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1.  Coordination of Cell Proliferation and Cell Fate Determination by CES-1 Snail 
PLoS Genetics  2013;9(10):e1003884.
The coordination of cell proliferation and cell fate determination is critical during development but the mechanisms through which this is accomplished are unclear. We present evidence that the Snail-related transcription factor CES-1 of Caenorhabditis elegans coordinates these processes in a specific cell lineage. CES-1 can cause loss of cell polarity in the NSM neuroblast. By repressing the transcription of the BH3-only gene egl-1, CES-1 can also suppress apoptosis in the daughters of the NSM neuroblasts. We now demonstrate that CES-1 also affects cell cycle progression in this lineage. Specifically, we found that CES-1 can repress the transcription of the cdc-25.2 gene, which encodes a Cdc25-like phosphatase, thereby enhancing the block in NSM neuroblast division caused by the partial loss of cya-1, which encodes Cyclin A. Our results indicate that CDC-25.2 and CYA-1 control specific cell divisions and that the over-expression of the ces-1 gene leads to incorrect regulation of this functional ‘module’. Finally, we provide evidence that dnj-11 MIDA1 not only regulate CES-1 activity in the context of cell polarity and apoptosis but also in the context of cell cycle progression. In mammals, the over-expression of Snail-related genes has been implicated in tumorigenesis. Our findings support the notion that the oncogenic potential of Snail-related transcription factors lies in their capability to, simultaneously, affect cell cycle progression, cell polarity and apoptosis and, hence, the coordination of cell proliferation and cell fate determination.
Author Summary
Animal development is a complex process and requires the coordination in space and time of various processes. These processes include the controlled production of cells, also referred to as ‘cell proliferation’, and the adoption by cells of specific fates, also referred to as ‘cell fate determination’. The observation that uncontrolled cell proliferation and cell fate determination contribute to conditions such as cancer, demonstrates that a precise coordination of these processes is not only important for development but for the prevention of disease throughout life. Snail-related transcription factors have previously been shown to be involved in the regulation of cell proliferation and cell fate determination. For example, the Caenorhabditis elegans Snail-related protein CES-1 affects cell fate determination in a specific cell lineage, the NSM (neurosecretory motorneuron) lineage. We now present evidence that CES-1 also controls cell proliferation in this lineage. Within a short period of time, CES-1 therefore coordinates cell proliferation and cell fate determination in one and the same lineage. Based on this finding, we propose that CES-1 is an important coordinator that is involved in the precise control - in space (NSM lineage) and time (<150 min) - of processes that are critical for animal development.
doi:10.1371/journal.pgen.1003884
PMCID: PMC3814331  PMID: 24204299
2.  Deletion of microRNA-80 Activates Dietary Restriction to Extend C. elegans Healthspan and Lifespan 
PLoS Genetics  2013;9(8):e1003737.
Caloric/dietary restriction (CR/DR) can promote longevity and protect against age-associated disease across species. The molecular mechanisms coordinating food intake with health-promoting metabolism are thus of significant medical interest. We report that conserved Caenorhabditis elegans microRNA-80 (mir-80) is a major regulator of the DR state. mir-80 deletion confers system-wide healthy aging, including maintained cardiac-like and skeletal muscle-like function at advanced age, reduced accumulation of lipofuscin, and extended lifespan, coincident with induction of physiological features of DR. mir-80 expression is generally high under ad lib feeding and low under food limitation, with most striking food-sensitive expression changes in posterior intestine. The acetyltransferase transcription co-factor cbp-1 and interacting transcription factors daf-16/FOXO and heat shock factor-1 hsf-1 are essential for mir-80(Δ) benefits. Candidate miR-80 target sequences within the cbp-1 transcript may confer food-dependent regulation. Under food limitation, lowered miR-80 levels directly or indirectly increase CBP-1 protein levels to engage metabolic loops that promote DR.
Author Summary
Dietary restriction, limitation of calorie intake with maintained vitamin and mineral support, can extend lifespan and protect against diseases of age across many species. Elaboration of molecular mechanisms that control dietary restriction in simple animal models may therefore inform on strategies to activate health-promoting metabolism to help address clinical challenges associated with aging and age-associated disease. We characterize a single Caenorhabditis elegans microRNA gene that keeps dietary restriction programs off when food is abundant. A mir-80 deletion exhibits beneficial features of dietary restriction regardless of food availability, including extended maintenance of mobility and cardiac-like muscle function later into life as well as lifespan extension. We identify three key longevity genes that are required for these benefits. We hypothesize that miR-80 is a core regulator by which diverse and intersecting metabolic pathways are coordinately regulated to respond to nutrient availability.
doi:10.1371/journal.pgen.1003737
PMCID: PMC3757059  PMID: 24009527
3.  The modular era of functional genomics 
Genome Biology  2003;4(5):317.
A report on the Keystone Symposium 'Functional Genomics: Global Analysis of Complex Biological Systems', Santa Fe, USA, 20-24 February 2003.
A report on the Keystone Symposium 'Functional Genomics: Global Analysis of Complex Biological Systems', Santa Fe, USA, 20-24 February 2003.
doi:10.1186/gb-2003-4-5-317
PMCID: PMC156581  PMID: 12734004
4.  The GATA Transcription Factor egl-27 Delays Aging by Promoting Stress Resistance in Caenorhabditis elegans 
PLoS Genetics  2012;8(12):e1003108.
Stress is a fundamental aspect of aging, as accumulated damage from a lifetime of stress can limit lifespan and protective responses to stress can extend lifespan. In this study, we identify a conserved Caenorhabditis elegans GATA transcription factor, egl-27, that is involved in several stress responses and aging. We found that overexpression of egl-27 extends the lifespan of wild-type animals. Furthermore, egl-27 is required for the pro-longevity effects from impaired insulin/IGF-1 like signaling (IIS), as reduced egl-27 activity fully suppresses the longevity of worms that are mutant for the IIS receptor, daf-2. egl-27 expression is inhibited by daf-2 and activated by pro-longevity factors daf-16/FOXO and elt-3/GATA, suggesting that egl-27 acts at the intersection of IIS and GATA pathways to extend lifespan. Consistent with its role in IIS signaling, we found that egl-27 is involved in stress response pathways. egl-27 expression is induced in the presence of multiple stresses, its targets are significantly enriched for many types of stress genes, and altering levels of egl-27 itself affects survival to heat and oxidative stress. Finally, we found that egl-27 expression increases between young and old animals, suggesting that increased levels of egl-27 in aged animals may act to promote stress resistance. These results identify egl-27 as a novel factor that links stress and aging pathways.
Author Summary
Stress is a fundamental aspect of aging, but it is unclear whether the molecular mechanisms underlying stress response become altered during normal aging and whether these alterations can affect the aging process. In this study, we found a GATA transcription factor called egl-27, whose targets are significantly enriched for age-dependent genes and stress response genes, and whose expression increases with age. In contrast to previous work describing factors that are causal for aging, we found that egl-27 activity is likely beneficial for survival since egl-27 overexpression extends lifespan. egl-27 promotes longevity by enhancing stress response; specifically, increased levels of egl-27 protect animals against heat stress, while reduced egl-27 activity impairs survival following heat and oxidative stress. These results suggest that aging is not simply a process of constant decline. Some factors, such as egl-27, are more active in old animals, working to restore organismal function and to improve survival.
doi:10.1371/journal.pgen.1003108
PMCID: PMC3521710  PMID: 23271974
5.  Seeing elegance in the gene regulatory networks of the worm 
Summary
There has been a recent explosion in the wealth of genomic data available to C. elegans researchers, as efforts to characterize gene expression and its regulators at a molecular level have borne significant fruit. Detailed measurement of gene expression at a variety of developmental stages, and in numerous individual tissues, has dramatically increased our understanding of cell-type-specific gene expression networks. Characterization of the targets of transcription factors, chromatin-binding proteins, and miRNAs has provided genome-wide insights into the mechanisms governing gene expression. Development of new techniques have allowed this characterization to begin to shift from whole-organism studies to tissue-, and even single-cell-level profiling, creating a first glimpse into gene regulatory circuits at the single-cell level in a living organism. Integration of these datasets has yielded novel insights into evolution, gene expression regulation, and the link between sequence and phenotype.
doi:10.1016/j.gde.2011.08.007
PMCID: PMC3224770  PMID: 21963133
6.  An Engineering Approach to Extending Lifespan in C. elegans 
PLoS Genetics  2012;8(6):e1002780.
We have taken an engineering approach to extending the lifespan of Caenorhabditis elegans. Aging stands out as a complex trait, because events that occur in old animals are not under strong natural selection. As a result, lifespan can be lengthened rationally using bioengineering to modulate gene expression or to add exogenous components. Here, we engineered longer lifespan by expressing genes from zebrafish encoding molecular functions not normally present in worms. Additionally, we extended lifespan by increasing the activity of four endogenous worm aging pathways. Next, we used a modular approach to extend lifespan by combining components. Finally, we used cell- and worm-based assays to analyze changes in cell physiology and as a rapid means to evaluate whether multi-component transgenic lines were likely to have extended longevity. Using engineering to add novel functions and to tune endogenous functions provides a new framework for lifespan extension that goes beyond the constraints of the worm genome.
Author Summary
We used bioengineering to extend the lifespan of C. elegans by expressing genes acting in critical aging pathways. We overexpressed five genes that act in endogenous worm aging pathways, as well as two genes from zebrafish encoding molecular functions not normally present in worms. For example, we used zebrafish genes to alter mitochondrial function and innate immunity in ways not normally available to C. elegans and extended worm lifespan by ∼40%. Next, we used a modular approach to extend lifespan by 130% by combining up to four components in the same strain. These results provide a platform to build worms having progressively longer lifespans. This project is conceptually similar to using engineering to increase the useful lifespan of a primitive machine (1931 Model T) using both parts from the model T as well as parts from a more advanced machine (2012 Toyota Corolla). Our results open the door to use engineering to go beyond the constraints of the C. elegans genome to extend its lifespan by adding non-native components.
doi:10.1371/journal.pgen.1002780
PMCID: PMC3380832  PMID: 22737090
7.  Down-Regulating Sphingolipid Synthesis Increases Yeast Lifespan 
PLoS Genetics  2012;8(2):e1002493.
Knowledge of the mechanisms for regulating lifespan is advancing rapidly, but lifespan is a complex phenotype and new features are likely to be identified. Here we reveal a novel approach for regulating lifespan. Using a genetic or a pharmacological strategy to lower the rate of sphingolipid synthesis, we show that Saccharomyces cerevisiae cells live longer. The longer lifespan is due in part to a reduction in Sch9 protein kinase activity and a consequent reduction in chromosomal mutations and rearrangements and increased stress resistance. Longer lifespan also arises in ways that are independent of Sch9 or caloric restriction, and we speculate on ways that sphingolipids might mediate these aspects of increased lifespan. Sch9 and its mammalian homolog S6 kinase work downstream of the target of rapamycin, TOR1, protein kinase, and play evolutionarily conserved roles in regulating lifespan. Our data establish Sch9 as a focal point for regulating lifespan by integrating nutrient signals from TOR1 with growth and stress signals from sphingolipids. Sphingolipids are found in all eukaryotes and our results suggest that pharmacological down-regulation of one or more sphingolipids may provide a means to reduce age-related diseases and increase lifespan in other eukaryotes.
Author Summary
Studies with rats in the 1930s showed a surprising increase in lifespan when the diet contained 30%–40% fewer calories than normal. This experiment has been repeated on many organisms and is the gold standard for extending lifespan. While we are beginning to understand how calorie restriction regulates lifespan, the mechanisms are complex and much remains to be learned. In the work presented here, we demonstrate a novel way to increase lifespan in the budding yeast Saccharomyces cerevisiae. Our strategy is to lower the rate of sphingolipid synthesis either by reducing the synthesis of the first enzyme in the biosynthesis pathway or by using a drug to reduce enzyme activity. This strategy works in part by lowering the activity of a protein kinase, termed Sch9 in yeast and S6K in mammals, both of which are involved in the processes affected by calorie restriction and that control lifespan. In addition, we find that reducing sphingolipid synthesis increases lifespan in ways that are independent of Sch9 and calorie restriction. Since sphingolipids are found in all eukaryotes, our results suggest that pharmacological down-regulation of one or more sphingolipids may provide a means to reduce age-related diseases and increase lifespan in other eukaryotes.
doi:10.1371/journal.pgen.1002493
PMCID: PMC3271065  PMID: 22319457
8.  Systems Biology of Aging in Four Species 
Current opinion in biotechnology  2007;18(4):355-359.
Using DNA microarrays to generate transcriptional profiles of the aging process is a powerful tool for identifying biomarkers of aging. In C. elegans, a number of whole-genome profiling studies identified genes that change expression levels with age. High-throughput RNAi screens in worms determined a number of genes that modulate lifespan when silenced. Transcriptional profiling of the fly head identified a molecular pathway, the ‘response to light’ gene set, that increases expression with age and could be directly related to the tendency for a reduction in light levels to extend fly lifespan. In mouse, comparing the gene expression profiles of several drugs to the gene expression profile of caloric restriction identified metformin as a drug whose action could potentially mimic caloric restriction in vivo. Finally, genes in the mitochondrial electron transport chain group decrease expression with age in the human, mouse, fly, and worm.
doi:10.1016/j.copbio.2007.07.004
PMCID: PMC3224768  PMID: 17681777
9.  The LIN-2/LIN-7/LIN-10 Complex Mediates Basolateral Membrane Localization of the C. elegans EGF Receptor LET-23 in Vulval Epithelial Cells 
Cell  1998;94(6):761-771.
In C. elegans, the LET-23 receptor tyrosine kinase is localized to the basolateral membranes of polarized vulval epithelial cells. lin-2, lin-7, and lin-10 are required for basolateral localization of LET-23, since LET-23 is mislocalized to the apical membrane in lin-2, lin-7, and lin-10 mutants. Yeast two-hybrid, in vitro binding, and in vivo coimmunoprecipitation experiments show that LIN-2, LIN-7, and LIN-10 form a protein complex. Furthermore, compensatory mutations in lin-7 and let-23 exhibit allele-specific suppression of apical mislocalization and signaling-defective phenotypes. These results present a mechanism for basolateral localization of LET-23 receptor tyrosine kinase by direct binding to the LIN-2/LIN-7/LIN-10 complex. Each of the binding interactions within this complex is conserved, suggesting that this complex may also mediate basolateral localization in mammals.
PMCID: PMC3224769  PMID: 9753323
10.  MicroRNA Predictors of Longevity in Caenorhabditis elegans 
PLoS Genetics  2011;7(9):e1002306.
Neither genetic nor environmental factors fully account for variability in individual longevity: genetically identical invertebrates in homogenous environments often experience no less variability in lifespan than outbred human populations. Such variability is often assumed to result from stochasticity in damage accumulation over time; however, the identification of early-life gene expression states that predict future longevity would suggest that lifespan is least in part epigenetically determined. Such “biomarkers of aging,” genetic or otherwise, nevertheless remain rare. In this work, we sought early-life differences in organismal robustness in unperturbed individuals and examined the utility of microRNAs, known regulators of lifespan, development, and robustness, as aging biomarkers. We quantitatively examined Caenorhabditis elegans reared individually in a novel apparatus and observed throughout their lives. Early-to-mid–adulthood measures of homeostatic ability jointly predict 62% of longevity variability. Though correlated, markers of growth/muscle maintenance and of metabolic by-products (“age pigments”) report independently on lifespan, suggesting that graceful aging is not a single process. We further identified three microRNAs in which early-adulthood expression patterns individually predict up to 47% of lifespan differences. Though expression of each increases throughout this time, mir-71 and mir-246 correlate with lifespan, while mir-239 anti-correlates. Two of these three microRNA “biomarkers of aging” act upstream in insulin/IGF-1–like signaling (IIS) and other known longevity pathways, thus we infer that these microRNAs not only report on but also likely determine longevity. Thus, fluctuations in early-life IIS, due to variation in these microRNAs and from other causes, may determine individual lifespan.
Author Summary
Why do some individuals live longer than others? Unexpectedly, genetic differences contribute surprisingly little to lifespan variation in humans. The situation is thrown into relief in studies of C. elegans, in which genetically identical siblings reared in identical environments usually experience different lifespans. In this work, we show that physiological differences between identical animals begin to appear relatively early in life and that markers of ill health in young adulthood presage shorter lifespans. Using fluorescent markers to examine the level of activation of several genes, we found three regulatory microRNA genes that vary in activity between individuals in a manner that predicts future lifespan. Moreover, two of these regulate insulin signaling, which is well known to alter lifespan in diverse species when experimentally manipulated. This indicates that different levels of insulin signaling in otherwise identical individuals may determine differences in lifespan.
doi:10.1371/journal.pgen.1002306
PMCID: PMC3183074  PMID: 21980307
11.  Variable Pathogenicity Determines Individual Lifespan in Caenorhabditis elegans 
PLoS Genetics  2011;7(4):e1002047.
A common property of aging in all animals is that chronologically and genetically identical individuals age at different rates. To unveil mechanisms that influence aging variability, we identified markers of remaining lifespan for Caenorhabditis elegans. In transgenic lines, we expressed fluorescent reporter constructs from promoters of C. elegans genes whose expression change with age. The expression levels of aging markers in individual worms from a young synchronous population correlated with their remaining lifespan. We identified eight aging markers, with the superoxide dismutase gene sod-3 expression being the best single predictor of remaining lifespan. Correlation with remaining lifespan became stronger if expression from two aging markers was monitored simultaneously, accounting for up to 49% of the variation in individual lifespan. Visualizing the physiological age of chronologically-identical individuals allowed us to show that a major source of lifespan variability is different pathogenicity from individual to individual and that the mechanism involves variable activation of the insulin-signaling pathway.
Author Summary
One of the long-standing mysteries in aging is that some individuals die early whereas others die late. The age at which a specific individual will die is difficult or impossible to predict, and thus a fundamental aspect of aging in all animals is that it is stochastic. Aging stochasticity is particularly interesting in model organisms such as C. elegans because they are genetically inbred, can have the exact same chronological age, and can be grown under standard lab conditions. In this paper, we uncover a major mechanism underlying stochasticity in aging. To do this, we first developed a fluorescent aging marker (sod-3::GFP) whose expression declines with age and can be used to measure physiological age. In young animals, the level of expression of this fluorescent marker indicates which animals will live longer and which will die earlier. We used this fluorescent aging marker to show that variable pathogenicity from individual to individual is a major source of lifespan variability and that the mechanism involves variable activation of the insulin-signaling pathway.
doi:10.1371/journal.pgen.1002047
PMCID: PMC3077391  PMID: 21533182
12.  Genetics and genomics of human ageing 
Ageing in humans is typified by the decline of physiological functions in various organs and tissues leading to an increased probability of death. Some individuals delay, escape or survive much of this age-related decline and live past age 100. Studies comparing centenarians to average-aged individuals have found polymorphisms in genes that are associated with long life, including APOE and FOXOA3, which have been replicated many times. However, the associations found in humans account for small percentages of the variance in lifespan and many other gene associations have not been replicated in additional populations. Therefore, ageing is probably a highly polygenic trait. In humans, it is important to also consider differences in age-related decline that occur within and among tissues. Longitudinal data of age-related traits can be used in association studies to test for polymorphisms that predict how an individual will change over time. Transcriptional and genetic association studies of different tissues have revealed common and unique pathways involved in human ageing. Genomic convergence is a method that combines multiple types of functional genomic information such as transcriptional profiling, expression quantitative trait mapping and gene association. The genomic convergence approach has been used to implicate the gene MMP20 in human kidney ageing. New human genetics technologies are continually in development and may lead to additional breakthroughs in human ageing in the near future.
doi:10.1098/rstb.2010.0259
PMCID: PMC3001305  PMID: 21115529
human ageing; centenarians; tissue ageing; longitudinal studies; genomic convergence
13.  A Developmental Timing Switch Promotes Axon Outgrowth Independent of Known Guidance Receptors 
PLoS Genetics  2010;6(8):e1001054.
To form functional neuronal connections, axon outgrowth and guidance must be tightly regulated across space as well as time. While a number of genes and pathways have been shown to control spatial features of axon development, very little is known about the in vivo mechanisms that direct the timing of axon initiation and elongation. The Caenorhabditis elegans hermaphrodite specific motor neurons (HSNs) extend a single axon ventrally and then anteriorly during the L4 larval stage. Here we show the lin-4 microRNA promotes HSN axon initiation after cell cycle withdrawal. Axons fail to form in lin-4 mutants, while they grow prematurely in lin-4–overexpressing animals. lin-4 is required to down-regulate two inhibitors of HSN differentiation—the transcriptional regulator LIN-14 and the “stemness” factor LIN-28—and it likely does so through a cell-autonomous mechanism. This developmental switch depends neither on the UNC-40/DCC and SAX-3/Robo receptors nor on the direction of axon growth, demonstrating that it acts independently of ventral guidance signals to control the timing of HSN axon elongation.
Author Summary
During development, nerve cells extend long structures called axons which are required for communication across distant brain regions and/or with other tissues. Many of the signals controlling the direction of axon extension are well understood, but much less is known about the factors that control when this growth occurs. Ultimately, failure to coordinate the direction and timing of axon elongation could lead to dramatic defects in the way our brains function. By studying the simple soil nematode C. elegans, we have identified mutations in three timing genes that result in either premature or delayed axon growth. These genes function independently from known directional signals as well as axon position. Since two of the genes are shared with mammals, findings presented here will help expand our understanding of human axon development, and could potentially lead to novel strategies for promoting growth in injured adult nerve cells.
doi:10.1371/journal.pgen.1001054
PMCID: PMC2916846  PMID: 20700435
14.  A 3D Digital Atlas of C. elegans and Its Application To Single-Cell Analyses 
Nature methods  2009;6(9):667-672.
We have built a digital nuclear atlas of the newly hatched, first larval stage (L1) of the wild type hermaphrodite of C. elegans at single cell resolution from confocal image stacks of 15 individuals. The atlas quantifies the stereotypy of the locations and provides for other statistics on the spatial patterns of the 357 nuclei that could be faithfully segmented and annotated of the 558 present at this developmental stage. Given this atlas we then developed an automated approach to assign cell names to each nucleus in a 3D image of an L1 worm. We achieve 86% accuracy in identifying the 357 nuclei automatically. This computational method is essential for high-throughput single cell analyses of the worm at post-embryonic stages, such as determining the expression of every gene in every cell during development from the L1 onward, or ablating or stimulating cells under computer control in a high-throughput functional screen.
doi:10.1038/nmeth.1366
PMCID: PMC2882208  PMID: 19684595
15.  Manipulation of Behavioral Decline in Caenorhabditis elegans with the Rag GTPase raga-1 
PLoS Genetics  2010;6(5):e1000972.
Normal aging leads to an inexorable decline in motor performance, contributing to medical morbidity and decreased quality of life. While much has been discovered about genetic determinants of lifespan, less is known about modifiers of age-related behavioral decline and whether new gene targets may be found which extend vigorous activity, with or without extending lifespan. Using Caenorhabditis elegans, we have developed a model of declining neuromuscular function and conducted a screen for increased behavioral activity in aged animals. In this model, behavioral function suffers from profound reductions in locomotory frequency, but coordination is strikingly preserved until very old age. By screening for enhancers of locomotion at advanced ages we identified the ras-related Rag GTPase raga-1 as a novel modifier of behavioral aging. raga-1 loss of function mutants showed vigorous swimming late in life. Genetic manipulations revealed that a gain of function raga-1 curtailed behavioral vitality and shortened lifespan, while a dominant negative raga-1 lengthened lifespan. Dietary restriction results indicated that a raga-1 mutant is relatively protected from the life-shortening effects of highly concentrated food, while RNAi experiments suggested that raga-1 acts in the highly conserved target of rapamycin (TOR) pathway in C. elegans. Rag GTPases were recently shown to mediate nutrient-dependent activation of TOR. This is the first demonstration of their dramatic effects on behavior and aging. This work indicates that novel modulators of behavioral function can be identified in screens, with implications for future study of the clinical amelioration of age-related decline.
Author Summary
As humans and animals age, there is an inevitable decrease in functional capacity. Elderly individuals can suffer from a decline in motor function, or the ability to move. Genetic studies in model organisms have led to the identification of genes that can prolong lifespan. Elongation of lifespan is less appealing, however, if there is not also an extension of vitality or enhanced functionality. Here, we have used a genetic model organism, the nematode worm Caenorhabditis elegans, to screen for mutations that result in enhanced vitality in older animals. We identified a new modifier of the aging of motor function, RAGA-1, a protein present in species from worms and fruit flies to humans. Animals with a raga-1 mutation move more vigorously at advanced ages and also live longer, on average, than wild-type. In contrast, animals engineered with an excessively active version of RAGA-1 show decreases in behavioral activity earlier in life than wild-type and a strikingly shortened lifespan. This offers the possibility that manipulating raga-1 could also produce beneficial effects, such as enhanced vitality, in aging humans.
doi:10.1371/journal.pgen.1000972
PMCID: PMC2877737  PMID: 20523893
16.  Properties of Balanced Permutations 
Journal of Computational Biology  2009;16(4):625-638.
Abstract
This paper takes a close look at balanced permutations, a recently developed sample reuse method with applications in bioinformatics. It turns out that balanced permutation reference distributions do not have the correct null behavior, which can be traced to their lack of a group structure. We find that they can give p-values that are too permissive to varying degrees. In particular the observed test statistic can be larger than that of all B balanced permutations of a data set with a probability much higher than 1/(B + 1), even under the null hypothesis.
doi:10.1089/cmb.2008.0144
PMCID: PMC3148117  PMID: 19361331
functional genomics; gene expression; genomics; statistics
17.  TGF-ß Sma/Mab Signaling Mutations Uncouple Reproductive Aging from Somatic Aging 
PLoS Genetics  2009;5(12):e1000789.
Female reproductive cessation is one of the earliest age-related declines humans experience, occurring in mid-adulthood. Similarly, Caenorhabditis elegans' reproductive span is short relative to its total life span, with reproduction ceasing about a third into its 15–20 day adulthood. All of the known mutations and treatments that extend C. elegans' reproductive period also regulate longevity, suggesting that reproductive span is normally linked to life span. C. elegans has two canonical TGF-ß signaling pathways. We recently found that the TGF-ß Dauer pathway regulates longevity through the Insulin/IGF-1 Signaling (IIS) pathway; here we show that this pathway has a moderate effect on reproductive span. By contrast, TGF-ß Sma/Mab signaling mutants exhibit a substantially extended reproductive period, more than doubling reproductive span in some cases. Sma/Mab mutations extend reproductive span disproportionately to life span and act independently of known regulators of somatic aging, such as Insulin/IGF-1 Signaling and Dietary Restriction. This is the first discovery of a pathway that regulates reproductive span independently of longevity and the first identification of the TGF-ß Sma/Mab pathway as a regulator of reproductive aging. Our results suggest that longevity and reproductive span regulation can be uncoupled, although they appear to normally be linked through regulatory pathways.
Author Summary
Female reproductive cessation is the earliest aging phenotype humans experience, and its importance as a clinical issue is growing as more women opt to have children later in life. While much work has been done to understand the general aging process, little is currently known about the regulation of reproductive aging. Like longevity, the ability to produce progeny with advanced age is likely to be genetically regulated. Thus, understanding the processes that regulate reproductive aging may allow us to address the problems of maternal age-related infertility and birth defects. C. elegans and humans both have long post-reproductive life spans, leaving open the possibility that their reproductive spans might be extendable. C. elegans has been used previously to discover conserved regulators of aging, and here we use worms to identify a new regulator of reproductive aging, a highly conserved TGF-ß signaling pathway. We find that TGF-ß signaling regulates reproductive aging independently of somatic aging. This is the first identification of a pathway that breaks the coupling that normally links the two processes. Our work will provide new insights into the improvement of human fertility and prevention of age-related birth defects, and it has implications for the evolutionary relationship between reproduction and longevity regulation.
doi:10.1371/journal.pgen.1000789
PMCID: PMC2791159  PMID: 20041217
18.  Aging Mice Show a Decreasing Correlation of Gene Expression within Genetic Modules 
PLoS Genetics  2009;5(12):e1000776.
In this work we present a method for the differential analysis of gene co-expression networks and apply this method to look for large-scale transcriptional changes in aging. We derived synonymous gene co-expression networks from AGEMAP expression data for 16-month-old and 24-month-old mice. We identified a number of functional gene groups that change co-expression with age. Among these changing groups we found a trend towards declining correlation with age. In particular, we identified a modular (as opposed to uniform) decline in general correlation with age. We identified potential transcriptional mechanisms that may aid in modular correlation decline. We found that computationally identified targets of the NF-ΚB transcription factor decrease expression correlation with age. Finally, we found that genes that are prone to declining co-expression tend to be co-located on the chromosome. Our results conclude that there is a modular decline in co-expression with age in mice. They also indicate that factors relating to both chromosome domains and specific transcription factors may contribute to the decline.
Author Summary
There is mounting evidence that mammalian aging is marked by increased gene transcriptional variation. This trend was shown not only by studying gene expression in single cells (Bahar et al. 2006), but at the coarse tissue resolution as well (Somel et al. 2006; Li et al. 2009). These led us to believe that looking at absolute changes in expression level alone may not tell the whole story of transcriptional changes in age. Instead the story may be in the more subtle changes in the coordination of expression among multiple genes. For this reason, we decided to look at changes in co-expression relationships with age. To this end, we developed a methodology for differential co-expression network analysis for the comparison gene co-expression on a global scale. We applied this methodology to compare co-expression between young (16-month) and old (24-month) mice. This allowed us to find both gene groups whose coordination appear to be affected by age and to propose potential mechanisms for the change. We believe our work is of broad importance because it represents a different paradigm for looking not only at aging but also at any complex condition or disease—away from changes in individual genes towards changes in gene relationships.
doi:10.1371/journal.pgen.1000776
PMCID: PMC2788246  PMID: 20019809
19.  Mutations in the Caenorhabditis elegans U2AF Large Subunit UAF-1 Alter the Choice of a 3′ Splice Site In Vivo 
PLoS Genetics  2009;5(11):e1000708.
The removal of introns from eukaryotic RNA transcripts requires the activities of five multi-component ribonucleoprotein complexes and numerous associated proteins. The lack of mutations affecting splicing factors essential for animal survival has limited the study of the in vivo regulation of splicing. From a screen for suppressors of the Caenorhabditis elegans unc-93(e1500) rubberband Unc phenotype, we identified mutations in genes that encode the C. elegans orthologs of two splicing factors, the U2AF large subunit (UAF-1) and SF1/BBP (SFA-1). The uaf-1(n4588) mutation resulted in temperature-sensitive lethality and caused the unc-93 RNA transcript to be spliced using a cryptic 3′ splice site generated by the unc-93(e1500) missense mutation. The sfa-1(n4562) mutation did not cause the utilization of this cryptic 3′ splice site. We isolated four uaf-1(n4588) intragenic suppressors that restored the viability of uaf-1 mutants at 25°C. These suppressors differentially affected the recognition of the cryptic 3′ splice site and implicated a small region of UAF-1 between the U2AF small subunit-interaction domain and the first RNA recognition motif in affecting the choice of 3′ splice site. We constructed a reporter for unc-93 splicing and using site-directed mutagenesis found that the position of the cryptic splice site affects its recognition. We also identified nucleotides of the endogenous 3′ splice site important for recognition by wild-type UAF-1. Our genetic and molecular analyses suggested that the phenotypic suppression of the unc-93(e1500) Unc phenotype by uaf-1(n4588) and sfa-1(n4562) was likely caused by altered splicing of an unknown gene. Our observations provide in vivo evidence that UAF-1 can act in regulating 3′ splice-site choice and establish a system that can be used to investigate the in vivo regulation of RNA splicing in C. elegans.
Author Summary
Eukaryotic genes contain intervening intronic sequences that must be removed from pre-mRNA transcripts by RNA splicing to generate functional messenger RNAs. While studying genes that encode and control a presumptive muscle potassium channel complex in the nematode Caenorhabditis elegans, we found that mutations in two splicing factors, the U2AF large subunit and SF1/BBP suppress the rubberband Unc phenotype caused by a rare missense mutation in the gene unc-93. Mutations affecting the U2AF large subunit caused the recognition of a cryptic 3′ splice site generated by the unc-93 mutation, providing in vivo evidence that the U2AF large subunit can affect splice-site selection. By contrast, an SF1/BBP mutation that suppressed the rubberband Unc phenotype did not cause splicing using this cryptic 3′ splice site. Our genetic studies identified a region of the U2AF large subunit important for its effect on 3′ splice-site choice. Our mutagenesis analysis of in vivo transgene splicing identified a positional effect on weak 3′ splice site selection and nucleotides of the endogenous 3′ splice site important for recognition. The system we have defined should facilitate future in vivo analyses of pre–mRNA splicing.
doi:10.1371/journal.pgen.1000708
PMCID: PMC2762039  PMID: 19893607
20.  A Mechanistic Basis for the Coordinated Regulation of Pharyngeal Morphogenesis in Caenorhabditis elegans by LIN-35/Rb and UBC-18–ARI-1 
PLoS Genetics  2009;5(6):e1000510.
Genetic redundancy, whereby two genes carry out seemingly overlapping functions, may in large part be attributable to the intricacy and robustness of genetic networks that control many developmental processes. We have previously described a complex set of genetic interactions underlying foregut development in the nematode Caenorhabditis elegans. Specifically, LIN-35/Rb, a tumor suppressor ortholog, in conjunction with UBC-18–ARI-1, a conserved E2/E3 complex, and PHA-1, a novel protein, coordinately regulates an early step of pharyngeal morphogenesis involving cellular re-orientation. Functional redundancy is indicated by the observation that lin-35; ubc-18 double mutants, as well as certain allelic combinations of pha-1 with either lin-35 or ubc-18, display defects in pharyngeal development, whereas single mutants do not. Using a combination of genetic and molecular analyses, we show that sup-35, a strong recessive suppressor of pha-1–associated lethality, also reverts the synthetic lethality of lin-35; ubc-18, lin-35; pha-1, and ubc-18 pha-1 double mutants. SUP-35, which contains C2H2-type Zn-finger domains as well as a conserved RMD-like motif, showed a dynamic pattern of subcellular localization during embryogenesis. We find that mutations in sup-35 specifically suppress hypomorphic alleles of pha-1 and that SUP-35, acting genetically upstream of SUP-36 and SUP-37, negatively regulates pha-1 transcription. We further demonstrate that LIN-35, a transcriptional repressor, and UBC-18–ARI-1, a complex involved in ubiquitin-mediated proteolysis, negatively regulate SUP-35 abundance through distinct mechanisms. We also show that HCF-1, a C. elegans homolog of host cell factor 1, functionally antagonizes LIN-35 in the regulation of sup-35. Our cumulative findings piece together the components of a novel regulatory network that includes LIN-35/Rb, which functions to control organ morphogenesis. Our results also shed light on general mechanisms that may underlie developmental genetic redundancies as well as principles that may govern complex disease traits.
Author Summary
One of the more puzzling aspects of genetics is that the inactivation of many genes fails to produce strong deleterious effects on the organisms that carry those genes. In some cases, however, the combined inactivation of two or more such genes can lead to the expression of robust abnormal phenotypes. These types of synthetic genetic interactions are thought to reflect the presence of functional overlap or redundancy between the involved genes. The root mechanisms that underlie synthetic interactions are thought to be complex and are in most cases poorly understood. Our work here focuses on one case study where we have uncovered the molecular basis underlying a complex set of genetic redundancies in C. elegans. More specifically, we have discovered a novel regulatory network that connects eight genes controlling embryonic foregut development in the nematode C. elegans. By solving mechanisms of this nature, our analysis provides a means for understanding more generally the principles that govern genetic redundancies. Our work also provides insight into the bases of complex disease traits, where the combined interactions of multiple genetic factors leads to outcomes that determine health or disease.
doi:10.1371/journal.pgen.1000510
PMCID: PMC2686152  PMID: 19521497
21.  Deletion of the Mitochondrial Superoxide Dismutase sod-2 Extends Lifespan in Caenorhabditis elegans 
PLoS Genetics  2009;5(2):e1000361.
The oxidative stress theory of aging postulates that aging results from the accumulation of molecular damage caused by reactive oxygen species (ROS) generated during normal metabolism. Superoxide dismutases (SODs) counteract this process by detoxifying superoxide. It has previously been shown that elimination of either cytoplasmic or mitochondrial SOD in yeast, flies, and mice results in decreased lifespan. In this experiment, we examine the effect of eliminating each of the five individual sod genes present in Caenorhabditis elegans. In contrast to what is observed in other model organisms, none of the sod deletion mutants shows decreased lifespan compared to wild-type worms, despite a clear increase in sensitivity to paraquat- and juglone-induced oxidative stress. In fact, even mutants lacking combinations of two or three sod genes survive at least as long as wild-type worms. Examination of gene expression in these mutants reveals mild compensatory up-regulation of other sod genes. Interestingly, we find that sod-2 mutants are long-lived despite a significant increase in oxidatively damaged proteins. Testing the effect of sod-2 deletion on known pathways of lifespan extension reveals a clear interaction with genes that affect mitochondrial function: sod-2 deletion markedly increases lifespan in clk-1 worms while clearly decreasing the lifespan of isp-1 worms. Combined with the mitochondrial localization of SOD-2 and the fact that sod-2 mutant worms exhibit phenotypes that are characteristic of long-lived mitochondrial mutants—including slow development, low brood size, and slow defecation—this suggests that deletion of sod-2 extends lifespan through a similar mechanism. This conclusion is supported by our demonstration of decreased oxygen consumption in sod-2 mutant worms. Overall, we show that increased oxidative stress caused by deletion of sod genes does not result in decreased lifespan in C. elegans and that deletion of sod-2 extends worm lifespan by altering mitochondrial function.
Author Summary
In this paper, we examine the oxidative stress theory of aging using C. elegans as a model system. This theory proposes that aging results from the accumulation of molecular damage caused by reactive oxygen species (ROS). To test this theory, we examined the effect of deleting each of the five individual superoxide dismutase (SOD) genes on lifespan and sensitivity to oxidative stress. Since SOD acts to detoxify ROS, the oxidative stress theory predicts that deletion of sod genes should increase oxidative stress and decrease lifespan. However, in contrast to yeast, flies, and mice, where loss of either cytoplasmic or mitochondrial SOD results in decreased lifespan, we find that none of the sod deletion mutants in C. elegans exhibits a shortened lifespan despite increased sensitivity to oxidative stress. Surprisingly, we find that sod-2 mutant worms have extended lifespan and even worms with the primary cytoplasmic, mitochondrial, and extracellular sod genes deleted can live longer than wild-type worms. By examining genetic interactions with other genes known to extend lifespan and by comparing the phenotype of worms lacking sod-2 to that of known long-lived mitochondrial mutants such as clk-1 or isp-1, we provide evidence that the loss of sod-2 extends lifespan through alteration of mitochondrial function.
doi:10.1371/journal.pgen.1000361
PMCID: PMC2628729  PMID: 19197346
22.  Profiling Synaptic Proteins Identifies Regulators of Insulin Secretion and Lifespan 
PLoS Genetics  2008;4(11):e1000283.
Cells are organized into distinct compartments to perform specific tasks with spatial precision. In neurons, presynaptic specializations are biochemically complex subcellular structures dedicated to neurotransmitter secretion. Activity-dependent changes in the abundance of presynaptic proteins are thought to endow synapses with different functional states; however, relatively little is known about the rules that govern changes in the composition of presynaptic terminals. We describe a genetic strategy to systematically analyze protein localization at Caenorhabditis elegans presynaptic specializations. Nine presynaptic proteins were GFP-tagged, allowing visualization of multiple presynaptic structures. Changes in the distribution and abundance of these proteins were quantified in 25 mutants that alter different aspects of neurotransmission. Global analysis of these data identified novel relationships between particular presynaptic components and provides a new method to compare gene functions by identifying shared protein localization phenotypes. Using this strategy, we identified several genes that regulate secretion of insulin-like growth factors (IGFs) and influence lifespan in a manner dependent on insulin/IGF signaling.
Author Summary
Cells are divided into multiple subcellular compartments that perform diverse functions. In neurons, synapses mediate transmission of information between cells and they comprise hundreds of proteins dedicated for this purpose. Changes in the protein composition of synapses are thought to produce changes in synaptic transmission, such as those that occur during development, learning, and memory. Here, we describe a systematic genetic strategy for analyzing the protein composition of synapses. Using this strategy, we identified sets of genes that alter synapses in similar ways, and identified novel regulatory relationships between particular synaptic proteins. One set of genes regulated secretion of insulin-like hormones from neurons and had corresponding effects on lifespan, which is controlled by insulin signaling. These results illustrate how changes in synaptic composition can be utilized as a probe to explain changes in physiology. Our approach can be expanded to include a larger set of synaptic proteins or to analyze other subcellular compartments.
doi:10.1371/journal.pgen.1000283
PMCID: PMC2582949  PMID: 19043554
23.  C. elegans Nucleostemin Is Required for Larval Growth and Germline Stem Cell Division 
PLoS Genetics  2008;4(8):e1000181.
The nucleolus has shown to be integral for many processes related to cell growth and proliferation. Stem cells in particular are likely to depend upon nucleolus-based processes to remain in a proliferative state. A highly conserved nucleolar factor named nucleostemin is proposed to be a critical link between nucleolar function and stem-cell–specific processes. Currently, it is unclear whether nucleostemin modulates proliferation by affecting ribosome biogenesis or by another nucleolus-based activity that is specific to stem cells and/or highly proliferating cells. Here, we investigate nucleostemin (nst-1) in the nematode C. elegans, which enables us to examine nst-1 function during both proliferation and differentiation in vivo. Like mammalian nucleostemin, the NST-1 protein is localized to the nucleolus and the nucleoplasm; however, its expression is found in both differentiated and proliferating cells. Global loss of C. elegans nucleostemin (nst-1) leads to a larval arrest phenotype due to a growth defect in the soma, while loss of nst-1 specifically in the germ line causes germline stem cells to undergo a cell cycle arrest. nst-1 mutants exhibit reduced levels of rRNAs, suggesting defects in ribosome biogenesis. However, NST-1 is generally not present in regions of the nucleolus where rRNA transcription and processing occurs, so this reduction is likely secondary to a different defect in ribosome biogenesis. Transgenic studies indicate that NST-1 requires its N-terminal domain for stable expression and both its G1 GTPase and intermediate domains for proper germ line function. Our data support a role for C. elegans nucleostemin in cell growth and proliferation by promoting ribosome biogenesis.
Author Summary
Stem cells are carefully poised between the alternate fates of proliferation and differentiation. The regulation of this choice is a complex one that occurs on many different levels. One major influence controlling this choice derives signals emanating from the nucleolus, which serves dual roles as the site of ribosome biogenesis and as a repository for sequestered key regulatory factors. The nucleolar GTPase nucleostemin has recently been identified as a potential link between stem cell proliferation and nucleolar function, but its exact role in the nucleolus has not been directly addressed in a metazoan. Here, we use the model organism C. elegans to investigate the function of nucleostemin in both differentiated cells and proliferating stem cells. We show that nucleostemin probably acts to regulate ribosome biogenesis, and through this process controls cell proliferation. We also suggest that, at least in C. elegans, the function of nucleostemin is not restricted to proliferating stem cells, but that it also functions in differentiated cells to control cell growth. Our study highlights the complexity of the role of the nucleolus in regulation of cell growth and division.
doi:10.1371/journal.pgen.1000181
PMCID: PMC2515194  PMID: 18725931
24.  Sensory Perception of Food and Insulin-Like Signals Influence Seizure Susceptibility 
PLoS Genetics  2008;4(7):e1000117.
Food deprivation is known to affect physiology and behavior. Changes that occur could be the result of the organism's monitoring of internal and external nutrient availability. In C. elegans, male mating is dependent on food availability; food-deprived males mate with lower efficiency compared to their well-fed counterparts, suggesting that the mating circuit is repressed in low-food environments. This behavioral response could be mediated by sensory neurons exposed to the environment or by internal metabolic cues. We demonstrated that food-deprivation negatively regulates sex-muscle excitability through the activity of chemosensory neurons and insulin-like signaling. Specifically, we found that the repressive effects of food deprivation on the mating circuit can be partially blocked by placing males on inedible food, E. coli that can be sensed but not eaten. We determined that the olfactory AWC neurons actively suppress sex-muscle excitability in response to food deprivation. In addition, we demonstrated that loss of insulin-like receptor (DAF-2) signaling in the sex muscles blocks the ability of food deprivation to suppress the mating circuit. During low-food conditions, we propose that increased activity by specific olfactory neurons (AWCs) leads to the release of neuroendocrine signals, including insulin-like ligands. Insulin-like receptor signaling in the sex muscles then reduces cell excitability via activation of downstream molecules, including PLC-γ and CaMKII.
Author Summary
We demonstrate that lack of sensation of food in the environment can alleviate spontaneous muscle seizures via an insulin-like mediated pathway. Food restriction is known to promote many adaptive physiological responses, including the mobilization of fat-stores, increases in life span, and suppression of seizures. Consequently, a better understanding of the exact cellular and molecular details involved in these responses could lead to better health treatments. Here, we identify a novel mechanism activated by food restriction that occurs as a response to decreased sensation of food in the environment, rather than a response to decreased ingestion. Specifically, we show that suppression of C. elegans mutant-induced muscle seizures by food deprivation requires the activity of the AWC olfactory neurons and insulin-like signaling. We elucidate a novel role of insulin-like signaling in response to caloric restriction that does not involve the canonical FOXO/DAF-16 pathway. Instead, we propose that insulin-like control of muscle excitability activates downstream signaling molecules that include phospholipase C-γ, calcium/calmodulin-dependent kinase II (CaMKII), and ether-a-go-go K+ channels. These molecules identify a novel mechanism used by organisms to regulate multiple physiological responses to changing environmental conditions.
doi:10.1371/journal.pgen.1000117
PMCID: PMC2432499  PMID: 18604269
25.  Phospholipase C-ε Regulates Epidermal Morphogenesis in Caenorhabditis elegans 
PLoS Genetics  2008;4(3):e1000043.
Migration of cells within epithelial sheets is an important feature of embryogenesis and other biological processes. Previous work has demonstrated a role for inositol 1,4,5-trisphosphate (IP3)-mediated calcium signalling in the rearrangement of epidermal cells (also known as hypodermal cells) during embryonic morphogenesis in Caenorhabditis elegans. However the mechanism by which IP3 production is stimulated is unknown. IP3 is produced by the action of phospholipase C (PLC). We therefore surveyed the PLC family of C. elegans using RNAi and mutant strains, and found that depletion of PLC-1/PLC-ε produced substantial embryonic lethality. We used the epithelial cell marker ajm-1::gfp to follow the behaviour of epidermal cells and found that 96% of the arrested embryos have morphogenetic defects. These defects include defective ventral enclosure and aberrant dorsal intercalation. Using time-lapse confocal microscopy we show that the migration of the ventral epidermal cells, especially of the leading cells, is slower and often fails in plc-1(tm753) embryos. As a consequence plc-1 loss of function results in ruptured embryos with a Gex phenotype (gut on exterior) and lumpy larvae. Thus PLC-1 is involved in the regulation of morphogenesis. Genetic studies using gain- and loss-of-function alleles of itr-1, the gene encoding the IP3 receptor in C. elegans, demonstrate that PLC-1 acts through ITR-1. Using RNAi and double mutants to deplete the other PLCs in a plc-1 background, we show that PLC-3/PLC-γ and EGL-8/PLC-β can compensate for reduced PLC-1 activity. Our work places PLC-ε into a pathway controlling epidermal cell migration, thus establishing a novel role for PLC-ε.
Author Summary
Morphogenesis is a fundamental part of development which underlies the ability of animals, including humans, to define the shape of their tissues and organs and thus enable their proper function. To understand morphogenesis we need to understand the signalling networks that regulate coordinated changes in cell morphology, movement and adhesion. We know that in C. elegans intracellular signalling through the messenger inositol 1,4,5-trisphosphate (IP3) is required for the proper completion of the morphogenetic processes. However the mechanism by which this signal is produced remains unclear. In this work we define the mechanism responsible for IP3 production in C. elegans. We use a combination of genetic and morphological analysis to show that phospholipase C-epsilon (PLC-ε) is the molecule responsible for IP3 production. In worms with disrupted PLC-ε the embryonic epidermal cells fail to migrate properly so that morphogenesis fails. PLC-ε was only discovered relatively recently and interacts directly with a wide range of signalling pathways, including others that are known to regulate important cellular properties during morphogenesis such as small GTPases. Therefore we establish a potential link between IP3 signalling and other pathways that are known to be involved in cell movements. This is an important advance in defining the network of interactions that regulate epithelial cell movements in morphogenesis.
doi:10.1371/journal.pgen.1000043
PMCID: PMC2274882  PMID: 18369461

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