Cytosolic microRNA-inducible nuclear translocation of Cas9 protein for disease-specific genome modification.

MicroRNA-dependent mRNA decay plays an important role in gene silencing by facilitating posttranscriptional and translational repression. Inspired by this intrinsic nature of microRNA-mediated mRNA cleavage, here, we describe a microRNA-targeting mRNA as a switch platform called mRNA bridge mimetics to regulate the translocation of proteins. We applied the mRNA bridge mimetics platform to Cas9 protein to confer it the ability to translocate into the nucleus via cleavage of the nuclear export signal. This system performed programmed gene editing in vitro and in vivo. Combinatorial treatment with cisplatin and miR-21-EZH2 axis-targeting CRISPR Self Check-In improved sensitivity to chemotherapeutic drugs in vivo. Using the endogenous microRNA-mediated mRNA decay mechanism, our platform is able to remodel a cell's natural biology to allow the entry of precise drugs into the nucleus, devoid of non-specific translocation. The mRNA bridge mimetics strategy is promising for applications in which the reaction must be controlled via intracellular stimuli and modulates Cas9 proteins to ensure safe genome modification in diseased conditions.

Recombination and mutational robustness in neutral fitness landscapes.

Mutational robustness quantifies the effect of random mutations on fitness. When mutational robustness is high, most mutations do not change fitness or have only a minor effect on it. From the point of view of fitness landscapes, robust genotypes form neutral networks of almost equal fitness. Using deterministic population models it has been shown that selection favors genotypes inside such networks, which results in increased mutational robustness. Here we demonstrate that this effect is massively enhanced by recombination. Our results are based on a detailed analysis of mesa-shaped fitness landscapes, where we derive precise expressions for the dependence of the robustness on the landscape parameters for recombining and non-recombining populations. In addition, we carry out numerical simulations on different types of random holey landscapes as well as on an empirical fitness landscape. We show that the mutational robustness of a genotype generally correlates with its recombination weight, a new measure that quantifies the likelihood for the genotype to arise from recombination. We argue that the favorable effect of recombination on mutational robustness is a highly universal feature that may have played an important role in the emergence and maintenance of mechanisms of genetic exchange.

Isoform-Specific Lysine Methylation of RORα2 by SETD7 Is Required for Association of the TIP60 Coactivator Complex in Prostate Cancer Progression.

The retinoid acid-related orphan receptor α (RORα), a member of the orphan nuclear receptor superfamily, functions as an unknown ligand-dependent transcription factor. RORα was shown to regulate a broad array of physiological processes such as Purkinje cell development in the cerebellum, circadian rhythm, lipid and bone metabolism, inhibition of inflammation, and anti-apoptosis. The human RORα gene encodes at least four distinct isoforms (RORα1, -2, -3, -4), which differ only in their N-terminal domain (NTD). Two isoforms, RORα2 and 3, are not expressed in mice, whereas RORα1 and 4 are expressed both in mice and humans. In the present study, we identified the specific NTD of RORα2 that enhances prostate tumor progression and proliferation via lysine methylation-mediated recruitment of coactivator complex pontin/Tip60. Upregulation of the RORα2 isoform in prostate cancers putatively promotes tumor formation and progression. Furthermore, binding between coactivator complex and RORα2 is increased by lysine methylation of RORα2 because methylation permits subsequent interaction with binding partners. This methylation-dependent activation is performed by SET domain containing 7 (SETD7) methyltransferase, inducing the oncogenic potential of RORα2. Thus, post-translational lysine methylation of RORα2 modulates oncogenic function of RORα2 in prostate cancer. Exploration of the post-translational modifications of RORα2 provides new avenues for the development of tumor-suppressive therapeutic agents through modulating the human isoform-specific tumorigenic role of RORα2.

N-Terminal Domain Mediated Regulation of RORα1 Inhibits Invasive Growth in Prostate Cancer.

Four members of the retinoic acid-related orphan receptor α (RORα) family (RORα1, RORα2, RORα3 and RORα4) are transcription factors that regulate several processes including circadian rhythm, lipid metabolism, cerebellar development, immune function, and cancer. Only two isoforms, RORα1 and 4, are specifically co-expressed in the murine and human. In the present study, we identified a specific N-terminal domain (NTD) of RORα1 that potentiated the downregulation of target genes involved in tumor progression and proliferation, based on results from RORα-deficient mouse embryonic fibroblasts and prostate carcinoma tissues. The hyperactivation of proliferative target genes were observed in RORα-deficient embryonic fibroblasts, and reconstitution of RORα1 inhibited this activation by a NTD dependent manner. Downregulation of RORα1 and upregulation of Wnt/ß-catenin target genes were correlated in prostate cancer patients. These findings revealed the control of invasive growth by NTD-mediated RORα1 signaling, suggesting advanced approaches for the development of therapeutic drugs.

Greedy adaptive walks on a correlated fitness landscape.

We study adaptation of a haploid asexual population on a fitness landscape defined over binary genotype sequences of length L. We consider greedy adaptive walks in which the population moves to the fittest among all single mutant neighbors of the current genotype until a local fitness maximum is reached. The landscape is of the rough mount Fuji type, which means that the fitness value assigned to a sequence is the sum of a random and a deterministic component. The random components are independent and identically distributed random variables, and the deterministic component varies linearly with the distance to a reference sequence. The deterministic fitness gradient c is a parameter that interpolates between the limits of an uncorrelated random landscape (c=0) and an effectively additive landscape (c→∞). When the random fitness component is chosen from the Gumbel distribution, explicit expressions for the distribution of the number of steps taken by the greedy walk are obtained, and it is shown that the walk length varies non-monotonically with the strength of the fitness gradient when the starting point is sufficiently close to the reference sequence. Asymptotic results for general distributions of the random fitness component are obtained using extreme value theory, and it is found that the walk length attains a non-trivial limit for L→∞, different from its values for c=0 and c=∞, if c is scaled with L in an appropriate combination.

Ezh2 promotes TRß lysine methylation-mediated degradation in hepatocellular carcinoma.

BACKGROUND: Post-translational modification (PTM) of proteins controls various cellular functions of transcriptional regulators and participates in diverse signal transduction pathways in cancer. The thyroid hormone (triiodothyronine, T3) plays a critical role in metabolic homeostasis via its direct interaction with the thyroid hormone receptor beta (TRß). TRß is involved in physiological processes, such as cell growth, differentiation, apoptosis, and maintenance of metabolic homeostasis through transcriptional regulation of target genes. OBJECTIVE: This study was performed to characterize the specific PTM of TRß is an active control mechanism for the proteasomal degradation of TRß in transcriptional signaling pathways in hepatocellular carcinoma cells. METHODS: Based on a previous study, we predicted that the lysine methyltransferase and methylation sites of TRß by comparing the amino acid sequences of histone H3 and TRß. Methyl-acceptor site of TRß was confirmed by point mutation. TRß protein stability was evaluated by ubiquitination assay with MG132. For glucose starvation, HepG2 cells were incubated in media without D-glucose. Proliferation-related proteins were detected by western blotting. MicroRNA level and autophagy marker were measured by real-time qPCR. RESULTS: The presence of enhancer of zeste homolog 2 (Ezh2), a methyltransferase of H3 lysine 27, as a methyltransferase of TRß also revealed that direct lysine methylation and consequent stimulated protein degradation of TRß underlies the negative correlation between Ezh2 and TRß. Notably, glucose starvation significantly increased lysine methylation, and methylated TRß showed further protein instability leading to an increase in the proliferation and growth of hepatocellular carcinoma cells. CONCLUSIONS: TRß functions as a tumor suppressor in various cancers; therefore, we evaluated the effect of TRß degradation on oncogenesis during glucose starvation. These data clearly define a functional model and provide a link between metabolism and cancer by regulating methyl-dependent protein levels of tumor suppressors. Taken together, maintaining TRß against methyl-dependent degradation is considered a possible therapeutic target for cancer progression.

Bistability in two-locus models with selection, mutation, and recombination.

The evolutionary effect of recombination depends crucially on the epistatic interactions between linked loci. A paradigmatic case where recombination is known to be strongly disadvantageous is a two-locus fitness landscape displaying reciprocal sign epistasis with two fitness peaks of unequal height. Although this type of model has been studied since the 1960s, a full analytic understanding of the stationary states of mutation-selection balance was not achieved so far. Focusing on the bistability arising due to the recombination, we consider here the deterministic, haploid two-locus model with reversible mutations, selection and recombination. We find analytic formulae for the critical recombination probability r ( c ) above which two stable stationary solutions appear which are localized on each of the two fitness peaks. We also derive the stationary genotype frequencies in various parameter regimes. In particular, when the recombination rate is close to r ( c ) and the fitness difference between the two peaks is small, we obtain a compact description in terms of a cubic polynomial which is analogous to the Landau theory of physical phase transitions.

The consequences of yield stress on deployment of a non-Newtonian anti-HIV microbicide gel.

A recent study in South Africa has confirmed, for the first time, that a vaginal gel formulation of the antiretroviral drug Tenofovir, when applied topically, significantly inhibits sexual HIV transmission to women [10]. However the gel for this drug, and anti-HIV microbicide gels in general, have not been designed using full understanding of how gel spreading and retention in the vagina govern successful drug delivery. Elastohydrodynamic lubrication theory can be applied to model such spreading of microbicide gels, which are inherently non-Newtonian [13,15]. A yield stress is emerging as one of the important properties of microbicide gel vehicle deployment, as this may improve retention within the vaginal canal. On the other hand, a yield stress may decrease the initial extent of the coating flow. Here, we first explain a certain yield stress paradox observed generally in many lubrication flows. Four conditions are determined, via scaling analysis, which mitigate the inconsistency in the use of lubrication theory to analyze the specific problem of elastic wall squeezing flow of yield stress fluid. Parameters characterizing these conditions are obtained experimentally for a test gel. Using them, it is shown that the lubrication approximation may be applied to the elastic wall-squeezing problem for this gel.

Clonal interference in large populations.

Clonal interference, the competition between lineages arising from different beneficial mutations in an asexually reproducing population, is an important factor determining the tempo and mode of microbial adaptation. The standard theory of this phenomenon neglects the occurrence of multiple mutations as well as the correlation between loss by genetic drift and clonal competition, which is questionable in large populations. Working within the Wright-Fisher model with multiplicative fitness (no epistasis), we determine the rate of adaptation asymptotically for very large population sizes and show that the standard theory fails in this regime. Our study also explains the success of the standard theory in predicting the rate of adaptation for moderately large populations. Furthermore, we show that the nature of the substitution process changes qualitatively when multiple mutations are allowed for, because several mutations can be fixed in a single fixation event. As a consequence, the index of dispersion for counts of the fixation process displays a minimum as a function of population size, whereas the origination process of fixed mutations becomes completely regular for very large populations. We find that the number of mutations fixed in a single event is geometrically distributed as in the neutral case. These conclusions are based on extensive simulations combined with analytic results for the limit of infinite population size.

One-dimensional annihilating random walk with long-range interaction.

We study the annihilating random walk with long-range interaction in one dimension. Each particle performs random walks on a one-dimensional ring in such a way that the probability of hopping toward the nearest particle is W=[1-ɛ(x+µ)^{-σ}]/2 (the probability of moving away from its nearest particle is 1-W), where x is the distance from the hopping particle to its nearest particle and ɛ, µ, and σ are parameters. For positive (negative) ɛ, a particle is effectively repulsed (attracted) by its nearest particle and each hopping is generally biased. On encounter, two particles are immediately removed from the system. We first study the survival probability and the mean spreading behaves in the long-time limit if there are only two particles in the beginning. Then we study how the density decays to zero if all sites are occupied at the outset. We find that the asymptotic behaviors are classified by seven categories: (i) σ>1 or ɛ=0, (ii) σ=1 and 2ɛ>1, (iii) σ=1 and 2ɛ=1, (iv) σ=1 and 2ɛ<1, (v) σ<1 and ɛ>0, (vi) σ=0 and ɛ<0, and (vii) 0<σ<1 and ɛ<0. The asymptotic behaviors in each category are universal in the sense that µ (and sometimes ɛ) cannot affect the asymptotic behaviors.

Branching annihilating random walks with long-range attraction in one dimension.

We introduce and numerically study the branching annihilating random walks with long-range attraction (BAWL). The long-range attraction makes hopping biased in such a manner that particle's hopping along the direction to the nearest particle has larger transition rate than hopping against the direction. Still, unlike the Lévy flight, a particle only hops to one of its nearest-neighbor sites. The strength of bias takes the form x^{-σ} with non-negative σ, where x is the distance to the nearest particle from a particle to hop. By extensive Monte Carlo simulations, we show that the critical decay exponent δ varies continuously with σ up to σ=1 and δ is the same as the critical decay exponent of the directed Ising (DI) universality class for σ≥1. Investigating the behavior of the density in the absorbing phase, we argue that σ=1 is indeed the threshold that separates the DI and non-DI critical behavior. We also show by Monte Carlo simulations that branching bias with symmetric hopping exhibits the same critical behavior as the BAWL.

Crossover behaviors in branching annihilating attracting walk.

We introduce branching annihilating attracting walk (BAAW) in one dimension. The attracting walk is implemented by a biased hopping in such a way that a particle prefers hopping to a nearest neighbor located on the side where the nearest particle is found within the range of attraction. We study the BAAW with four offspring by extensive Monte Carlo simulation. At first, we find the critical exponents of the BAAW with infinite range of attraction, which are different from those of the directed Ising (DI) universality class. Our results are consistent with the recent observation [Daga and Ray, Phys. Rev. E 99, 032104 (2019)2470-004510.1103/PhysRevE.99.032104]. Then, by studying crossover behaviors, we show that as far as the range of attraction is finite the BAAW belongs to the DI class. We conclude that the origin of non-DI critical behavior of the BAAW with infinite range of attraction is the long-range nature of the attraction.

Order-parameter critical exponent of absorbing phase transitions in one-dimensional systems with two symmetric absorbing states.

Via extensive Monte Carlo simulations along with systematic analyses of corrections to scaling, we estimate the order parameter critical exponent ß of absorbing phase transitions in systems with two symmetric absorbing states. The value of ß was conjectured to be 13/14≈0.93 and Monte Carlo simulation studies in the literature have repeatedly reproduced values consistent with the conjecture. In this paper, we systematically estimate ß by analyzing the effective exponent after finding how strong corrections to scaling are. We show that the widely accepted numerical value of ß is not correct. Rather, we obtain ß=1.020(5) from different models with two symmetric absorbing states.

Exploring the effect of sex on empirical fitness landscapes.

The nature of epistasis has important consequences for the evolutionary significance of sex and recombination. Recent efforts to find negative epistasis as a source of negative linkage disequilibrium and associated long-term advantage to sex have yielded little support. Sign epistasis, where the sign of the fitness effects of alleles varies across genetic backgrounds, is responsible for the ruggedness of the fitness landscape, with several unexplored implications for the evolution of sex. Here, we describe fitness landscapes for two sets of strains of the asexual fungus Aspergillus niger involving all combinations of five mutations. We find that approximately 30% of the single-mutation fitness effects are positive despite their negative effect in the wild-type strain and that several local fitness maxima and minima are present. We then compare adaptation of sexual and asexual populations on these empirical fitness landscapes by using simulations. The results show a general disadvantage of sex on these rugged landscapes, caused by the breakdown by recombination of genotypes on fitness peaks. Sex facilitates movement to the global peak only for some parameter values on one landscape, indicating its dependence on the landscape's topography. We discuss possible reasons for the discrepancy between our results and the reports of faster adaptation of sexual populations.

Dynamic correlation between intrahost HIV-1 quasispecies evolution and disease progression.

Quantifying the dynamics of intrahost HIV-1 sequence evolution is one means of uncovering information about the interaction between HIV-1 and the host immune system. In the chronic phase of infection, common dynamics of sequence divergence and diversity have been reported. We developed an HIV-1 sequence evolution model that simulated the effects of mutation and fitness of sequence variants. The amount of evolution was described by the distance from the founder strain, and fitness was described by the number of offspring a parent sequence produces. Analysis of the model suggested that the previously observed saturation of divergence and decrease of diversity in later stages of infection can be explained by a decrease in the proportion of offspring that are mutants as the distance from the founder strain increases rather than due to an increase of viral fitness. The prediction of the model was examined by performing phylogenetic analysis to estimate the change in the rate of evolution during infection. In agreement with our modeling, in 13 out of 15 patients (followed for 3-12 years) we found that the rate of intrahost HIV-1 evolution was not constant but rather slowed down at a rate correlated with the rate of CD4+ T-cell decline. The correlation between the dynamics of the evolutionary rate and the rate of CD4+ T-cell decline, coupled with our HIV-1 sequence evolution model, explains previously conflicting observations of the relationships between the rate of HIV-1 quasispecies evolution and disease progression.

Crossover from the parity-conserving pair contact process with diffusion to other universality classes.

The pair contact process with diffusion (PCPD) with modulo 2 conservation (PCPD2) [ 2A-->4A , 2A-->0 ] is studied in one dimension, focused on the crossover to other well established universality classes: the directed Ising (DI) and the directed percolation (DP). First, we show that the PCPD2 shares the critical behaviors with the PCPD, both with and without directional bias. Second, the crossover from the PCPD2 to the DI is studied by including a parity-conserving single-particle process (A-->3A) . We find the crossover exponent 1/varphi_{1}=0.57(3) , which is argued to be identical to that of the PCPD-to-DP crossover by adding A-->2A . This suggests that the PCPD universality class has a well-defined fixed point distinct from the DP. Third, we study the crossover from a hybrid-type reaction-diffusion process belonging to the DP [ 3A-->5A , 2A-->0 ] to the DI by adding A-->3A . We find 1/varphi_{2}=0.73(4) for the DP-to-DI crossover. The inequality of varphi_{1} and varphi_{2} further supports the non-DP nature of the PCPD scaling. Finally, we introduce a symmetry-breaking field in the dual spin language to study the crossover from the PCPD2 to the DP. We find 1/varphi_{3}=1.23(10) , which is associated with a new independent route from the PCPD to the DP.

Reentrant phase transition in a predator-prey model.

We numerically investigate the six-species predator-prey game in complex networks as well as in d -dimensional regular hypercubic lattices with d=1,2,...,6 . The food-web topology of the six species contains two directed loops, each of which is composed of cyclically predating three species. As the mutation rate is lowered below the well-defined phase transition point, the Z2 symmetry related with the interchange in the two loops is spontaneously broken, and it has been known that the system develops the defensive alliance in which three cyclically predating species defend each other against the invasion of other species. In the Watts-Strogatz small-world network structure characterized by the rewiring probability alpha , the phase diagram shows the reentrant behavior as alpha is varied, indicating a twofold role of the shortcuts. In d -dimensional regular hypercubic lattices, the system also exhibits the reentrant phase transition as d is increased. We identify universality class of the phase transition and discuss the proper mean-field limit of the system.

Three different routes from the directed Ising to the directed percolation class.

The scaling nature of absorbing critical phenomena is well understood for the directed percolation (DP) and the directed Ising (DI) systems. However, a full analysis of the crossover behavior is still lacking, which is of our interest in this study. In one dimension, we find three different routes from the DI to the DP classes by introducing a symmetry-breaking field (SB), breaking a modulo 2 conservation (CB), or making channels connecting two equivalent absorbing states (CC). Each route can be characterized by a crossover exponent, which is found numerically as phi=2.1+/-0.1 (SB), 4.6+/-0.2 (CB), and 2.9+/-0.1 (CC), respectively. The difference between the SB and CB crossover can be understood easily in the domain wall language, while the CC crossover involves an additional critical singularity in the auxiliary field density with the memory effect to identify itself independent.

Absorbing phase transitions in deterministic fixed-energy sandpile models.

We investigate the origin of the difference, which was noticed by Fey et al. [Phys. Rev. Lett. 104, 145703 (2010)PRLTAO0031-900710.1103/PhysRevLett.104.145703], between the steady state density of an Abelian sandpile model (ASM) and the transition point of its corresponding deterministic fixed-energy sandpile model (DFES). Being deterministic, the configuration space of a DFES can be divided into two disjoint classes such that every configuration in one class should evolve into one of absorbing states, whereas no configurations in the other class can reach an absorbing state. Since the two classes are separated in terms of toppling dynamics, the system can be made to exhibit an absorbing phase transition (APT) at various points that depend on the initial probability distribution of the configurations. Furthermore, we show that in general the transition point also depends on whether an infinite-size limit is taken before or after the infinite-time limit. To demonstrate, we numerically study the two-dimensional DFES with Bak-Tang-Wiesenfeld toppling rule (BTW-FES). We confirm that there are indeed many thresholds. Nonetheless, the critical phenomena at various transition points are found to be universal. We furthermore discuss a microscopic absorbing phase transition, or a so-called spreading dynamics, of the BTW-FES, to find that the phase transition in this setting is related to the dynamical isotropic percolation process rather than self-organized criticality. In particular, we argue that choosing recurrent configurations of the corresponding ASM as an initial configuration does not allow for a nontrivial APT in the DFES.

Nontrivial critical crossover between directed percolation models: effect of infinitely many absorbing states.

At nonequilibrium phase transitions into absorbing (trapped) states, it is well known that the directed percolation (DP) critical scaling is shared by two classes of models with a single (S) absorbing state and with infinitely many (IM) absorbing states. We study the crossover behavior in one dimension, arising from a considerable reduction of the number of absorbing states (typically from the IM-type to the S -type DP models) by following two different (excitatory or inhibitory) routes which make the auxiliary field density abruptly jump at the crossover. Along the excitatory route, the system becomes overly activated even for an infinitesimal perturbation and its crossover becomes discontinuous. Along the inhibitory route, we find a continuous crossover with universal crossover exponent phi approximately=1.78(6), which is argued to be equal to nu||, the relaxation time exponent of the DP universality class on a general footing. This conjecture is also confirmed in the case of the directed Ising (parity-conserving) class. Finally, we discuss the effect of diffusion on the IM-type models and suggest an argument why diffusive models with some hybrid-type reactions should belong to the DP class.