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Epigenetics and Evolution: Transposons and the Stochastic Epigenetic Modification Model

机译：表观遗传学和进化：转座子和随机表观遗传修饰模型

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In addition to genetic variation, epigenetic variation and transposons can greatly affect the evolutionary fitnesses landscape and gene expression. Previously we proposed a mathematical treatment of a general epigenetic variation model that we called Stochastic Epigenetic Modification (SEM) model. In this study we follow up with a special case, the Transposon Silencing Model (TSM), with, once again, emphasis on quantitative treatment. We have investigated the evolutionary effects of epigenetic changes due to transposon ( T ) insertions; in particular, we have considered a typical gene locus A and postulated that (i) the expression level of gene A depends on the epigenetic state (active or inactive) of a cis - located transposon element T , (ii) stochastic variability in the epigenetic silencing of T occurs only in a short window of opportunity during development, (iii) the epigenetic state is then stable during further development, and (iv) the epigenetic memory is fully reset at each generation. We develop the model using two complementary approaches: a standard analytical population genetics framework (di usion equations) and Monte-Carlo simulations. Both approaches led to similar estimates for the probability of fixation and time of fixation of locus TA with initial frequency P in a randomly mating diploid population of effective size Ne . We have ascertained the e ect that ρ , the probability of transposon Modification during the developmental window, has on the population (species). One of our principal conclusions is that as ρ increases, the pattern of fixation of the combined TA locus goes from "neutral" to "dominant" to "over-dominant". We observe that, under realistic values of ρ , epigenetic Modifications can provide an e cient mechanism for more rapid fixation of transposons and cis-located gene alleles. The results obtained suggest that epigenetic silencing, even if strictly transient (being reset at each generation), can still have signi cant macro-evolutionary effects. Importantly, this conclusion also holds for the static fitness landscape. To the best of our knowledge, no previous analytical modeling has treated stochastic epigenetic changes during a window of opportunity.
机译：除了遗传变异外，表观遗传变异和转座子还可以极大地影响进化适应性景观和基因表达。以前，我们提出了一种一般表观遗传变异模型的数学处理方法，我们将其称为随机表观遗传修饰（SEM）模型。在这项研究中，我们以特例转座子沉默模型（TSM）为重点，再次强调定量治疗。我们已经研究了由于转座子（T）插入而引起的表观遗传变化的进化影响。特别是，我们已经考虑了一个典型的基因座A，并假设（i）基因A的表达水平取决于顺式转座子元件T的表观遗传状态（活跃或不活跃），（ii）表观遗传的随机变异性T的沉默仅发生在发育过程中的短时机中，（iii）表观遗传状态随后在进一步的发育中是稳定的，并且（iv）表观遗传记忆在每一代都被完全重置。我们使用两种互补的方法来开发模型：标准的分析种群遗传学框架（二维方程式）和蒙特卡洛模拟。在有效大小为N e 的随机交配的二倍体种群中，两种方法均得出了以初始频率P定位轨迹TA的固定概率和固定时间的相似估计。我们已经确定了ρ，即发育窗口中转座子修饰的概率对种群（物种）的影响。我们的主要结论之一是，随着ρ的增加，组合TA位点的固定模式从“中性”变为“显性”再到“过度显性”。我们观察到，在ρ的实际值下，表观遗传修饰可以为更快速固定转座子和顺式定位的基因等位基因提供有效的机制。获得的结果表明，表观遗传沉默，即使严格地是瞬态的（每一代都被重置），仍然可以具有明显的宏观进化作用。重要的是，该结论也适用于静态健身态势。据我们所知，在机会之窗内，以前的分析模型都没有处理随机表观遗传的变化。

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