The composition of piRNA clusters in Drosophila melanogaster deviates from expectations under the trap model.

BACKGROUND: It is widely assumed that the invasion of a transposable element (TE) in mammals and invertebrates is stopped when a copy of the TE jumps into a piRNA cluster (i.e., the trap model). However, recent works, which for example showed that deletion of three major piRNA clusters has no effect on TE activity, cast doubt on the trap model. RESULTS: Here, we test the trap model from a population genetics perspective. Our simulations show that the composition of regions that act as transposon traps (i.e., potentially piRNA clusters) ought to deviate from regions that have no effect on TE activity. We investigated TEs in five Drosophila melanogaster strains using three complementary approaches to test whether the composition of piRNA clusters matches these expectations. We found that the abundance of TE families inside and outside of piRNA clusters is highly correlated, although this is not expected under the trap model. Furthermore, the distribution of the number of TE insertions in piRNA clusters is also much broader than expected. CONCLUSIONS: We found that the observed composition of piRNA clusters is not in agreement with expectations under the simple trap model. Dispersed piRNA producing TE insertions and temporal as well as spatial heterogeneity of piRNA clusters may account for these deviations.

A population genetics theory for piRNA-regulated transposable elements.

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.

An entropy trap model of thermodynamic anomalies for dual-amorphous water undergoing liquid-liquid phase transition.

Water displays numerous anomalously thermodynamic behaviors. However, the working principles behind these anomalies are not well understood, and the liquid-liquid phase transition (LLPT) is often regarded as the potential reason. In this study, we developed an entropy trap model to characterize the thermodynamic LLPT in dual-amorphous water, i.e. having both low-density and high-density liquid water. From the Adam-Gibbs model and free-volume theory, thermodynamic behaviors of water have been described using the proposed model, in which the constitutive relationships among density, heat capacity, thermal expansivity and glass transition temperature have been formulated. Moreover, the glass transition and its connection to thermodynamic behaviors were also investigated for dual-amorphous water. Finally, experimental data reported in the literature were used to verify effectiveness of the proposed model. This study is expected to provide a physical insight into the anomalous thermodynamics of dual-amorphous water undergoing the LLPT.