×

A population genetics theory for piRNA-regulated transposable elements. (English) Zbl 07702605

Summary: Transposable elements (TEs) are self-reproducing selfish DNA sequences that can invade the genome of virtually all living species. Population genetics models have shown that TE copy numbers generally reach a limit, either because the transposition rate decreases with the number of copies (transposition regulation) or because TE copies are deleterious, and thus purged by natural selection. Yet, recent empirical discoveries suggest that TE regulation may mostly rely on piRNAs, which require a specific mutational event (the insertion of a TE copy in a piRNA cluster) to be activated – the so-called TE regulation “trap model”. We derived new population genetics models accounting for this trap mechanism, and showed that the resulting equilibria differ substantially from previous expectations based on a transposition-selection equilibrium. We proposed three sub-models, depending on whether or not genomic TE copies and piRNA cluster TE copies are selectively neutral or deleterious, and we provide analytical expressions for maximum and equilibrium copy numbers, as well as cluster frequencies for all of them. In the full neutral model, the equilibrium is achieved when transposition is completely silenced, and this equilibrium does not depend on the transposition rate. When genomic TE copies are deleterious but not cluster TE copies, no long-term equilibrium is possible, and active TEs are eventually eliminated after an active incomplete invasion stage. When all TE copies are deleterious, a transposition-selection equilibrium exists, but the invasion dynamics is not monotonic, and the copy number peaks before decreasing. Mathematical predictions were in good agreement with numerical simulations, except when genetic drift and/or linkage disequilibrium dominates. Overall, the trap-model dynamics appeared to be substantially more stochastic and less repeatable than traditional regulation models.

MSC:

92-XX Biology and other natural sciences

Software:

diffEq; NumPy; deSolve; R; phaseR
Full Text: DOI

References:

[1] Adams, M. D.; Tarng, R. S.; Rio, D. C., The alternative splicing factor PSI regulates P-element third intron splicing in vivo, Genes Dev., 11, 1, 129-138 (1997)
[2] Arkhipova, I.; Meselson, M., Deleterious transposable elements and the extinction of asexuals, Bioessays, 27, 1, 76-85 (2005)
[3] Bergman, C. M.; Quesneville, H.; Anxolabéhère, D.; Ashburner, M., Recurrent insertion and duplication generate networks of transposable element sequences in the Drosophila melanogaster genome, Genome Biol., 7, 11, 1-21 (2006)
[4] Brennecke, J.; Aravin, A. A.; Stark, A.; Dus, M.; Kellis, M.; Sachidanandam, R.; Hannon, G. J., Discrete small RNA-generating loci as master regulators of transposon activity in Drosophila, Cell, 128, 6, 1089-1103 (2007)
[5] Brookfield, J. F.; Badge, R. M., Population genetics models of transposable elements, Genetica, 100, 1, 281-294 (1997)
[6] Charlesworth, B.; Charlesworth, D., The population dynamics of transposable elements, Genet. Res., 42, 1, 1-27 (1983)
[7] Deniz, Ö.; Frost, J. M.; Branco, M. R., Regulation of transposable elements by DNA modifications, Nature Rev. Genet., 20, 7, 417-431 (2019)
[8] Dolgin, E. S.; Charlesworth, B., The fate of transposable elements in asexual populations, Genetics, 174, 2, 817-827 (2006)
[9] Doolittle, W. F.; Sapienza, C., Selfish genes, the phenotype paradigm and genome evolution, Nature, 284, 5757, 601-603 (1980)
[10] Gilbert, C.; Feschotte, C., Horizontal acquisition of transposable elements and viral sequences: patterns and consequences, Curr. Opin. Genet. Dev., 49, 15-24 (2018)
[11] Gladyshev, E., Repeat-induced point mutation and other genome defense mechanisms in fungi, (Heitman, J.; Howlett, B. J.; Crous, P. W.; Stukenbrock, E. H.; James, T. Y.; Gow, N. A.R., The fungal kingdom (2017), Wiley Online Library), 687-699
[12] Goriaux, C.; Théron, E.; Brasset, E.; Vaury, C., History of the discovery of a master locus producing piRNAs: the flamenco/COM locus in Drosophila melanogaster, Front. Genet., 5, 257 (2014)
[13] Grayling, M. J., phaseR: An R package for phase plane analysis of autonomous ODE systems, R J., 6, 2, 43-51 (2014)
[14] Harris, C. R.; Millman, K. J.; van der Walt, S. J.; Gommers, R.; Virtanen, P.; Cournapeau, D.; Wieser, E.; Taylor, J.; Berg, S.; Smith, N. J.; Kern, R.; Picus, M.; Hoyer, S.; van Kerkwijk, M. H.; Brett, M.; Haldane, A.; del Río, J. F.; Wiebe, M.; Peterson, P.; Gérard-Marchant, P.; Sheppard, K.; Reddy, T.; Weckesser, W.; Abbasi, H.; Gohlke, C.; Oliphant, T. E., Array programming with NumPy, Nature, 585, 7825, 357-362 (2020)
[15] Hartl, D.; Lozovskaya, E.; Lawrence, J., Nonautonomous transposable elements in prokaryotes and eukaryotes, Genetica, 86, 1, 47-53 (1992)
[16] Huang, S.; Yoshitake, K.; Asakawa, S., A review of discovery profiling of PIWI-interacting RNAs and their diverse functions in Metazoans, Int. J. Mol. Sci., 22, 20, 11166 (2021)
[17] Kelleher, E. S.; Azevedo, R. B.; Zheng, Y., The evolution of small-RNA-mediated silencing of an invading transposable element, Genome Biol. Evol., 10, 11, 3038-3057 (2018)
[18] Khan, A. I.; Dinh, D. M.; Schneider, D.; Lenski, R. E.; Cooper, T. F., Negative epistasis between beneficial mutations in an evolving bacterial population, Science, 332, 6034, 1193-1196 (2011)
[19] Kidwell, M. G.; Lisch, D. R., Perspective: transposable elements, parasitic DNA, and genome evolution, Evolution, 55, 1, 1-24 (2001)
[20] Kofler, R., Dynamics of transposable element invasions with piRNA clusters, Mol. Biol. Evol., 36, 7, 1457-1472 (2019)
[21] Kofler, R., piRNA clusters need a minimum size to control transposable element invasions, Genome Biol. Evol., 12, 5, 736-749 (2020)
[22] Kofler, R.; Nolte, V.; Schlötterer, C., The transposition rate has little influence on the plateauing level of the P-element, Mol. Biol. Evol., 39, 7, msac141 (2022)
[23] Kouyos, R. D.; Silander, O. K.; Bonhoeffer, S., Epistasis between deleterious mutations and the evolution of recombination, Trends Ecol. Evol., 22, 6, 308-315 (2007)
[24] Le Rouzic, A., Estimating directional epistasis, Front. Genet., 5, 198 (2014)
[25] Le Rouzic, A.; Capy, P., The first steps of transposable elements invasion: parasitic strategy vs. genetic drift, Genetics, 169, 2, 1033-1043 (2005)
[26] Le Rouzic, A.; Capy, P., Population genetics models of competition between transposable element subfamilies, Genetics, 174, 2, 785-793 (2006)
[27] Lee, Y. C.G., Synergistic epistasis of the deleterious effects of transposable elements, Genetics, 220, 2, iyab211 (2022)
[28] Lohe, A. R.; Hartl, D. L., Autoregulation of mariner transposase activity by overproduction and dominant-negative complementation, Mol. Biol. Evol., 13, 4, 549-555 (1996)
[29] Lu, J.; Clark, A. G., Population dynamics of PIWI-interacting RNAs (piRNAs) and their targets in Drosophila, Genome Res., 20, 2, 212-227 (2010)
[30] Lynch, M.; Conery, J. S., The origins of genome complexity, Science, 302, 5649, 1401-1404 (2003)
[31] Maisnier-Patin, S.; Roth, J. R.; Fredriksson, A.s.; Nyström, T.; Berg, O. G.; Andersson, D. I., Genomic buffering mitigates the effects of deleterious mutations in bacteria, Nature Genet., 37, 12, 1376-1379 (2005)
[32] Malone, C. D.; Hannon, G. J., Small RNAs as guardians of the genome, Cell, 136, 4, 656-668 (2009)
[33] Nuzhdin, S. V., Sure facts, speculations, and open questions about the evolution of transposable element copy number, (Transposable Elements and Genome Evolution (2000), Springer), 129-137
[34] Orgel, L. E.; Crick, F. H., Selfish DNA: the ultimate parasite, Nature, 284, 5757, 604-607 (1980)
[35] Ozata, D. M.; Gainetdinov, I.; Zoch, A.; O’Carroll, D.; Zamore, P. D., PIWI-interacting RNAs: small RNAs with big functions, Nature Rev. Genet., 20, 2, 89-108 (2019)
[36] R. Core Team, D. M., R: A language and environment for statistical computing (2020), URL https://www.R-project.org/
[37] Robillard, É.; Le Rouzic, A.; Zhang, Z.; Capy, P.; Hua-Van, A., Experimental evolution reveals hyperparasitic interactions among transposable elements, Proc. Natl. Acad. Sci., 113, 51, 14763-14768 (2016)
[38] Roessler, K.; Bousios, A.; Meca, E.; Gaut, B. S., Modeling interactions between transposable elements and the plant epigenetic response: a surprising reliance on element retention, Genome Biol. Evol., 10, 3, 803-815 (2018)
[39] Roze, D., Causes and consequences of linkage disequilibrium among transposable elements within eukaryotic genomes, BioRxiv (2022)
[40] Saint-Leandre, B.; Capy, P.; Hua-Van, A.; Filée, J., PiRNA and transposon dynamics in drosophila: A female story, Genome Biol. Evol., 12, 6, 931-947 (2020)
[41] Selker, E. U.; Stevens, J. N., DNA methylation at asymmetric sites is associated with numerous transition mutations, Proc. Natl. Acad. Sci., 82, 23, 8114-8118 (1985)
[42] Soetaert, K.; Petzoldt, T.; Setzer, R. W., Solving differential equations in R: Package desolve, J. Stat. Softw., 33, 9, 1-25 (2010), URL http://www.jstatsoft.org/v33/i09
[43] Sousa, A.; Bourgard, C.; Wahl, L. M.; Gordo, I., Rates of transposition in Escherichia coli, Biol. Lett., 9, 6, Article 20130838 pp. (2013)
[44] Wallau, G. L.; Capy, P.; Loreto, E.; Le Rouzic, A.; Hua-Van, A., VHICA, a new method to discriminate between vertical and horizontal transposon transfer: Application to the mariner family within drosophila, Mol. Biol. Evol., 33, 4, 1094-1109 (2016)
[45] Zanni, V.; Eymery, A.; Coiffet, M.; Zytnicki, M.; Luyten, I.; Quesneville, H.; Vaury, C.; Jensen, S., Distribution, evolution, and diversity of retrotransposons at the flamenco locus reflect the regulatory properties of piRNA clusters, Proc. Natl. Acad. Sci., 110, 49, 19842-19847 (2013)
[46] Zhang, S.; Pointer, B.; Kelleher, E. S., Rapid evolution of piRNA-mediated silencing of an invading transposable element was driven by abundant de novo mutations, Genome Res., 30, 4, 566-575 (2020)
This reference list is based on information provided by the publisher or from digital mathematics libraries. Its items are heuristically matched to zbMATH identifiers and may contain data conversion errors. In some cases that data have been complemented/enhanced by data from zbMATH Open. This attempts to reflect the references listed in the original paper as accurately as possible without claiming completeness or a perfect matching.