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What sex did to X

What sex did to X. Mark Ross, HGM2006 Helsinki. Sex chromosome evolution. SRY. X. Y. X. Y. autosomes. Outstanding features of the X chromosome. X chromosome inactivation X-linked disease Reduced levels of heterozygosity Increased levels of linkage disequilibrium

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What sex did to X

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  1. What sex did to X Mark Ross, HGM2006 Helsinki

  2. Sex chromosome evolution SRY X Y X Y autosomes

  3. Outstanding features of the X chromosome • X chromosome inactivation • X-linked disease • Reduced levels of heterozygosity • Increased levels of linkage disequilibrium • Enrichment for genes expressed in testis, particularly CT-antigens • Enrichment for palindromic repeats • Enrichment for interspersed repeats of the LINE1 class

  4. LD in the human genomeThe International HapMap consortium, 2005

  5. Outstanding features of the X chromosome • X chromosome inactivation • X-linked disease • Reduced levels of heterozygosity • Increased levels of linkage disequilibrium • Enrichment for genes expressed in testis, particularly CT-antigens • Enrichment for palindromic repeats • Enrichment for interspersed repeats of the LINE1 class

  6. Sex chromosome evolution Human XX/XY Mouse XX/XY Wallaby XX/XY Opossum XX/XY Platypus X1X1X2X2X3X3X4X4X5X5/ X1Y1X2Y2X3Y3X4Y4X5Y5 Chicken ZZ/ZW MYR 300 280 260 240 220 200 180 160 140 120 100 80 60 40 20 0

  7. Autosomal origins of the human X chromosome Chicken chromosome 1q Chicken chromosome 4p X added region (XAR) X conserved region (XCR) Xp Xq

  8. Chicken chromosome 12 15 10 5 48 50 52 54 56 Autosomal origins of the human X chromosome Chicken chromosome 1q Chicken chromosome 4p X added region (XAR) X conserved region (XCR) Xp Xq

  9. Autosomal origins of the human X chromosome UBE1 ARAF1 SYN1 TIMP OATL1 GATA1 SMCX ACRC PIN4 RS4X PHKA1 Scaffold 134 Opossum sequence scaffolds X added region (XAR) X conserved region (XCR) Xp Xq

  10. Evolutionary strata on the X chromosome PAR1 S4 S3 S2 S1

  11. Evolutionary strata on the X chromosome Stratum 5 Stratum 4 Stratum 3 1 2 3 4 5 6 7 8 9 10 11 12 PAR1

  12. Evolutionary strata on the X chromosome Stratum 5 Stratum 4 Stratum 3 1 2 3 4 5 6 7 8 9 10 11 12 PAR1

  13. Sex chromosome evolution S3-S5 S2 X Y X Y X Y ancestor of eutheria/metatheria eutheria human S1 autosomes ancestral mammal

  14. LINE1 elements on the human X chromosome 1 0 XIST 1 L1 0 PAR1 S5 S4 S3 S2 S1 7% 9% 11% 20% 32% 34%

  15. L1 levels in other mammals

  16. Opossum sequence scaffolds X added region (XAR) X conserved region (XCR) Xp Xq

  17. L1 levels in other mammals

  18. LINE1 elements on the human X chromosome 1 L1M 0 1 L1P 0 XIST 1 L1 0 PAR1 S5 S4 S3 S2 S1 7% 9% 11% 20% 32% 34%

  19. Are compositional differences a reflection of mutational biases?

  20. L1 levels at chromosome ends L1P LINE1

  21. Regional variation in L1P elements L1P count L1P length

  22. LINE1 elements on the human X chromosome XIST 1 L1 0 PAR1 S5 S4 S3 S2 S1 7% 9% 11% 20% 32% 34%

  23. Acknowledgements Mapping & Sequencing Sequence Analysis & Gene Annotation Adam Frankish Kevin Howe David Jackson Jennifer Ashurst Matthew Hurles Dan Andrews Steven Searle Tim Hubbard Richard Durbin Mathias Platzer Hunt Willard Mary Schueler Sanger Institute Darren Grafham Alison Coffey Kirsten McLay Gareth Howell Christine Burrows Christine Bird Frances Lovell Matt Jones Carol Scott Nigel Carter Mark Vaudin Baylor College of Medicine Steve Scherer Donna Muzny Richard Gibbs IMB, Jena Matthias Platzer Gaiping Wen Andre Rosenthal WUGSC Bob Fulton Rick Wilson Bob Waterston MPIMG, Berlin Ralf Sudbrak Hans Lehrach Stephan Beck John Sulston Jane Rogers David Bentley Genome community

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