L3genetics_epigenetics_genomcs_2024.pptx

evolution

1. L3 Evolutionary Genetics [email protected]

2. Molecular Evolution, but not as you know it… Genome Structural Evolution and Epigenetics

3. Following this lecture you should be able to: Understand the role non-sequence based heritable variation plays in adaptation and evolution Discuss copy number variation, genome duplication and genome rearrangement in the context of molecular evolution Discuss the historical development of definitions and concepts about epigenetics Understand the basic mechanisms by which epigenetic changes are mediated Discuss what is meant by trans-generational epigenetic inheritance, including its scale and importance

4. Genome Structural evolution

5. Whole genomic approaches allow more than just the analysis of genomic sequence diversity Structural variation can be defined via inter- or intra- species comparison between assembled genomes Duplications, inversions, deletions, insertions, translocations etc Can also occur at the scale of whole chromosomes (aneuploidies, polyploidies) Can have profound fitness consequences – not necessarily just negative (e.g. disease) We’ll look a few examples: Jumbled enomeGs HGT and genome rearrangements in bacteria Genome duplications in Yeast Gene family expansion and adaptation

6. Gene family expansion and adaptation Numerous examples of adaptive expansion of gene families by gene duplication Gene duplication a solution to Susumu Ohno’s dilemma – How do new genes evolve under continuous selection ? So long as duplicates are not lost to drift or null mutations, neofunctionalisation is possible Can have immediate ‘dosage effects’ – a brute way of modulating gene expression. Underlies copy number variation in Leishmania and T. cruzi for example https://doi.org/10.1093/nar/gkab1203

7. Gene family expansion – Monkey business Two copies of RNAase1 in Douc langur Only one in other primates RNAase in primates has antiviral ( dsRNA ) properties – optimum pH 7.4 RNAase1B in Douc langur optimum pH 6.4 Douc langur ferments bacteria in its gut (like ruminants) and uses RNAase1B Original copy retains function Zhang J1, Zhang YP, Rosenberg HF. 2002 Adaptive evolution of a duplicated pancreatic ribonuclease gene in a leaf-eating monkey. Nat Genet. 2002 Apr;30(4):411-5.

8. Whole Genome duplications ( Ploidy / Aneuploidy) Ancestor Sarcomyces lineage Kluyvermyces lineage Comparative genomics of modern day yeast Coordinate duplication of the genome can allow for large scale adaptation to novel environments Most of the genome underwent massive mutation and gene loss One from each set maintained in the majority of cases Where duplicates are retained – abundant neofunctionalisation Conserved synteny of duplicated genes is clue to ancient event 95% of cases of accelerated evolution involve only one member of a gene pair https:// www.nature.com /articles/nature02424

9. Genome structural evolution in bacteria Growing concept of ‘core genomes’ and ‘pan-genomes’ within the same bacterial species Core genome is stereotypical of a given species, Pan-genomes are rapidly exchanged mobile genes / genetic elements / virulence elements etc Mobile elements play a role in driving rearrangements between closely related individuals Constant genome rearrangement can have adaptive and maladaptive consequences Genomic rearrangements more common in the ‘pan genomic regions’ Huge potential pool of genetic diversity and novel gene combinations Eight Yersinia pestis genomes- what a mess !

10. Epigenetics

11. Jean Baptiste Lamarck (Great-great grandfather of epigentics ) 1744-1829 First to use “biology” in its modern sense in 1802 publication Invertebrate biologist, malacologist , taxonomist (soldier, lover, bon viveur) Best known for his theory “inheritance of acquired characteristics” First real concept of evolution - adaptation through use and disuse Didn’t know about genetics Concept has been abused and has gone through cycles of disfavour and favour

12. “ In every animal which has not passed the limit of its development, a more frequent and continuous use of any organ gradually strengthens, develops and enlarges that organ, and gives it a power proportional to the length of time it has been so used; while the permanent disuse of any organ imperceptibly weakens and deteriorates it , and progressively diminishes its functional capacity, until it finally disappears” Lamarck’s First law AKA – adaptation

13. “All the acquisitions or losses wrought by nature on individuals, through the influence of the environment in which their race has long been placed, and hence through the influence of the predominant use or permanent disuse of any organ; all these are preserved by reproduction to the new individuals which arise, provided that the acquired modifications are common to both sexes , or at least to the individuals which produce the young ” Lamarck’s second law AKA – soft inheritance (and maternal effects)

14. What is Epigenetics and what might it explain? “ Norm of reaction ”: pattern of phenotypic expression of a single genotype across a range of environments (plasticity) “Genetic Assimilation” – the phenotype produced under a stressful condition becomes the phenotype for every condition “ Canalization ” (robustness): ability of a population to produce the same phenotype regardless of variability of its environment or genotype Based on J. Slack. 2002. Conrad Waddington : the last Renaissance biologist? Nature Reviews Genetics 3:889-895 genotype phenotype Great uncle of epigenetics

15. Berger et al. 2009. An operational definition of epigenetics . Genes and Development 23:781-783 Epigenator – environmental signal that triggers intracellular pathway; can be transient Epigenetic Initiator – signal that responds to the epigenator and defines location of the epigenetic chromatin environment (e.g. DNA-binding protein, noncoding RNA) Epigenetic Maintainer - signal that sustains the chromatin / RNA / protein environment in the first and subsequent generations (e.g. DNA methylation, histone modifications, histone variants etc ); Components of Epigenetic phenotype ‘reprogramming’ NOTE: In many respects epigenetics is a far larger and complex field than genetics itself. We will only skim the surface

16. Why are epigenetics important? Cancer – heritable changes in gene expression responsible for cancer (Holliday 1979); tumour cells ha ve aberrant, cell-heritable patterns of DNA methylation associated with silencing of tumour repressor genes ( Baylin & Herman 2000) Hereditary Disease – defects in imprinted genes (i.e. epigenetic state depends on whether inherited from mother or father; Murphy et al 2000); aging (Lamb 1994) & psychiatric disorders ( Petronis 2000) Epigenetic Defense Mechanisms - methylating foreign DNA or RNA-directed degradation of RNA transcripts are mechanisms used by cells to avoid or destroy parasites ( Wolffe et al.1999) Epigenetic Epidemiology – maternal starvation and stress can have persistent effects in children (Barker 1994), some lasting effects across generations (Campbell & Perkins 1988); thalidimide -induced (Holliday 1998); retrotransposon -related (Morgan et al. 1999); prion -related disease (BSE, scrapie , kuru , Creutzfeld -Jacob disease) Cloning – somatic cells used for cloning need to be epigenetically reprogrammed ( Wolffe & Matzke 1999) Agriculture – epigenetics causes problems for genetic engineering for crop improvement- newly inserted genes can be silenced by methylation Epigenetics role in human development http://www.scribd.com/doc/24900138/Epigenetics-Role-in-Human-Development

17. Morgan et al. 1999. Epigenetic inheritance at the agouti locus in the mouse. Nature Genetics  23: 314 - 318 Agouti Locus in Mice Dogma at the time was that epigenetic marks have effects on phenotype but that they are cleared on passage through germ line ( i.e. not inherited ) this paper was one of first to demonstrate inheritance of epigenetic modification transposable element inserted upstream of the agouti gene causes ectopic expression of agouti protein, resulting in yellow fur, obesity, diabetes and increased susceptibility to tumours variable expressivity of A VY traits due to methylation of inserted element screened for methylation using methylation-sensitive ( HpaI I ) and insensitive ( MspI ) enzymes (all first digested with BamHI ) in offspring Showed that pseudo- oagouti phenotype was passed by mother to offspring via incomplete erasure of maternal allele. IAP = intra- cisternal A particle (TE) A vy = allele with the IAP B = BamH I M = MspI H = HpaII

18. Transgenerational Epigenetics (our focus as evolutionary biologists) Epigenetic modification of genetic material and gene expression takes may forms More common in plants, fungal and microbes than in mammals which have a sequestered germline Epigenetic mechanisms RNA Feedback loops mRNA that promotes its own transcription chromatin marks binding of methyl or ethyl groups to DNA and histones, or directly to DNA non coding and coding RNA maternal m,si,lnc,pi RNA structural templating Prion proteins in yeasts / fungi

19. Evolutionary scaling of epigenetic effects Most cellular epigenetic modifications are reset during meiosis in primordial germ line cells Further epigenetic modifications are also reset at fertilization Relative contribution of different sexes to retained epigenetic variation in offspring can be different (?) Importantly, the frequency and longevity of epigenetic mutations is highly variable How much epigenetic information is transferred and how do epigenetics interface with molecular evolution ? Is it associated with heritable phenotypic traits ?

20. Cytosine methylation dynamics in Arabidopsis - epigenetic neutrality and an ‘ epimolecular clock’ ? Genome-wide CG meth genotyping across a A. thalania genome (CHH & CHG calculated but ignored) Compared temporal divergence within lineages Fitted data to model of neutral forward-backward epimutation Clock-like accumulation of differences. Mutation rate per site per generation = 10 -4 compared to 10 -9 DNA Decoupling of genetic and epigenetic evolutionary scales van der Graaf A, Wardenaar R, Neumann DA, Taudt A, Shaw RG, Jansen RC, Schmitz RJ*, Colomé-Tatché M*, Johannes F*. (2015). Rate, spectrum and evolutionary dynamics of spontaneous epimutations . Proc. Natl. Acad. Sci. USA

21. Mapping the epigenetic basis of complex traits ? (pause for a quick QTL primer)

22. Rudiments of QTL theory p values Cosegregation of (epi)genetic markers and phenotype

23. Mapping the epigenetic basis of complex traits ? Establish monogenic A. thalania lines Only differences are based on cytosine methylation Focused on flowering time and root lengths as their phenotypic traits Board sense heritability clearly demonstrated Paves the way for top down / bottom down analyses… what next … population epigenomics ? Sandra Cortijo, et al 2014 Mapping the Epigenetic Basis of Complex Traits Science March 2014: 343 (6175), 1145-1148.

24. Structural mutations, genome duplications HGT, mobile genetic elements are a powerful force in molecular evolution If genetics is a solar system, epigentics is a galaxy, them the potential combinations between the two systems are infinite (almost) For evolutionary biologists, trans-generational effects are of most interest (imprinting, maternal effects) Multiple transgenerational epigenetic mechanisms exist Epigenet control of phenotypes, links with Lamarckian Inheritance and Genetic Assimilation (adapt first mutate later, so long as the environment stays fixed) Much still to be understood…. Take homes

25. Projects

26. Further reading…. Bergthorsson, U, Andersson , DI & Roth, JR Ohno's dilemma: Evolution of new genes under continuous selection. Proc Natl Acad Sci U S A. 2007 Oct 23; 104(43): 17004–17009. Zhang, J 2003 Evolution by gene dupliclication – an update TREE: 18 Darling AE, Miklós I, Ragan MA (2008) Dynamics of Genome Rearrangement in Bacterial Populations. PLoS Genet 4(7): e1000128. Johnson & Tricker . 2010. Epigenomic plasticity within populations: its evolutionary significance and potential. Heredity 105 : 113-121 Siddle et al. 2013. Reversible epigenetic down- regulaiton of MHC molecules by devil facial tumour disease illustrates immune escape by a contagious cancer. PNAS 110 : 5103-5108 Heard E 1 , Martienssen RA 2 . 2014 Transgenerational epigenetic inheritance: myths and mechanisms. Cell. 27;157(1):95-109. doi : 10.1016/j.cell.2014.02.045. van der Graaf A, Wardenaar R, Neumann DA, Taudt A, Shaw RG, Jansen RC, Schmitz RJ*, Colomé-Tatché M*, Johannes F*. (2015). Rate, spectrum and evolutionary dynamics of spontaneous epimutations.Proc . Natl. Acad. Sci. USA. Cortijo S, Wardenaar R,, Colot V*, Johannes F* (2014).Mapping the epigenetic basis of complex traits. Science doi:10.1126/science.1248127. http:// www.johanneslab.org /

27. Computer lab: Genomic signals of selection and demographic change in the kinetoplastid parasite Leishmania infantum Leishmania infantum is a kinetoplastid parasite of the Trypanosomatidae Pathogenic agent of visceral leishmaniasis in humans. Parasite’s life cycle consists of two major developmental stages, one stage in an invertebrate host, the phlebotomine sand fly, and one stage in a vertebrate host, often the common dog. Upon vertebrate infection, the parasite quickly invades host macrophages and proliferates in ‘ amastigote ’ form. Human infection generally leads to death without chemotherapy. Treatment is highly problematic (high toxicity, prohibitive cost, resistance issues, etc.) and vaccines have yet to be found.

28. Computer lab continued ….. Calculate summary statistics (genetic diversity Fstats etc ) Look for signatures of selection (Tajima’s D, dN / dS ) Build some phylogenetic trees Answer some questions about disease diversity and dispersal