo human images from Wikipedia Nature (2005) 437: 69

6. FOXP2 is involved in the developmental process that culminates in speech and language Affected individuals are indicated by filled symbols. Asterisks indicate those individuals who were unavailable for genetic analyses. Squares are males, circles are females, and a line through a symbol indicates that the person is deceased. • Individuals with a mutation in this gene do not have an overall impairment but a lesion in the neural circuitry that affects language processes • This gene is a transcription factor Lai et al. Nature 2001

7. The FOXP2 area shows the hallmarks of a selective sweep Enard et al. Nature 2002 Image from Carroll. Nature 2003

8. FOXP2 is not unique to humans Enard et al. Nature 2002 • The human FOXP2 protein differs from the gorilla and chimpanzee sequence at just two residues, and from the orangutan and mouse sequences at three and four residues, respectively.

9. However, birds showthat regulatory changes are at work Song by birds and human speech have similarities at the behavioral and neuronal level. Comparing the coding sequences, there is no difference between song-learner birds and non-song-learner bird. Foxp2 mRNA levels are increased in area x (a center necessary for vocal learning that is absent from non-learners). Seasonal changes of foxp2 expression were correlated with changes of the stability of the bird song. Carroll. Plos Biology 2005

10. A humanized version of Foxp2 affects cortico-basal ganglia circuits in mice Cell. 2009 May 29;137(5):961-71. 

11. A recent change to FOXP2 affects a regulatory element Mol BiolEvol. 2013 Apr;30(4):844-52.

12. Changes in gene expression are particularly pronounced in the human brain Enard et al. Science 2002

13. http://www.biotechnologie.de/BIO/Navigation/DE/root,did=109516.htmlhttp://www.biotechnologie.de/BIO/Navigation/DE/root,did=109516.html Regulation in E. coli

14. The fundamental discovery of genome regulation

15. The lacOperon involves DNA-binding proteins that regulate expression from Wikipedia http://www.youtube.com/watch?v=oBwtxdI1zvk See the movie:

16. Encoding a lock-in switch with positive feedback Without feedback With feedback Bolouri and Davidson. BioEssays, 2002

17. Motifs in the networks • Deployed a motif detection algorithm on the transcriptional regulation network. • Identified three recurring motifs (significant with respect to random graphs). Shai S. Shen-Orr, Ron Milo, Shmoolik Mangan & Uri Alon (2002) Nature Genetics 31 64 - 68

18. The transcriptional regulation network of Escherichia coli Shai S. Shen-Orr, Ron Milo, Shmoolik Mangan & Uri Alon (2002) Nature Genetics 31 64 - 68

19. The transcription network of E. coli http://www.mrc-lmb.cam.ac.uk/genomes/madanm/chalancon_chapter.pdf

20. 46,XX and 46,XY disorder of sex development (DSD) is correlated with a genomic duplication event Pedigrees of 46,XX and 46,XY disorder of sex development (DSD) families. (A) A ∼605–695 kb duplication occurred de novo in the DSD1 sporadic case of 46,XX DSD. (B) A ∼148 kb duplication in the DSD2 case with a 46,XX DSD is inherited from the father and from the unaffected paternal grandmother. (C) In the DSD3 case, a ∼762–780 kb duplication in the two affected 46,XX probands was inherited from their healthy 46,XY father and grandfather. (D) The ∼240 kb DSD4 deletion is shared between two 46,XY DSD patients of the same family (one with a female phenotype, the other with severe ambiguous and asymmetric external genitalia). The deletion is transmitted by unaffected 46,XX mothers. dup: duplication within chromosome 17q24.3; del: deletion within chromosome 17q24.3. Open squares: normal males; open circles: normal females; black filled symbols, isolated 46,XY or 46,XX DSD. XX males XY females Benko S et al. J Med Genet 2011;48:825-830 Benko S et al. J Med Genet 2011;48:825-830

21. Rearrangements in the SOX9 centromeric gene desert are associated with isolated 46,XX and 46,XY disorders of sex development (DSD). The region surrounding SOX9 is represented as a grey bar with genes depicted in black, and proximal and distal campomelic dysplasia (CD) translocation breakpoint clusters (BPCs) as shadows within the locus. The copy number gains associated with ovotesticular 46,XX DSD (DSD1,DSD2 and DSD3) and with complete 46,XX DSD reported by Cox et al. (duplication; Dup4) and Vetro et al. (triplication; Trip1) are depicted as bars above the proximal SOX9 gene desert. Brachydactyly-anonychia duplications are indicated as BA1, BA2, BA3 and BA4.13 The XX DSD translocation breakpoint is indicated by an arrow.9 The deletions associated with syndromic 46,XY DSD (CD1, CD2, and CD3, 10–12) and isolated 46,XY DSD (DSD4) are represented as bars below the proximal SOX9 gene desert. The TESCO element and the mandibular enhancer HCNE-F2 are represented as dots. The minimal 78 kb RevSex region, shared among DSD1, DSD2, DSD3, Dup4 and Trip1 copy number gains and DSD4, CD1, CD2 and CD3 deletions is indicated as a shadow within the locus. Coordinates are according to the GRCh37/hg19 genome assembly. The duplications occur in the SOX9 gene desert At the center: the transcription factor SOX9 In early embryos, SOX9 is expressed regardless of sex Benko S et al. J Med Genet 2011;48:825-830

22. A regulatory network of genes lead to sex determination Ono, M. & Harley, V. R. (2012) Disorders of sex development: new genes, new concepts Nat. Rev. Endocrinol. doi:10.1038/nrendo.2012.235

23. SOX is important for sex determination In females: Gonads also express the signaling protein beta-catenin Beta-catenin proteins bind to SOX9 proteins This marks both of them for destruction Additional regulatory proteins interfere with transcription of SOX9 In males: The transcription factor Sf1 increases expression of the SRY protein Sf1 and SRY together induce SOX9 Once SOX9 rises to sufficient levels, it starts inducing itself in a positive feedback loop beta-catenin – if present – binds to SOX9 and is removed

24. SOX9 is activated by a positive feedback loop SF1 SRY SOX9 The SOX9 positive feedback loop: a one-way switch once it is switched on (protein level above threshold), it stays switched on The SF1 → SRY → SOX9 feed-forward loop: a filter against short fluctuations only together, the two proteins can boost the core player SOX9 SF1 may be expressed briefly by accident in a female embryo but only when SF1 protein has been around long enough, there will have accumulated enough of SRY to boost SOX9 with joined forces.

25. SOX9 is pleiotropic Apart from its role in sex determination, the transcription factor SOX9 plays a role in: Cartilage / bone formation Certain mutations to SOX9 cause campomelic dysplasia Facio-cranial development Certain muations to SOX9 causeRobin sequence (cleft palate, small chin) Depending on where the mutation is (coding region or regulatory regions), one or all three of the syndromes may occur in a patient

26. Orthologous transcription factors often govern the expression of different gene sets in related bacterial species The orthologs of 10 genes whose expression is controlled by the stress response sigma factor RpoE in E. coli and Shigella do not appear to harbor RpoE-regulated promoters in Salmonella Perez & Groisman. Cell 2009

27. Evolution by re-wiring • cis-regulatory sequences are degenerate and short (approximately 5e10 nt). • Mutations in the so-called “consensus” regulatory sequences will not only cause quan- titative change on the binding affinity, but also lead to complete dissociation or even substitution to rewire novel TFs (Gelfand, 2006). • Network motifs do not arise by duplications of existing motifs, but by re-wiring (point substitutions) (Teichmann and Babu 2004),(Conant and Wagner 2003) • -> convergent evolution • organisms with similar lifestyle tend to conserve similar interactions and similar motifs (MadanBabu et al. 2006) Perez & Groisman. Cell 2009 Regulatory Circuits Governing Resistance to an Antibiotic

28. in animal genomes

29. Complex promoters are a hallmark of the human genome Levin & Tijan. Nature 2003

30. Metazoan strategies for specific transcription Levin & Tijan. Nature 2003

31. Trifonov periodicity of nucleotides in the genome Trifonov. NAR 1980 Segal et al. Nature 2006

32. Two of each of the core histones assemble to form one octameric nucleosome core particle, and 147 base pairs of DNA wrap around this core particle Wikipedia

33. A genomic code for chromatic binding Segal et al. Nature 2006

34. Predicting chromatin location Segal et al. Nature 2006

35. There are four levels of genome regulation Hurst, Pal, Lercher, Nature Reviews Genet. 2004