1. Chromosome inversions in human populations Marta Ruiz Fernández Master in Advanced Genetics 17 December 2014

2. INTRODUCTION Inversions occur when a chromosome breaks at two points and the segment between the breakpoints is reinserted in the reverse orientation. Do not change the amount of genetic material  Generally viable and show no particular abnormalities at phenotypic level

3. TYPES OF INVERSIONS Paracentric inversion: Pericentric inversion:

4. Problems in recombination Paracentric inversion Pericentric inversion

5. MECHANISMS OF INVERSION Double strand break is needed for the inversion “Hotspots” – Usually contains segmental duplications (SD) – Distance between SD = 10-400kb – 95 – 97% identity Mechanisms – Non-allelic homologous recombination (NAHR) – Non-homologous end joining (NHEJ) – Fork stalling and template switching

6. CONSEQUENCES OF INVERSIONS Recombination suppressed in heterozygotes – Reducing cross-over within inverted regions – If recombination occurs  Not viable cells Inversions could lead to insertions or deletions Depending on the breakpoints position: – Gene disruption – Alter gene expression – Generate new splicing sites – Gene fusion NEUTRAL DELETERIOUS ADAPTATIVE

7. HOW TO DETECT INVERSIONS Problems – Inversions do not change genome size – The genome is full of GAPs and the inversions flanked by repetitive sequences International Human Genome Sequencing Consortium (2004) Nature 409: 931-945.

8. HOW TO DETECT INVERSIONS Problems – Inversions do not change genome size – The genome is full of GAPs and the inversions flanked by repetitive sequences Methods – Cytogenetic (conventional, FISH, FISH-based assay) – Pair-end sequencing – Genome assembly

9. IMPLICATIONS OF INVERSIONS INVERSIONS Generating variability Speciation Local adaptation Human diseases

10. HapMap project  Structural Variations The role of inversions in human diversity

11. The role of inversions in speciation Speciation Prezygotic INVERSIONS Postzygotic

12. The role of inversions in local adaptation -Annual -Found in DRY environments in the INLAND -Flowering time BEFORE hot -Perennial -Found in WET and COOL environments in the coast -Flowering time LATER - Flowering time - Morphological differences Monkeyflower ( Mimulus guttatus)

13. Inversions related to diseases Chr. locationConsequences X intron 22Haemophilia 4 p14q21Behavioural disorders X q11q28Klinefelter –like Sd 8 p11.2q23.1Ambras Syndrome -X-linked disease -Factor VIII  26 exons and 25 introns -Inversion of the intron 22 by NAHR

14. CONCLUSIONS Several studies have reported many inversions Way to generate variation between and within species Diversity of effects depending on: – Where? (Coding/Non-coding, introns, exons) – Is any gene affected? – Does the inversion imply another chromosomal arrangement?

15. REFERENCES Antonacci F, Kidd JM, Marques-Bonet T, Ventura M, Siswara P, Jiang Z, et al. Characterization of six human disease-associated inversion polymorphisms. Hum Mol Genet. 2009;18:2555–66. Gu W, Zhang F, Lupski JR. Mechanisms for human genomic rearrangements. Pathogenetics. 2008;1:4. Bansal V, Bashir A, Bafna V. Evidence for large inversion polymorphisms in the human genome from HapMap data 2007:219–30. Lee J, Han K, Meyer TJ, Kim H-S, Batzer M a. Chromosomal inversions between human and chimpanzee lineages caused by retrotransposons. PLoS One. 2008;3:e4047. Kirkpatrick M. How and why chromosome inversions evolve. PLoS Biol. 2010;8. Lowry DB, Willis JH. A widespread chromosomal inversion polymorphism contributes to a major life-history transition, local adaptation, and reproductive isolation. PLoS Biol. 2010;8.

16. Chromosome inversions in human populations Marta Ruiz Fernández Master in Advanced Genetics 17 December 2014

18. MECHANISMS OF INVERSION 1. Non-allelic homologous recombination (NAHR)

19. MECHANISMS OF INVERSION 1b. NAHR and Transposable Elements – Some transposable elements contains LTR – By homology two TE containing LTR can recombine – If the TE are in opposite orientation they could cause inversions Retrotransposon recombination-mediated inversion

20. MECHANISMS OF INVERSION 2. Fork stalling and template switching (FoSTeS) Gu W. Pathogenetics. 2008;1:4

21. HOW TO DETECT INVERSIONS Methods: – Cytogenetic: FISH The problem of this techniques is the resolution (2Mbp) Solution  FISH-based assay Antonacci F.Hum Mol Genet. 2009;18:2555–66

22. HOW TO DETECT INVERSIONS Methods: – FISH – Pair-end sequencing method (variants >5kb) + ++ ++ +++ + + - -- -- --- -+

23. HOW TO DETECT INVERSIONS Methods: – FISH – End-pair sequencing method – Genome assembly