Timescales of genetic and epigenetic inheritance

Yeast flocculation and its biotechnological relevance

Adhesion properties of microorganisms are crucial for many essential biological processes such as sexual reproduction, tissue or substrate invasion, biofilm formation and others. Most, if not all microbial adhesion phenotypes are controlled by factors such as nutrient availability or the presence of pheromones. One particular form of controlled cellular adhesion that occurs in liquid environments is a process of asexual aggregation of cells which is also referred to as flocculation. This process has been the subject of significant scientific and biotechnological interest because of its relevance for many industrial fermentation processes. Specifically adjusted flocculation properties of industrial microorganisms could indeed lead to significant improvements in the processing of biotechnological fermentation products such as foods, biofuels and industrially produced peptides. This review briefly summarises our current scientific knowledge on the regulation of flocculation-related phenotypes, their importance for different biotechnological industries, and possible future applications for microorganisms with improved flocculation properties.

Short-term memory in gene induction reveals the regulatory principle behind stochastic IL-4 expression

Combining experiments on primary T cells and mathematical modeling, we characterized the stochastic expression of the interleukin-4 cytokine gene in its physiologic context, showing that a two-step model of transcriptional regulation acting on chromatin rearrangement and RNA polymerase recruitment accounts for the level, kinetics, and population variability of expression.

A rate-limiting step upstream of transcription initiation, but occurring at the level of an individual allele, controls whether the interleukin-4 gene is expressed during antigenic stimulation, suggesting that the observed stochasticity of expression is linked to the dynamics of chromatin rearrangement.

The computational analysis predicts that the probability to re-express an interleukin-4 gene that has been expressed once is transiently increased. In support, we experimentally demonstrate a short-term memory for interleukin-4 expression at the predicted time scale of several days.

The model provides a unifying framework that accounts for both graded and binary modes of gene regulation. Graded changes in expression level can be achieved by controlling transcription initiation, whereas binary regulation acts at the level of chromatin rearrangement and is targeted during the differentiation of T cells that specialize in interleukin-4 production.

Cell populations are typically heterogeneous with respect to protein expression even when clonally derived from a single progenitor. In bacteria and yeast, such heterogeneity has been shown to be due to intrinsically stochastic dynamics of gene expression (Raj and van Oudenaarden, 2008). Thus, cross-population heterogeneity may be an unavoidable by-product of random fluctuations in molecular interactions (Raser and O'Shea, 2004; Pedraza and van Oudenaarden, 2005). The phenotypic variability deriving from it may also be beneficial for cell function, differentiation, or adaptation to changing environments (Chang et al, 2008; Feinerman et al, 2008; Losick and Desplan, 2008). However, little is known about how gene-expression variability is caused in mammalian cells.

Two principal modes of gene regulation have been identified: graded and binary. In the graded mode, transcriptional regulators can tune the level of a gene product in a continuous manner (Hazzalin and Mahadevan, 2002). In the binary mode, the gene is expressed at an invariant level, whereas its probability of being expressed in a given cell is regulated, so that the gene has discrete ‘on' and ‘off' states (Walters et al, 1995; Hume, 2000; Biggar and Crabtree, 2001). In humans and mice, cytokine genes are expressed in a binary manner (Bix and Locksley, 1998; Riviere et al, 1998; Hu-Li et al, 2001; Apostolou and Thanos, 2008). A particularly well-studied case is the interleukin-4 (il4) gene that is critical for antibody-based immune responses. This gene is expressed by antigen-stimulated T cells initially with low probability, so that in most IL-4-positive cells only one allele is active (Bix and Locksley, 1998; Riviere et al, 1998). The expressed allele is not imprinted but chosen stochastically during each cell stimulation (Hu-Li et al, 2001).

Here, we have studied the dynamics of IL-4 expression quantitatively. Primary murine CD4⁺ T cells have been differentiated uniformly into type-2 T-helper (Th2) cells that express the lineage-specifying transcription factor (TF) Gata-3 and are competent to activate the il4 gene upon challenge with antigen. Using T cells heterozygous for an il4 wild-type allele and an il4 allele with GFP knock-in after the promoter, the alleles are found to be expressed stochastically and in an uncorrelated manner (Figure 2A; Hu-Li et al, 2001). To account for the observed stochastic dynamics of IL-4 expression, we considered a basic model of gene transcription, mRNA translation, turnover, and protein secretion (Figure 2B). However, our experimental estimates of the intracellular life times of IL-4 mRNA and protein (∼1 h) and their absolute numbers (mRNA∼10³, protein∼10⁵) rule out random fluctuations in transcription, translation as well as mRNA and protein turnover as an explanation for the observed stochastic properties of IL-4 expression (Thattai and van Oudenaarden, 2001; Paulsson, 2004).

As il4 is known to be strongly regulated at the chromatin level (Ansel et al, 2006), we included in the model a reversible step of chromatin opening that is permissive for transcription (Figure 2C and D). Both chromatin opening and transcription initiation are driven by TFs that are transiently activated during the antigen stimulus, with NFAT1 playing a prominent role (Agarwal et al, 2000; Avni et al, 2002; Guo et al, 2004). The model accounts for the kinetics of NFAT1 TF activity (Figure 2E) (Loh et al, 1996). Using a best-fit procedure for estimating the kinetics of the chromatin transition and TF activity from experimental data, we found that the model accurately reproduces the distribution of IL-4 expression within the cell population over the entire time course of a stimulation (Figure 3A). At the same time, it accounts for the measured kinetics of IL-4 mRNA, intracellular and secreted protein (Figure 3B). Additional data show that the model can also explain IL-4 expression at different stages of Th2 differentiation and upon pharmacological inhibition of NFAT1 activity. In each case, the model predicts a slow and stochastic chromatin opening (Step 1 in Figure 2C) that is the limiting step for the activation of the gene.

The slowness of chromatin opening inferred by the model implies an extended lifetime of the open chromatin state (several days), which lasts longer than TF activity during antigenic stimulation (several hours). This indicates that acute IL-4 expression is terminated by the cessation of TF activity (Step 2 in Figure 2C), rather than by the closing of the chromatin (Step 1). In support of this prediction, we observed an elevated fraction of IL-4-producing cells after secondary stimulations administered within a few days of the primary stimulus. Consistent with the model, this elevation disappeared with a half-life of ∼3 days (Figure 4B). To test whether this ‘short-term memory' for activation of the il4 gene is indeed due to the IL-4 producers in the primary stimulation, we sorted stimulated Th2 cells into viable IL-4-producing and non-producing fractions using the cytokine secretion assay (Ouyang et al, 2000) and cultured them separately for different resting periods. The probability of IL-4 re-expression in the positive-sorted cells was consistently larger than in negative-sorted cells and decreased progressively over several days (Figure 4C). By contrast, the sorted IL-4 negative cells exhibited a constant induction probability indistinguishable from the unsorted population. This behavior was not due to differential cell proliferation in the sorted populations or different success of Th2 differentiation. Moreover, using heterozygous il4-wild-type/il4-gfp cells, and sorting for expression of the wild-type allele, we observed that expression of the il4-gfp allele was similar in IL-4-positive and negative sorted fractions. Taken together, these findings imply that stochastic, slow chromatin changes at individual il4 genes govern the binary expression pattern of this cytokine.

In conclusion, we propose an experimentally based model of inducible gene expression where strong stochasticity arises from slow (hours to days) chromatin opening and closing transitions, rather than being due to small numbers of mRNA or protein molecules or transcriptional bursting (Raj et al, 2006). This rate-limiting step upstream of transcription initiation (which may entail several interacting epigenetic processes) naturally gives rise to a binary expression pattern of the gene. By contrast, regulation at the level of transcription initiation can have a graded effect on the expression level. We provide evidence that both binary and graded regulation can occur for the il4 gene. Physiological regulation of il4 seems to be mainly binary, thus enabling a dose–response within a population while producing an unequivocal all-or-none signal at the single-cell level.

Although cell-to-cell variability has been recognized as an unavoidable consequence of stochasticity in gene expression, it may also serve a functional role for tuning physiological responses within a cell population. In the immune system, remarkably large variability in the expression of cytokine genes has been observed in homogeneous populations of lymphocytes, but the underlying molecular mechanisms are incompletely understood. Here, we study the interleukin-4 gene (il4) in T-helper lymphocytes, combining mathematical modeling with the experimental quantification of expression variability and critical parameters. We show that a stochastic rate-limiting step upstream of transcription initiation, but acting at the level of an individual allele, controls il4 expression. Only a fraction of cells reaches an active, transcription-competent state in the transient time window determined by antigen stimulation. We support this finding by experimental evidence of a previously unknown short-term memory that was predicted by the model to arise from the long lifetime of the active state. Our analysis shows how a stochastic mechanism acting at the chromatin level can be integrated with transcriptional regulation to quantitatively control cell-to-cell variability.

Regulation of phenotypic variability by a threshold-based mechanism underlies bacterial persistence

In the face of antibiotics, bacterial populations avoid extinction by harboring a subpopulation of dormant cells that are largely drug insensitive. This phenomenon, termed "persistence," is a major obstacle for the treatment of a number of infectious diseases. The mechanism that generates both actively growing as well as dormant cells within a genetically identical population is unknown. We present a detailed study of the toxin-antitoxin module implicated in antibiotic persistence of Escherichia coli. We find that bacterial cells become dormant if the toxin level is higher than a threshold, and that the amount by which the threshold is exceeded determines the duration of dormancy. Fluctuations in toxin levels above and below the threshold result in coexistence of dormant and growing cells. We conclude that toxin-antitoxin modules in general represent a mixed network motif that can serve to produce a subpopulation of dormant cells and to supply a mechanism for regulating the frequency and duration of growth arrest. Toxin-antitoxin modules thus provide a natural molecular design for implementing a bet-hedging strategy.

Chromatin as a potential carrier of heritable information

Organisms with the same genome can inherit information in addition to that encoded in the DNA sequence-this is known as epigenetic inheritance. Epigenetic inheritance is responsible for many of the phenotypic differences between different cell types in multicellular organisms. Work by many investigators over the past decades has suggested that a great deal of epigenetic information might be carried in the pattern of post-translational modifications of the histone proteins, although this is not as well established as many believe. For example, it is unclear whether and how the histones, which are displaced from the chromosome during passage of the replication fork and are often exchanged from the DNA template at other times, carry information from one cellular generation to the next. Here, we briefly review the evidence that some chromatin states are indeed heritable, and then focus on the mechanistic challenges that remain in order to understand how this inheritance can be achieved.

Rapid expansion and functional divergence of subtelomeric gene families in yeasts

BACKGROUND

Subtelomeres, regions proximal to telomeres, exhibit characteristics unique to eukaryotic genomes. Genes residing in these loci are subject to epigenetic regulation and elevated rates of both meiotic and mitotic recombination. However, most genome sequences do not contain assembled subtelomeric sequences, and, as a result, subtelomeres are often overlooked in comparative genomics.

RESULTS

We studied the evolution and functional divergence of subtelomeric gene families in the yeast lineage. Our computational results show that subtelomeric families are evolving and expanding much faster than families that do not contain subtelomeric genes. Focusing on three related subtelomeric MAL gene families involved in disaccharide metabolism that show typical patterns of rapid expansion and evolution, we show experimentally how frequent duplication events followed by functional divergence yield novel alleles that allow the metabolism of different carbohydrates.

CONCLUSIONS

Taken together, our computational and experimental analyses show that the extraordinary instability of eukaryotic subtelomeres supports rapid adaptation to novel niches by promoting gene recombination and duplication followed by functional divergence of the alleles.

Transgenerational inheritance and resetting of stress-induced loss of epigenetic gene silencing in Arabidopsis

Plants, as sessile organisms, need to sense and adapt to heterogeneous environments and have developed sophisticated responses by changing their cellular physiology, gene regulation, and genome stability. Recent work demonstrated heritable stress effects on the control of genome stability in plants--a phenomenon that was suggested to be of epigenetic nature. Here, we show that temperature and UV-B stress cause immediate and heritable changes in the epigenetic control of a silent reporter gene in Arabidopsis. This stress-mediated release of gene silencing correlated with pronounced alterations in histone occupancy and in histone H3 acetylation but did not involve adjustments in DNA methylation. We observed transmission of stress effects on reporter gene silencing to non-stressed progeny, but this effect was restricted to areas consisting of a small number of cells and limited to a few non-stressed progeny generations. Furthermore, stress-induced release of gene silencing was antagonized and reset during seed aging. The transient nature of this phenomenon highlights the ability of plants to restrict stress-induced relaxation of epigenetic control mechanisms, which likely contributes to safeguarding genome integrity.

A LINE-1 component to human aging: do LINE elements exact a longevity cost for evolutionary advantage?

Advancing age remains the largest risk factor for devastating diseases, such as heart disease, stroke, and cancer. The mechanisms by which advancing age predisposes to disease are now beginning to unfold, due in part, to genetic and environmental manipulations of longevity in lower organisms. Converging lines of evidence suggest that DNA damage may be a final common pathway linking several proposed mechanisms of aging. The present review forwards a theory for an additional aging pathway that involves modes of inherent genetic instability. Long interspersed nuclear elements (LINEs) are endogenous non-LTR retrotransposons that compose about 20% of the human genome. The LINE-1 (L1) gene products, ORF1p and ORF2p, possess mRNA binding, endonuclease, and reverse transcriptase activity that enable retrotransposition. While principally active only during embryogenesis, L1 transcripts are detected in adult somatic cells under certain conditions. The present hypothesis proposes that L1s act as an 'endogenous clock', slowly eroding genomic integrity by competing with the organism's double-strand break repair mechanism. Thus, while L1s are an accepted mechanism of genetic variation fueling evolution, it is proposed that longevity is negatively impacted by somatic L1 activity. The theory predicts testable hypotheses about the relationship between L1 activity, DNA repair, healthy aging, and longevity.

Epigenomic plasticity within populations: its evolutionary significance and potential

Epigenetics has progressed rapidly from an obscure quirk of heredity into a data-heavy 'omic' science. Our understanding of the molecular mechanisms of epigenomic regulation, and the extent of its importance in nature, are far from complete, but in spite of such drawbacks, population-level studies are extremely valuable: epigenomic regulation is involved in several processes central to evolutionary biology including phenotypic plasticity, evolvability and the mediation of intragenomic conflicts. The first studies of epigenomic variation within populations suggest high levels of phenotypically relevant variation, with the patterns of epigenetic regulation varying between individuals and genome regions as well as with environment. Epigenetic mechanisms appear to function primarily as genome defences, but result in the maintenance of plasticity together with a degree of buffering of developmental programmes; periodic breakdown of epigenetic buffering could potentially cause variation in rates of phenotypic evolution.

Measuring behavior in mice with chronic stress depression paradigm

Many studies with chronic stress, a common depression paradigm, lead to inconsistent behavioral results. We are introducing a new model of stress-induced anhedonia, which provides more reproducible induction and behavioral measuring of depressive-like phenotype in mice. First, a 4-week stress procedure induces anhedonia, defined by decreased sucrose preference, in the majority of but not all C57BL/6 mice. The remaining 30-50% non-anhedonic animals are used as an internal control for stress effects that are unrelated to anhedonia. Next, a modified sucrose test enables the detection of inter-individual differences in mice. Moreover, testing under dimmed lighting precludes behavioral artifacts caused by hyperlocomotion, a major confounding factor in stressed mice. Finally, moderation of the stress load increases the reproducibility of anhedonia induction, which otherwise is difficult to provide because of inter-batch variability in laboratory mice. We believe that our new mouse model overcomes some major difficulties in measuring behavior with chronic stress depression models.

Environmentally induced phenotypes and DNA methylation: how to deal with unpredictable conditions until the next generation and after

Organisms often respond to environmental changes by producing alternative phenotypes. Epigenetic processes such as DNA methylation may contribute to environmentally induced phenotypic variation by modifying gene expression. Changes in DNA methylation, unlike DNA mutations, can be influenced by the environment; they are stable at the time scale of an individual and present different levels of heritability. These characteristics make DNA methylation a potentially important molecular process to respond to environmental change. The aim of this review is to present the implications of DNA methylation on phenotypic variations driven by environmental changes. More specifically, we explore epigenetic concepts concerning phenotypic change in response to the environment and heritability of DNA methylation, namely the Baldwin effect and genetic accommodation. Before addressing this point, we report major differences in DNA methylation across taxa and the role of this modification in producing and maintaining environmentally induced phenotypic variation. We also present the different methods allowing the detection of methylation polymorphism. We believe this review will be helpful to molecular ecologists, in that it highlights the importance of epigenetic processes in ecological and evolutionary studies.

The role of REST in transcriptional and epigenetic dysregulation in Huntington's disease

Huntington's disease (HD) is a devastating disorder that affects approximately 1 in 10,000 people and is accompanied by neuronal dysfunction and neurodegeneration. HD manifests as a progressive chorea, a decline in mental abilities accompanied by behavioural, emotional and psychiatric problems followed by, dementia, and ultimately, death. The molecular pathology of HD is complex but includes widespread transcriptional dysregulation. Although many transcriptional regulatory molecules have been implicated in the pathogenesis of HD, a growing body of evidence points to the pivotal role of RE1 Silencing Transcription Factor (REST). In HD, REST, translocates from the cytoplasm to the nucleus in neurons resulting in repression of key target genes such as BDNF. Since these original observations, several thousand direct target genes of REST have been identified, including numerous non-coding RNAs including both microRNAs and long non-coding RNAs, several of which are dysregulated in HD. More recently, evidence is emerging that hints at epigenetic abnormalities in HD brain. This in turn, promotes the notion that targeting the epigenetic machinery may be a useful strategy for treatment of some aspects of HD. REST also recruits a host of histone and chromatin modifying activities that can regulate the local epigenetic signature at REST target genes. Collectively, these observations present REST as a hub that coordinates transcriptional, posttranscriptional and epigenetic programmes, many of which are disrupted in HD. We identify several spokes emanating from this REST hub that may represent useful sites to redress REST dysfunction in HD.

Oceanographic and biogeochemical insights from diatom genomes

Diatoms are the most successful group of eukaryotic phytoplankton in the modern ocean and have risen to dominance relatively quickly over the last 100 million years. Recently completed whole genome sequences from two species of diatom, Thalassiosira pseudonana and Phaeodactylum tricornutum, have revealed a wealth of information about the evolutionary origins and metabolic adaptations that have led to their ecological success. A major finding is that they have incorporated genes both from their endosymbiotic ancestors and by horizontal gene transfer from marine bacteria. This unique melting pot of genes encodes novel capacities for metabolic management, for example, allowing the integration of a urea cycle into a photosynthetic cell. In this review we show how genome-enabled approaches are being leveraged to explore major phenomena of oceanographic and biogeochemical relevance, such as nutrient assimilation and life histories in diatoms. We also discuss how diatoms may be affected by climate change-induced alterations in ocean processes.

Intraclonal protein expression heterogeneity in recombinant CHO cells

Therapeutic glycoproteins have played a major role in the commercial success of biotechnology in the post-genomic era. But isolating recombinant mammalian cell lines for large-scale production remains costly and time-consuming, due to substantial variation and unpredictable stability of expression amongst transfected cells, requiring extensive clone screening to identify suitable high producers. Streamlining this process is of considerable interest to industry yet the underlying phenomena are still not well understood. Here we examine an antibody-expressing Chinese hamster ovary (CHO) clone at single-cell resolution using flow cytometry and vectors, which couple light and heavy chain transcription to fluorescent markers. Expression variation has traditionally been attributed to genetic heterogeneity arising from random genomic integration of vector DNA. It follows that single cell cloning should yield a homogeneous cell population. We show, in fact, that expression in a clone can be surprisingly heterogeneous (standard deviation 50 to 70% of the mean), approaching the level of variation in mixed transfectant pools, and each antibody chain varies in tandem. Phenotypic variation is fully developed within just 18 days of cloning, yet is not entirely explained by measurement noise, cell size, or the cell cycle. By monitoring the dynamic response of subpopulations and subclones, we show that cells also undergo slow stochastic fluctuations in expression (half-life 2 to 11 generations). Non-genetic diversity may therefore play a greater role in clonal variation than previously thought. This also has unexpected implications for expression stability. Stochastic gene expression noise and selection bias lead to perturbations from steady state at the time of cloning. The resulting transient response as clones reestablish their expression distribution is not ordinarily accounted for but can contribute to declines in median expression over timescales of up to 50 days. Noise minimization may therefore be a novel strategy to reduce apparent expression instability and simplify cell line selection.

Epigenetics: molecular mechanisms and implications for disease

Epigenetics is rising to prominence in biology as a mechanism by which environmental factors have intermediate-term effects on gene expression without changing the underlying genetic sequence. This can occur through the selective methylation of DNA bases and modification of histones. There are wide-ranging implications for the gene-environment debate and epigenetic mechanisms are causing a reevaluation of many traditional concepts such as heritability. The reversible nature of epigenetics also provides plausible treatment or prevention prospects for diseases previously thought hard-coded into the genome. Here, we consider how growing knowledge of epigenetics is altering our understanding of biology and medicine, and its implications for future research.

Promoter architecture and the evolvability of gene expression

Evolutionary changes in gene expression are a main driver of phenotypic evolution. In yeast, genes that have rapidly diverged in expression are associated with particular promoter features, including the presence of a TATA box, a nucleosome-covered promoter and unstable tracts of tandem repeats. Here, we discuss how these promoter properties may confer an inherent capacity for flexibility of expression.

Genetic and epigenetic mechanisms underlying cell-surface variability in protozoa and fungi

Eukaryotic microorganisms have evolved ingenious mechanisms to generate variability at their cell surface, permitting differential adherence, rapid adaptation to changing environments, and evasion of immune surveillance. Fungi such as Saccharomyces cerevisiae and the pathogen Candida albicans carry a family of mucin and adhesin genes that allow adhesion to various surfaces and tissues. Trypanosoma cruzi, T. brucei, and Plasmodium falciparum likewise contain large arsenals of different cell surface adhesion genes. In both yeasts and protozoa, silencing and differential expression of the gene family results in surface variability. Here, we discuss unexpected similarities in the structure and genomic location of the cell surface genes, the role of repeated DNA sequences, and the genetic and epigenetic mechanisms-all of which contribute to the remarkable cell surface variability in these highly divergent microbes.

Non-genetic cell-to-cell variability and the consequences for pharmacology

Recent advances in single-cell assays have focused attention on the fact that even members of a genetically identical group of cells or organisms in identical environments can exhibit variability in drug sensitivity, cellular response, and phenotype. Underlying much of this variability is stochasticity in gene expression, which can produce unique proteomes even in genetically identical cells. Here we discuss the consequences of non-genetic cell-to-cell variability in the cellular response to drugs and its potential impact for the treatment of human disease.

Tracking lineages of single cells in lines using a microfluidic device

Cells within a genetically identical population exhibit phenotypic variation that in some cases can persist across multiple generations. However, information about the temporal variation and familial dependence of protein levels remains hidden when studying the population as an ensemble. To correlate phenotypes with the age and genealogy of single cells over time, we developed a microfluidic device that enables us to track multiple lineages in parallel by trapping single cells and constraining them to grow in lines for as many as 8 divisions. To illustrate the utility of this method, we investigate lineages of cells expressing one of 3 naturally regulated proteins, each with a different representative expression behavior. Within lineages deriving from single cells, we observe genealogically related clusters of cells with similar phenotype; cluster sizes vary markedly among the 3 proteins, suggesting that the time scale of phenotypic persistence is protein-specific. Growing lines of cells also allows us to dynamically track temporal fluctuations in protein levels at the same time as pedigree relationships among the cells as they divide in the chambers. We observe bursts in expression levels of the heat shock protein Hsp12-GFP that occur simultaneously in mother and daughter cells. In contrast, the ribosomal protein Rps8b-GFP shows relatively constant levels of expression over time. This method is an essential step toward understanding the time scales of phenotypic variation and correlations in phenotype among single cells within a population.

Epigenetic and conventional regulation is distributed among activators of FLO11 allowing tuning of population-level heterogeneity in its expression

Epigenetic switches encode their state information either locally, often via covalent modification of DNA or histones, or globally, usually in the level of a trans-regulatory factor. Here we examine how the regulation of cis-encoded epigenetic switches controls the extent of heterogeneity in gene expression, which is ultimately tied to phenotypic diversity in a population. We show that two copies of the FLO11 locus in Saccharomyces cerevisiae switch between a silenced and competent promoter state in a random and independent fashion, implying that the molecular event leading to the transition occurs locally at the promoter, in cis. We further quantify the effect of trans regulators both on the slow epigenetic transitions between a silenced and competent promoter state and on the fast promoter transitions associated with conventional regulation of FLO11. We find different classes of regulators affect epigenetic, conventional, or both forms of regulation. Distributing kinetic control of epigenetic silencing and conventional gene activation offers cells flexibility in shaping the distribution of gene expression and phenotype within a population.

In an uncertain and changing world, microbial populations with a diverse range of phenotypes may outperform a monolithic population. Over many generations, mutations can lead to genetic diversity in a population. However, microbes have strategies to generate such diversity quickly. For example, if multiple genes switch ON and OFF slowly, randomly, and independently of each other, then a large combination of gene expression states, and hence phenotypes, are possible. The different gene expression states do not involve changes in DNA sequence and are therefore epigenetically inherited. We show that the two copies of the FLO11 gene in S. cerevisiae can switch ON and OFF slowly and independently. In addition, we reveal a simple regulatory strategy by which cells can control the proportion of cells in different gene expression states. Because FLO11 encodes a cell-wall protein responsible for mediating cell–cell and cell–surface interactions, this control might literally allow natural populations to have a controllable fraction of cells “stick around” while the other fraction is easily washed away.

The evolution of reversible switches in the presence of irreversible mimics

Reversible phenotypic switching can be caused by a number of different mechanisms including epigenetic inheritance systems and DNA-based contingency loci. Previous work has shown that reversible switching systems may be favored by natural selection. Many switches can be characterized as "on/off" where the "off" state constitutes a temporary and reversible loss of function. Loss-of-function phenotypes corresponding to the "off" state can be produced in many different ways, all yielding identical fitness in the short term. In the long term, however, a switch-induced loss of function can be reversed, whereas many loss-of-function mutations, especially deletions, cannot. We refer to these loss-of-function mutations as "irreversible mimics" of the reversible switch. Here, we develop a model in which a reversible switch evolves in the presence of both irreversible mimics and metapopulation structure. We calculate that when the rate of appearance of irreversible mimics exceeds the migration rate, the evolved reversible switching rate will exceed the bet-hedging rate predicted by panmictic models.

Transgenerational epigenetic inheritance: prevalence, mechanisms, and implications for the study of heredity and evolution

This review describes new developments in the study of transgenerational epigenetic inheritance, a component of epigenetics. We start by examining the basic concepts of the field and the mechanisms that underlie epigenetic inheritance. We present a comprehensive review of transgenerational cellular epigenetic inheritance among different taxa in the form of a table, and discuss the data contained therein. The analysis of these data shows that epigenetic inheritance is ubiquitous and suggests lines of research that go beyond present approaches to the subject. We conclude by exploring some of the consequences of epigenetic inheritance for the study of evolution, while also pointing to the importance of recognizing and understanding epigenetic inheritance for practical and theoretical issues in biology.

Inheritance of acquired behaviour adaptations and brain gene expression in chickens

BACKGROUND

Environmental challenges may affect both the exposed individuals and their offspring. We investigated possible adaptive aspects of such cross-generation transmissions, and hypothesized that chronic unpredictable food access would cause chickens to show a more conservative feeding strategy and to be more dominant, and that these adaptations would be transmitted to the offspring.

METHODOLOGY/PRINCIPAL FINDINGS

Parents were raised in an unpredictable (UL) or in predictable diurnal light rhythm (PL, 12:12 h light:dark). In a foraging test, UL birds pecked more at freely available, rather than at hidden and more attractive food, compared to birds from the PL group. Female offspring of UL birds, raised in predictable light conditions without parental contact, showed a similar foraging behavior, differing from offspring of PL birds. Furthermore, adult offspring of UL birds performed more food pecks in a dominance test, showed a higher preference for high energy food, survived better, and were heavier than offspring of PL parents. Using cDNA microarrays, we found that the differential brain gene expression caused by the challenge was mirrored in the offspring. In particular, several immunoglobulin genes seemed to be affected similarly in both UL parents and their offspring. Estradiol levels were significantly higher in egg yolk from UL birds, suggesting one possible mechanism for these effects.

CONCLUSIONS/SIGNIFICANCE

Our findings suggest that unpredictable food access caused seemingly adaptive responses in feeding behavior, which may have been transmitted to the offspring by means of epigenetic mechanisms, including regulation of immune genes. This may have prepared the offspring for coping with an unpredictable environment.

Maternal obesity, inflammation, and fetal skeletal muscle development

Maternal obesity coupled with Western-style high-energy diets represents a special problem that can result in poor fetal development, leading to harmful, persistent effects on offspring, including predisposition to obesity and type 2 diabetes. Mechanisms linking maternal obesity to the increased incidence of obesity and other metabolic diseases in offspring remain poorly defined. Because skeletal muscle is the principal site for glucose and fatty acid utilization and composes 40%-50% of total body mass, changes in the properties of offspring skeletal muscle and its mass resulting from maternal obesity may be responsible for the increase in type 2 diabetes and obesity. Fetal stage is crucial for skeletal muscle development because there is no net increase in the muscle fiber number after birth. Fetal skeletal muscle development involves myogenesis, adipogenesis, and fibrogenesis, which are all derived from mesenchymal stem cells (MSCs). Shifting commitment of MSCs from myogenesis to adipogenesis and fibrogenesis will result in increased intramuscular fat and connective tissue, as well as reduced numbers of muscle fiber and/or diameter, all of which have lasting negative effects on offspring muscle function and properties. Maternal obesity leads to low-grade inflammation, which changes the commitment of MSCs in fetal muscle through several possible mechanisms: 1) inflammation downregulates wingless and int (WNT) signaling, which attenuates myogenesis; 2) inflammation inhibits AMP-activated protein kinase, which promotes adipogenesis; and 3) inflammation may induce epigenetic modification through polycomb group proteins. More studies are needed to further explore the underlying mechanisms associated with maternal obesity, inflammation, and the commitment of MSCs.

Unstable tandem repeats in promoters confer transcriptional evolvability

Relative to most regions of the genome, tandemly repeated DNA sequences display a greater propensity to mutate. A search for tandem repeats in the Saccharomyces cerevisiae genome revealed that the nucleosome-free region directly upstream of genes (the promoter region) is enriched in repeats. As many as 25% of all gene promoters contain tandem repeat sequences. Genes driven by these repeat-containing promoters show significantly higher rates of transcriptional divergence. Variations in repeat length result in changes in expression and local nucleosome positioning. Tandem repeats are variable elements in promoters that may facilitate evolutionary tuning of gene expression by affecting local chromatin structure.

Of elections and cell-death decisions

A new study in the journal Nature (Spencer et al., 2009) argues that cell-to-cell variation in the decision to undergo apoptosis is not due to genetic, epigenetic, or cell-cycle differences, nor due to random molecular noise, but instead is determined by differences in protein abundances.

Non-genetic origins of cell-to-cell variability in TRAIL-induced apoptosis

In microorganisms, noise in gene expression gives rise to cell-to-cell variability in protein concentrations1–7. In mammalian cells, protein levels also vary8–10 and individual cells differ widely in responsiveness to uniform physiological stimuli11–15. In the case of apoptosis mediated by TRAIL (TNF related apoptosis-inducing ligand) it is common for some cells in a clonal population to die while others survive – a striking divergence in cell fate. Among cells that die, the time between TRAIL exposure and caspase activation is highly variable. Here we image sister cells expressing reporters of caspase activation and mitochondrial outer membrane permeabilisation (MOMP) following exposure to TRAIL. We show that naturally occurring differences in the levels or states of proteins regulating receptor-mediated apoptosis are the primary causes of cell-to-cell variability in the timing and probability of death. Protein state is transmitted from mother to daughter, giving rise to transient heritability in fate, but protein synthesis promotes rapid divergence so that sister cells soon become no more similar to each other than pairs of cells chosen at random. Our results have implications for understanding “fractional killing” of tumor cells following exposure to chemotherapy, and for variability in mammalian signal transduction in general.

Limited tissue culture-induced mutations and linked epigenetic modifications in F hybrids of sorghum pure lines are accompanied by increased transcription of DNA methyltransferases and 5-methylcytosine glycosylases

In plant tissue culture, developmental disturbance and mutagenic factors are involved in channeling an individual totipotent cell to an intact plant. Comparing a pair of sorghum reciprocal F(1) hybrids with their parental pure lines revealed a dramatic difference in the occurrence of both genetic and DNA methylation alterations in the respective regenerated plants. In contrast to those of the pure lines, regenerated plants of hybrids exhibit significantly enhanced genetic and epigenetic stability. The genetic changes detected by amplified fragment length polymorphism and the DNA methylation alterations detected by methylation-sensitive amplified polymorphism are intimately correlated with each other, suggesting a common mechanism underlying both kinds of instabilities. Markedly altered transcription of genes encoding four putative sorghum DNA methyltransferases and two 5-methylcytosine glycosylases with nucleotide sequences orthologous to Arabidopsis counterparts was induced by tissue culture. The steady-state transcript levels of these genes were negatively correlated with genetic and methylation alterations. A salient observation is that tissue culture-induced transcription of genes encoding DNA methyltransferases and 5-methylcytosine glycosylases in calli and/or regenerated plants of the hybrids was remarkably coordinated, but is largely uncoordinated and stochastically altered in calli and/or regenerated plants of the pure lines. We suggest that the uncoordinated regulation of expression of DNA methyltransferases and 5-methylcytosine glycosylases is a major cause of the high incidence of genetic and DNA methylation alterations in cultures of pure lines, but coordinated up-regulated expression of these enzymes in cultures of the F(1) hybrids fortified their genetic and epigenetic stability.

The importance of being persistent: heterogeneity of bacterial populations under antibiotic stress

While the DNA sequence is largely responsible for transmitting phenotypic traits over evolutionary time, organisms are also considerably affected by phenotypic variations that persist for more than one generation, with no direct change in the organisms' DNA sequence. In contrast to genetic variation, which is passed on over many generations, the phenotypic variation generated by nongenetic mechanisms is difficult to study due to the inherently limited life time of states that are not encoded in the DNA sequence, but makes it possible for the 'memory' of past environments to influence future organisms. One striking example of phenotypic variation is the phenomenon of bacterial persistence, whereby genetically identical bacterial populations respond heterogeneously to antibiotic treatment. Our aim is to review several experimental and theoretical approaches to the study of persistence. We define persistence as a characteristic of a heterogeneous bacterial population that is taken as a generic example through which we illustrate the approach and study the dynamics of population variability. The clinical and evolutionary implications of persistence are discussed in light of the mathematical description. This approach should be of relevance to the study of other phenomena in which nongenetic variability is involved, such as cellular differentiation or the response of cancer cells to treatment.

Bistability, epigenetics, and bet-hedging in bacteria

Clonal populations of microbial cells often show a high degree of phenotypic variability under homogeneous conditions. Stochastic fluctuations in the cellular components that determine cellular states can cause two distinct subpopulations, a property called bistability. Phenotypic heterogeneity can be readily obtained by interlinking multiple gene regulatory pathways, effectively resulting in a genetic logic-AND gate. Although switching between states can occur within the cells' lifetime, cells can also pass their cellular state over to the next generation by a mechanism known as epigenetic inheritance and thus perpetuate the phenotypic state. Importantly, heterogeneous populations can demonstrate increased fitness compared with homogeneous populations. This suggests that microbial cells employ bet-hedging strategies to maximize survival. Here, we discuss the possible roles of interlinked bistable networks, epigenetic inheritance, and bet-hedging in bacteria.

Epigenome dynamics: a quantitative genetics perspective

Classically, quantitative geneticists have envisioned DNA sequence variants as the only source of heritable phenotypes. This view should be revised in light of accumulating evidence for widespread epigenetic variation in natural and experimental populations. Here we argue that it is timely to consider novel experimental strategies and analysis models to capture the potentially dynamic interplay between chromatin and DNA sequence factors in complex traits.

Molecular circuits for associative learning in single-celled organisms

We demonstrate how a single-celled organism could undertake associative learning. Although to date only one previous study has found experimental evidence for such learning, there is no reason in principle why it should not occur. We propose a gene regulatory network that is capable of associative learning between any pre-specified set of chemical signals, in a Hebbian manner, within a single cell. A mathematical model is developed, and simulations show a clear learned response. A preliminary design for implementing this model using plasmids within Escherichia coli is presented, along with an alternative approach, based on double-phosphorylated protein kinases.

A collective mechanism for phase variation in biofilms

Understanding how microbes gather into biofilm communities and maintain diversity remains one of the central questions of microbiology, requiring an understanding of microbes as communal rather then individual organisms. Phase variation plays an integral role in the formation of diverse phenotypes within biofilms. We propose a collective mechanism for phase variation based on gene transfer agents, and apply the theory to predict the population structure and growth dynamics of a biofilm. Our results describe quantitatively recent experiments, with the only adjustable parameter being the rate of intercellular horizontal gene transfer. Our approach derives from a more general picture for the emergence of cooperation between microbes.

The EDGE hypothesis: epigenetically directed genetic errors in repeat-containing proteins (RCPs) involved in evolution, neuroendocrine signaling, and cancer

Trans-generational epigenetic phenomena, such as contamination with endocrine-disrupting chemicals (EDCs) that decrease fertility and the global methylation status of DNA in the offspring, are of great concern because they may affect health, particularly the health of children. However, of even greater concern is the possibility that trans-generational changes in the methylation status of the DNA might lead to permanent changes in the DNA sequence itself. By contaminating the environment with EDCs, mankind might be permanently affecting the health of future generations. In this section, we present evidence from our laboratory and others that trans-generational epigenetic changes in DNA might lead to mutations directed to genes encoding amino acid repeat-containing proteins (RCPs) that are important for adaptive evolution or cancer progression. Such epigenetic changes can be induced "naturally" by hormones or "unnaturally" by EDCs or environmental stress. To illustrate the phenomenon, we present new bioinformatic evidence that the only RCP ontological categories conserved from Drosophila to humans are "regulation of splicing," "regulation of transcription," and "regulation of synaptogenesis," which are classes of genes likely to be important for evolutionary processes. Based on that and other evidence, we propose a model for evolution that we call the EDGE (Epigenetically Directed Genetic Errors) hypothesis for the mechanism by which mutations are targeted at epigenetically modified "contingency genes" encoding RCPs. In the model, "epigenetic assimilation" of metastable epialleles of RCPs over many generations can lead to mutations directed to those genes, thereby permanently stabilizing the adaptive phenotype.

Plasticity comparisons between plants and animals: Concepts and mechanisms

This review attempts to present an integrated update of the issue of comparisons of phenotypic plasticity between plants and animals by presenting the problem and its integrated solutions via a whole-organism perspective within an evolutionary framework. Plants and animals differ in two important aspects: mobility and longevity. These features can have important implications for plasticity, and plasticity may even have facilitated greater longevity in plants. Furthermore, somatic genetic mosaicism, intra-organismal selection, and genomic instability contribute to the maintenance of an adaptive phenotype that is especially relevant to long-lived plants. It is contended that a cross-kingdom phylogenetic examination of sensors, messengers and responses that constitute the plasticity repertoire would be more useful than dichotomizing the plant and animal kingdoms. Furthermore, physicochemical factors must be viewed cohesively in the signal reception and transduction pathways leading to plastic responses. Comparison of unitary versus modular organisms could also provide useful insights into the range of expected plastic responses. An integrated approach that combines evolutionary theory and evolutionary history with signal-response mechanisms will yield the most insights into phenotypic plasticity in all its forms.

Multicellular development and protein-protein interactions

The macroevolution of organs and tissues in higher plants and animals may have been contingent upon the expansion of numerous gene families encoding interacting proteins. For example, there are dozens of gene families encoding actin cytoskeletal proteins that elaborate intercellular structures influencing development. Once gene family members evolve compartmentalized expression, protein isovariants are free to coevolve new interacting partners that may be incompatible with other related protein networks. Ancient classes of actin isovariants and actin-binding proteins are clear examples of such coevolving networks. Ectopic expression and suppression studies were used to dissect these interactions. In higher plants, the ectopic expression of a reproductive actin isovariant in vegetative cell types causes aberrant reorganization of the F-actin cytoskeleton and bizarre development of most organs and tissues. In contrast, overexpression of vegetative actin in vegetative cell types has little effect. The extreme ectopic actin expression phenotypes are suppressed by the coectopic expression of reproductive profilin or actin depolymerizing factor (ADF/cofilin) isovariants, but not by the overexpression of vegetative profilin or ADF. These data provide evidence for the coevolution of organ-specific protein-protein interactions. Thus, understanding the contingent relationships between the evolution of organ-specific isovariant networks and organ origination may be key to explaining multicellular development.

Small RNA-directed epigenetic natural variation in Arabidopsis thaliana

Progress in epigenetics has revealed mechanisms that can heritably regulate gene function independent of genetic alterations. Nevertheless, little is known about the role of epigenetics in evolution. This is due in part to scant data on epigenetic variation among natural populations. In plants, small interfering RNA (siRNA) is involved in both the initiation and maintenance of gene silencing by directing DNA methylation and/or histone methylation. Here, we report that, in the model plant Arabidopsis thaliana, a cluster of approximately 24 nt siRNAs found at high levels in the ecotype Landsberg erecta (Ler) could direct DNA methylation and heterochromatinization at a hAT element adjacent to the promoter of FLOWERING LOCUS C (FLC), a major repressor of flowering, whereas the same hAT element in ecotype Columbia (Col) with almost identical DNA sequence, generates a set of low abundance siRNAs that do not direct these activities. We have called this hAT element MPF for Methylated region near Promoter of FLC, although de novo methylation triggered by an inverted repeat transgene at this region in Col does not alter its FLC expression. DNA methylation of the Ler allele MPF is dependent on genes in known silencing pathways, and such methylation is transmissible to Col by genetic crosses, although with varying degrees of penetrance. A genome-wide comparison of Ler and Col small RNAs identified at least 68 loci matched by a significant level of approximately 24 nt siRNAs present specifically in Ler but not Col, where nearly half of the loci are related to repeat or TE sequences. Methylation analysis revealed that 88% of the examined loci (37 out of 42) were specifically methylated in Ler but not Col, suggesting that small RNA can direct epigenetic differences between two closely related Arabidopsis ecotypes.

Invasion emerges from cancer cell adaptation to competitive microenvironments: quantitative predictions from multiscale mathematical models

In this review we summarize our recent efforts using mathematical modeling and computation to simulate cancer invasion, with a special emphasis on the tumor microenvironment. We consider cancer progression as a complex multiscale process and approach it with three single-cell-based mathematical models that examine the interactions between tumor microenvironment and cancer cells at several scales. The models exploit distinct mathematical and computational techniques, yet they share core elements and can be compared and/or related to each other. The overall aim of using mathematical models is to uncover the fundamental mechanisms that lend cancer progression its direction towards invasion and metastasis. The models effectively simulate various modes of cancer cell adaptation to the microenvironment in a growing tumor. All three point to a general mechanism underlying cancer invasion: competition for adaptation between distinct cancer cell phenotypes, driven by a tumor microenvironment with scarce resources. These theoretical predictions pose an intriguing experimental challenge: test the hypothesis that invasion is an emergent property of cancer cell populations adapting to selective microenvironment pressure, rather than culmination of cancer progression producing cells with the "invasive phenotype". In broader terms, we propose that fundamental insights into cancer can be achieved by experimentation interacting with theoretical frameworks provided by computational and mathematical modeling.

Using the SERV Applet to Detect Tandem Repeats in DNA Sequences and to Predict Their Variability

INTRODUCTIONTandem repeats (satellite repeats) are short stretches of DNA that are repeated head-to-tail. Tandem repeats mutate at rates that are between 100- and 10,000-fold greater than normal (point) mutation rates in the rest of the genome. As a consequence of these frequent mutation events, "homologous" tandem repeats in closely related species, strains, or even individuals in the same population often contain a different number of repeat units. This heterogeneity is extensively used in today's molecular forensics and genotyping research. However, while all repeats are unstable, precise mutation rates vary greatly between different repeat loci. This implies that not all tandem repeats are suited as markers for forensics, genotyping, or putative hypervariable functional modules. The SERV ("Sequence-Based Estimation of Repeats Variability") applet enables finding repeats in DNA sequences and estimating their variability. Hence, it can be used to select repeats that are suitable markers for genotyping or interesting candidates for functional studies.

Heritable stochastic switching revealed by single-cell genealogy

The partitioning and subsequent inheritance of cellular factors like proteins and RNAs is a ubiquitous feature of cell division. However, direct quantitative measures of how such nongenetic inheritance affects subsequent changes in gene expression have been lacking. We tracked families of the yeast Saccharomyces cerevisiae as they switch between two semi-stable epigenetic states. We found that long after two cells have divided, they continued to switch in a synchronized manner, whereas individual cells have exponentially distributed switching times. By comparing these results to a Poisson process, we show that the time evolution of an epigenetic state depends initially on inherited factors, with stochastic processes requiring several generations to decorrelate closely related cells. Finally, a simple stochastic model demonstrates that a single fluctuating regulatory protein that is synthesized in large bursts can explain the bulk of our results.

When cells divide, not only DNA but an entire pattern of gene expression can be passed from mother to daughter cell. Once cell division is complete, random processes cause this pattern to change, with closely related cells growing less similar over time. We measured inheritance of a dynamic gene-expression state in single yeast cells. We used an engineered network where individual cells switch between two semi-stable states (ON and OFF), even in a constant environment. Several generations after cells have physically separated, many pairs of closely related cells switch in near synchrony. We quantified this effect by measuring how likely a mother cell is to have switched given that the daughter cell has already switched. This yields a conditional probability distribution that is very different from the exponential one found in the entire population of switching cells. We measured the extent to which this correlation between switching cells persists by comparing our results with a model Poisson process. Together, these findings demonstrate the inheritance of a dynamic gene expression state whose post-division changes include both random factors arising from noise as well as correlated factors that originate in two related cells' shared history. Finally, we constructed a model that demonstrates that our major findings can be explained by burst-like fluctuations in the levels of a single regulatory protein.

When cells divide, each daughter cell inherits a share of the contents of the mother. If the contents include a regulatory system with a feedback loop, sister cells switch states in synchrony.

Bridging the gap: The developmental aspects of evolution

The commentaries onEvolution in Four Dimensionsreflect views ranging from total adherence to gene-centered neo-Darwinism, to the acceptance of non-genetic and Lamarckian processes in evolution. We maintain that genetic, epigenetic, behavioral, and cultural variations have all been significant, and that the developmental aspects of heredity and evolution are an important bridge that can unite seemingly conflicting research programs and different disciplines.

Sequence-based estimation of minisatellite and microsatellite repeat variability

Variable tandem repeats are frequently used for genetic mapping, genotyping, and forensics studies. Moreover, variation in some repeats underlies rapidly evolving traits or certain diseases. However, mutation rates vary greatly from repeat to repeat, and as a consequence, not all tandem repeats are suitable genetic markers or interesting unstable genetic modules. We developed a model, "SERV," that predicts the variability of a broad range of tandem repeats in a wide range of organisms. The nonlinear model uses three basic characteristics of the repeat (number of repeated units, unit length, and purity) to produce a numeric "VARscore" that correlates with repeat variability. SERV was experimentally validated using a large set of different artificial repeats located in the Saccharomyces cerevisiae URA3 gene. Further in silico analysis shows that SERV outperforms existing models and accurately predicts repeat variability in bacteria and eukaryotes, including plants and humans. Using SERV, we demonstrate significant enrichment of variable repeats within human genes involved in transcriptional regulation, chromatin remodeling, morphogenesis, and neurogenesis. Moreover, SERV allows identification of known and candidate genes involved in repeat-based diseases. In addition, we demonstrate the use of SERV for the selection and comparison of suitable variable repeats for genotyping and forensic purposes. Our analysis indicates that tandem repeats used for genotyping should have a VARscore between 1 and 3. SERV is publicly available from http://hulsweb1.cgr.harvard.edu/SERV/.

Neurotropic effects of venoms and other factors that promote prey acquisition

Mammals envenomed by either the Eastern diamondback rattlesnake (Crotalus adamanteus) or the cottonmouth (Agkistrodon piscivorus piscivorus) exhibit an immediate but transitory pupillar contraction, a parasympathomimetic effect mediated through the ciliary ganglion that can be prevented by a retrobulbar injection of anesthetic. The venom of the cottonmouth injected into the lymph spaces of the frog (Rana pipiens) produces an immediate and total collapse of the lung sacs. Applied locally to the surface, it produces a constriction that eventually collapses the entire sac. Tests of venoms and toxins from both anterior and posterior parts of the venom apparatus indicate that the lung-collapsing moiety originates in the accessory, not the main portion of the venom gland. This is the first example of a functional specialization within the whole structure. It seems that this factor is elaborated primarily in snakes that prey upon frogs, although insufficient data are available from this study to confirm this. In both reptile species, the predatory strike is accompanied by an immediate effect, perhaps mediated by the parasympathetic nervous system, designed to incapacitate the prey and facilitate capture. These effects cannot now be attributed to neurotoxins because the effect of the former is transitory (and not lethal) and neither has been purified sufficiently to determine potency or structure. Both take part in securing, but not killing, the prey, and both directly oppose the sympathetic nervous system "fright-fight/flight" response. Evidence is presented to support the possibility that known epigenetic mechanisms are capable of effecting heritable changes in gene expression that could allow for the development of factors that facilitate prey acquisition and promote rapid adaptation to environmental change.