Intro Gene regulation Synteny The End. Today. Gene regulation Synteny Good bye!

Transcription

1 Today Gene regulation Synteny Good bye!

2 Gene regulation What governs gene transcription? Genes active under different circumstances.

3 Gene regulation What governs gene transcription? Genes active under different circumstances. Transcription factors bind to transcription factor binding sites (TFBS).

4 Gene regulation What governs gene transcription? Genes active under different circumstances. Transcription factors bind to transcription factor binding sites (TFBS). TFBS also known as regulatory elements (RE)

5 Gene regulation What governs gene transcription? Genes active under different circumstances. Transcription factors bind to transcription factor binding sites (TFBS). TFBS also known as regulatory elements (RE) TFBS can be grouped in regulatory modules.

6 Gene regulation What governs gene transcription? Genes active under different circumstances. Transcription factors bind to transcription factor binding sites (TFBS). TFBS also known as regulatory elements (RE) TFBS can be grouped in regulatory modules. cis-regulatory elements appear before the gene

7 Gene regulation Core promoter: about 35 bp prior to TSS, includes TATA box

8 Gene regulation Core promoter: about 35 bp prior to TSS, includes TATA box Upstream promoter: bp prior to TSS, activates transcription

9 Gene regulation Core promoter: about 35 bp prior to TSS, includes TATA box Upstream promoter: bp prior to TSS, activates transcription Enhancers in a book: Up to 2000 bp before TSS.

10 Gene regulation Core promoter: about 35 bp prior to TSS, includes TATA box Upstream promoter: bp prior to TSS, activates transcription Enhancers in a book: Up to 2000 bp before TSS. These experiments showed that, on average, the sequence -300 to -50 bp of the TSS positively contributes to core promoter activity. Interestingly, putative negative elements were identified to -500 bp upstream of the TSS for 55 % of genes tested. (Cooper et al, Genome Res, 2005)

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12 Promoter and TSS Hard to recognize a TSS Many attempts, little success Recent understanding: several TSS may exist

13 Correctness of TSS prediction Fickett & Hatzigeorgiou, 1997

14 Regulatory elements Binding sites for transcription factors Motifs, about 10 bp wide Represent using PSSMs Search strategy: use PSSM and look upstream (2 kb 5 kb) from gene.

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16 Finding regulatory elements: ConSite Problem: Overpredicting TFBS Solution: Comparative genomics. Use nearby species, look at conservation.

17 Finding regulatory elements Need: de novo motif discovery Solution: Phylogenetic footprinting

18 Finding regulatory elements Need: de novo motif discovery Solution: Phylogenetic footprinting The mathematics: Gibbs sampling Popular software: MEME What it does: Iteratively improve a motif from naive start point

19 Case study: motifs for TPX2 genes Input: five sequences, 3000 nt long Motif 1, E = , width 39 bp Pt At Mt Zm Os TGCATGAGAGGGAGATTTAATCAGAAAGTTTGGTGCATGAGAGC TGCATGAGTGGGAGGTTTAATCAGAAAGTTTGTTGCATGAGAGC TGATTGAGAAGGAAATTTAATCAGAAAGTTTGGTGCAAGAGAGC -----GATCGGGATATATACTCAGAAGTTTGAGTCCCACCGCCC -----GACGGCAACGTCTCATCAGATGGTTGGTAGTAACACCAC Motif 2, E = , width 28 bp Pt At Mt Zm Os TTGAGCATGTTTGTGATGTAGCAACAGA TAAAGCTTGTTGCTGATGTAGCAACAGA TAGAGCATGTTTGTGATGTAGCAACAGA TAGAGCTAGCTAGCTAGGTGGTCGCAAA TGGGGATGGCTGGTGAAGTGGCAGATTA

20 Case study: upstream analysis ATG ATG ATG ATG ATG

21 Comparative Genomics: Synteny Synteny: Preserved gene order

22 Comparative Genomics: Synteny Synteny: Preserved gene order Syntenic regions: Orthologous regions with genes in synteny

23 Comparative Genomics: Synteny Synteny: Preserved gene order Syntenic regions: Orthologous regions with genes in synteny Applications: Species phylogeny Understandning evolution Gene finding, regulatory elements Support for orthology

24 Synteny background Macro-genomic mutations: Transpositions Segment moved Reversals/inversions Segment reversed Transversals End segment reversed

25 Populus chromosomes Science, 2006

26 Mouse chromosomes Nature, 2002

27 Synteny explained by reversals PNAS, 2003

28 Synteny explained by reversals PNAS, 2003

29 Computational problems How recognize orthologous regions? How recognize a syntenic region?

30 Computational problems How recognize orthologous regions? How recognize a syntenic region?

31 Computational problems How many mutations separate two regions? Which phylogeny explains synteny best?

32 Computational problems How many mutations separate two regions? Which phylogeny explains synteny best? Human Nematode Sea urchin 5 1 Fruit fly mtgenome, reversals

33 Synteny in day-to-day work Are these two really orthologous?

34 Synteny in day-to-day work Are these two really orthologous? Where is my gene? I cannot find it!

35 Synteny in day-to-day work Are these two really orthologous? Where is my gene? I cannot find it! Solutions 1. Look at neighbor genes 2. Look at synteny map

36 Case study: Testatin

37 Case study: Testatin

38 Case study: Testatin

39 Case study: functional pseudogenes? Target:

40 Case study: functional pseudogenes? Must avoid:

41 Filtering with synteny Require two predicted pseudogenes to be from the same syntenic region.

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43 For the exam No pre-registration Part 1: 15 p, bonus points apply Minimum 10 points. Part 2: 15 p, no bonus points Pass exam at 15 points.