-
[
RNA,
2013]
Early environmental experiences profoundly influence adult phenotypes through complex mechanisms that are poorly understood. We previously showed that adult Caenorhabditis elegans that transiently passed through the stress-induced dauer larval stage (post-dauer adults) exhibit significant changes in gene expression profiles, chromatin states, and life history traits when compared with adults that bypassed the dauer stage (control adults). These wild-type, isogenic animals of equivalent developmental stages exhibit different signatures of molecular marks that reflect their distinct developmental trajectories. To gain insight into the mechanisms that contribute to these developmental history-dependent phenotypes, we profiled small RNAs from post-dauer and control adults by deep sequencing. RNA interference (RNAi) pathways are known to regulate genome-wide gene expression both at the chromatin and post-transcriptional level. By quantifying changes in endogenous small interfering RNA (endo-siRNA) levels in post-dauer as compared with control animals, our analyses identified a subset of genes that are likely targets of developmental history-dependent reprogramming through a complex RNAi-mediated mechanism. Mutations in specific endo-siRNA pathways affect expected gene expression and chromatin state changes for a subset of genes in post-dauer animals, as well as disrupt their increased brood size phenotype. We also find that both chromatin state and endo-siRNA distribution in dauers are unique, and suggest that remodeling in dauers provides a template for the subsequent establishment of adult post-dauer profiles. Our results indicate a role for endo-siRNA pathways as a contributing mechanism to early experience-dependent phenotypic plasticity in adults, and describe how developmental history can program adult physiology and behavior via epigenetic mechanisms.
-
[
Curr Biol,
2010]
Early life experiences have a major impact on adult phenotypes [1-3]. However, the mechanisms by which animals retain a cellular memory of early experience are not well understood. Here we show that adult wild-type Caenorhabditis elegans that transiently pass through the stress-resistant dauer larval stage exhibit distinct gene expression profiles and life history traits, as compared to adult animals that bypassed this stage. Using chromatin immunoprecipitation experiments coupled with massively parallel sequencing, we found that genome-wide levels of specific histone tail modifications are markedly altered in postdauer animals. Mutations in subsets of genes implicated in chromatin remodeling abolish, or alter, the observed changes in gene expression and life history traits in postdauer animals. Modifications to the epigenome as a consequence of early experience may contribute in part to a memory of early experience and generate phenotypic variation in an isogenic population.
-
[
International Worm Meeting,
2017]
Environmental stress during early development in animals can have profound effects on adult phenotypes via programmed changes in gene expression. Using the nematode, C. elegans, we demonstrated previously that adults retain a cellular memory of their developmental experience that is manifested by differences in gene expression and life history traits; however, the sophistication of this system in response to different environmental stresses, and how it dictates phenotypic plasticity in adults that contribute to increased fitness in response to distinct environmental challenges, was unknown. Using transcriptional profiling, we show here that C. elegans adults indeed retain distinct cellular memories of different environmental conditions. We identified approximately 500 genes that exhibit highly significant and opposite ("seesaw") transcriptional phenotypes in adults that entered dauer due to starvation (PDStv) compared to adults that entered dauer due to crowding (PDPhe), and are distinct from animals that bypassed dauer (CON). Moreover, we show that two-thirds of the genes in the genome experience a 2-fold or greater seesaw trend in gene expression, and based upon the direction of change, are enriched in large, tightly linked regions on different chromosomes. Importantly, these transcriptional programs correspond to significant changes in brood size depending on the experienced stress, such that we observe a decrease or increase in PD/CON brood size for Stv or Phe conditions, respectively. In addition, we demonstrate that the observed seesaw gene expression and brood size differences require different signaling mechanisms for the Stv- and Phe-induced changes. The starvation program requires endocrine signaling and the germline, while the pheromone program is dependent on systemic RNAi signals from the soma. Interestingly, both transcriptional programs require the AGO CSR-1. Thus, signaling between the soma and the germline can generate phenotypic plasticity as a result of early environmental experience, and likely contribute to increased fitness in adverse conditions and the evolution of the C. elegans genome.
-
[
International Worm Meeting,
2017]
Environmental stress experienced during early development can affect adult phenotypes through stable changes in gene expression. In C. elegans, stress experienced during the first larval stage, including starvation, crowding, and high temperature, promotes entry into the non-aging, stress-resistant dauer stage. Larva will exit dauer and resume continuous development when conditions improve. We have shown previously that postdauer (PD) adults retain a cellular memory of their developmental history that is reflected in changes of gene expression and behavior compared to continuously developing adults (CON). Recently, we have shown that the
osm-9 TRPV channel gene is down-regulated in ADL neurons of PD adults, while remains expressed in CON adults, resulting in altered olfactory behavior in response to high concentration of ascr#3 pheromone component. We identified a cis-acting promoter element called the PD motif that is required for the down-regulation of
osm-9 in PD ADL neurons, which is composed of a DAF-3 SMAD binding site adjacent to a 29 bp conserved sequence region. The PD motif is present in the upstream regulatory regions of 977 C. elegans genes and is bound by DAF-3 and ZFP-1 in PD animals. However, our mutational analysis of the PD motif indicates that additional transcription factors bind to the PD motif to both positively and negatively regulate
osm-9 expression. We have used a yeast one-hybrid approach performed by undergraduates in the laboratory and classroom to determine what other transcription factors are binding to the sequence components of the PD motif to regulate gene expression based on developmental history. Our preliminary results suggest that additional SMAD proteins acting in the TFG- beta pathway, DAF-8 and SMA-4, are also directly interacting with the PD motif. We are currently verifying and characterizing the role of transcription factors identified in our screen in the regulation of
osm-9 in C. elegans animals. Given that the PD motif is present in numerous genes, our results will contribute to the understanding of their regulation due to a TGF- beta sensitive PD motif.
-
[
International Worm Meeting,
2011]
The PHA-4/FoxA forkhead transcription factor in nematodes plays an integral role in all aspects of pharyngeal development, from the earliest specification of pharyngeal precursors to the determination of definitive cell types (1-3). Previous studies in the Mango lab have suggested that PHA-4 activates the expression of many pharyngeal genes directly (4). Our previous studies revealed that binding site affinity for PHA-4 contributes to target diversity in vivo. In fact, the affinity between PHA-4 and its target promoters contributes to the timing of gene expression (4). Mutation of a high affinity PHA-4 binding site to a lower affinity site results in a later onset of expression; conversely, switching a low affinity site to a higher affinity advances gene activation (4). However, the exact mechanism by which PHA-4 temporally regulates all of its targets through binding site affinity remains unclear. To address this question, we employed the NSA (Nuclear Spot Assay) which uses LacO/LacI::CFP to mark pseudochromosome arrays and PHA-4::YFP to track
pha-4 (5-7). By tracking both YFP and CFP signals and their distributed domains in the nucleus, we can follow patterns of association between PHA-4 and its target promoters in living embryos with precise spatial and temporal resolution. Our data indicate that PHA-4::YFP binds to target promoters hours before the transcription firing and that the level of PHA-4::YFP association is significantly different between high versus low affinity sites at early embryonic stages. In addition, manipulation of PHA-4 levels at early embryonic stages (2E to 8E) by heatshock (over expression) or RNAi (reduced expression) can alter the onset of pharyngeal expression. These data suggest that PHA-4 binds to pharyngeal target promoters through different affinity sites at early embryonic stages and this binding may prime the timing of gene expression at later stages. We will further investigate the PHA-4 occupancy at endogenous loci during development by chromatin immunoprecipitation. Together, this study will help clarify how binding site affinity influences temporal regulation of transcription. Reference 1.Mango S.E., Lambie E.J., and Kimble J. Development 120 : 3019. (1994) 2.Horner M., Quintin S., Domeier M.E., Kimble J., Labouesse M. and Mango S.E. Gene & Development 12:1947. (1998). 3.Gaudet J., Muttumu S., Horner M., and Mango S.E. PLoS Biol 2 :
e352. (2004) 4.Gaudet J., and Mango S.E. Science 295 : 821. (2002) 5.Carmi I., JKopczynski J.B. and Meyer B.J. Nature 396:168. (1998) 6.Belmont A.S., Straight A.F. Trends Cell Biol 8:121. (1998) 7.Fakhouri T.H., Stevenson J., Chisholm A.D., Mango S.E. PLos Genet 6:
e1001060. (2010).
-
[
International Worm Meeting,
2017]
Long-term effects of extended starvation during L1 arrest have been shown to persist to the F3 generation, suggesting transgenerational epigenetic inheritance. Though effects on lifespan and gene expression have been reported (Rechavi et al), we have only observed relatively subtle transgenerational effects on L1 starvation survival and heat resistance (Jobson, Jordan et al). Furthermore, we found that a minority of starved worms transmitted these effects, requiring phenotype-based sorting of the starved population to detect transgenerational effects among their descendants. In contrast to L1 arrest, larvae can survive dauer arrest for months and the majority of C. elegans in the wild are found as dauers. Persistent effects of dauer arrest have been reported for adults (Hall et al), but transgenerational effects have not been reported. We reasoned that dauer arrest is likely a more ecologically relevant and robust model for transgenerational effects of starvation. Here, we used a liquid culture system carefully controlling worm density and food availability to cause virtually 100% of N2 larvae to enter dauer arrest. These worms remain dauers for months and become reproductive adults when allowed to recover on plates. By assessing various life-history traits, we found that worms subjected to long-term dauer arrest exhibit apparent fitness costs upon recovery, including maternal effects in the F1 generation. However, L1 starvation survival was increased population-wide in the F3 generation (without phenotypic sorting of ancestors), suggesting potentially adaptive transgenerational effects of long-term dauer arrest. This phenotypic effect depended on the length of time the P0 generation spent in dauer arrest, suggesting that dauer formation alone is not sufficient. Notably, the transgenerational effects occurred in the absence of detectable gene expression changes, as if the presumed epigenetic effect on gene expression is distributed over many genes with a small effect on each. This work suggests that experiencing a stress such as starvation can initially be costly, but future generations may exhibit increased fitness in particular circumstances. References: Hall, S.E. et al., A cellular memory of developmental history generates phenotypic diversity in C. elegans. Current Biology, 2010. 20(2): p. 149-155. Jobson, M.A., Jordan J.M. et al., Transgenerational Effects of Early Life Starvation on Growth, Reproduction, and Stress Resistance in Caenorhabditis elegans. Genetics, 2015. 201(1): p. 201-12. Rechavi, O. et al., Starvation-Induced Transgenerational Inheritance of Small RNAs in C. elegans. Cell, 2014. 158(2): p. 277-287.
-
[
Worm Breeder's Gazette,
1994]
The C. elegans genome sequencing project: A progress report. The C. elegans Genome Consortium, Genome Sequencing Center, Washington University School of Medicine, St. Louis, Missouri, USA and Sanger Centre, Hinxton Hall, Cambridge, UK.
-
[
Worm Breeder's Gazette,
1994]
The C. elegans genome sequencing project: A progress report. The C. elegans Genome Consortium, Genome Sequencing Center, Washington University School of Medicine, St. Louis, Missouri, USA and Sanger Centre, Hinxton Hall, Cambridge, UK.
-
[
Worm Breeder's Gazette,
1994]
Cytology of degenerin-induced cell death in the PVM neuron David H. Hall, Guoqiang Gu+, Lei Gong#, Monica Driscoll#, and Martin Chalfie+, * Dept. Neuroscience, Albert Einstein College of Medicine, Bronx, N.Y. 10461 + Dept. Biological Sciences, Columbia University, New York, N.Y. 10027 # Dept. Molecular Biology and Biochemistry, Rutgers University, Piscataway, N.J. 08855
-
[
International C. elegans Meeting,
2001]
One of the hallmarks of RNAi in C. elegans is the systemic effect: injecting gene specific dsRNA into one tissue interferes with the expression of that gene in other tissues (Fire, A. et. al, 1998). In order to elucidate the mechanisms of systemic RNAi, we have developed an assay that has allowed us to identify mutants that are specifically suppressed in their ability to execute systemic RNAi, but are still able to maintain cell autonomous RNAi. This assay has also been used to identify mutants that are apparently enhanced for RNAi. We have screened approximately 600,000 genomes in search of suppressor mutants and approximately 100,000 genomes for enhancer mutants. Towards our goal of identifying the genes necessary for systemic RNAi, we are placing the mutations into complementation groups, mapping representative mutants to linkage groups, and characterizing the gene and tissue specificity of the suppressor mutants. Fire, A., Xu, S., Montgomery, M.K., Kostas, S.A., Driver, S.E., Mello, C.C. (1998) Potent and specific genetic interference by double-stranded RNA in Caenorhabditis elegans . Nature 19;391(6669):806-11