We study gene regulatory mechanisms controlling the timing of animal development using the C. elegans model system. Developmental timing regulators in C.elegans include microRNAs that control the stage-specific expression of key transcription factors. We aim to understand the molecular mechanisms of post-transcriptional gene regulation by microRNAs, and how microRNAs function in regulatory networks affecting development and disease

Ward Figure

Circulating microRNA profiles in human patients with acetaminophen hepatotoxicity or ischemic hepatitis

McJunkin Figure

The embryonic mir-35 family of microRNAs promotes multiple aspects of fecundity in Caenorhabditis elegans

Sterling Figure

An efficient and sensitive method for preparing cDNA libraries from scarce biological samples

Zinovyeva Figure

Mutations in conserved residues of the C. elegans microRNA Argonaute ALG-1 identify separable functions in ALG-1 miRISC loading and target repression

Karp Figure

Dauer larva quiescence alters the circuitry of microRNA pathways regulating cell fate progression in C. elegans


Circulating microRNA profiles in human patients with acetaminophen hepatotoxicity or ischemic hepatitis


Current Opinion in Genetics & Development 2011, 21:511–517


MicroRNAs regulate temporal transitions in gene expression associated with cell fate progression and differentiation throughout animal development. Genetic analysis of developmental timing in the nematode Caenorhabditis elegans identified two evolutionarily conserved microRNAs, lin-4/mir-125 and let-7, that regulate cell fate progression and differentiation in C. elegans cell lineages. MicroRNAs perform analogous developmental timing functions in other animals, including mammals. By regulating cell fate choices and transitions between pluripotency and differentiation, microRNAs help to orchestrate developmental events throughout the developing animal, and to play tissue homeostasis roles important for disease, including cancer.


Evolutionary conservation of developmental timing roles for microRNAs. (a) In nematodes, insects and mammals, let-7 family microRNAs control progression from earlier, or more proliferative states, to later, more differentiated states. These conserved activities in developmental progression can involve explicitly conserved targets (red), and nonconserved targets (blue). C. elegans let-7 family microRNAs act in several cell types to control early-to-late cell fate progression. Examples of targets that are conserved between C. elegans and mammals and insects include LIN-28, LET-60/Ras and LIN-41. Non-conserved targets of let-7 can nevertheless mediate roles for let-7 in promoting transitions from more primitive to more differentiated developmental states: examples include in Drosophila the down regulation of Abrupt in the control of a reorganization of the neuromusculature at metamorphosis [45,46__], and in humans the down regulation of the oncogene HMGA2 [69_]. (b) MicroRNAs of families other than let-7 can also control temporal developmental transitions, such as the case of miR-96, which is required for a program of differentiation in mammalian inner ear hair cells [53__]. There could be multiple relevant targets of miR-96 in this context, since many mRNAs are deregulated in mir-96 mutant mice [51].

The embryonic mir-35 family of microRNAs promotes multiple aspects of fecundity in Caenorhabditis elegans


Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, Massachusetts 01605

Genetics 187: 345–353 ( January 2011)


Animals developing in the wild encounter a range of environmental conditions, and so developmental mechanisms have evolved that can accommodate different environmental contingencies. Harsh environmental conditions cause Caenorhabditis elegans larvae to arrest as stress-resistant "dauer" larvae after the second larval stage (L2), thereby indefinitely postponing L3 cell fates. HBL-1 is a key transcriptional regulator of L2 vs. L3 cell fate. Through the analysis of genetic interactions between mutations of hbl-1 and of genes encoding regulators of dauer larva formation, we find that hbl-1 can also modulate the dauer formation decision in a complex manner. We propose that dynamic interactions between genes that regulate stage-specific cell fate decisions and those that regulate dauer formation promote the robustness of developmental outcomes to changing environmental conditions.


FIGURE 5. A model for integration of hbl-1 activity with the regulation of dauer formation. Early in larval development, environmental cues signal through TGFb and IIS pathways to direct progression to either the rapid L2 that leads to continuous development or the extended L2d that can lead to dauer diapause. Downstream transcription factors DAF-3 (complexed with DAF-5) and DAF-16 regulate target genes that in turn regulate dauer formation. One consequence of this regulation is daf-9 expression in favorable environmental conditions. High levels of HBL-1 at this stage promote L2 cell fates and also oppose dauer formation, perhaps by regulating common targets with DAF-3-DAF-5 and DAF-16 (blue arrow). By the time of the L2d-to-dauer molt, HBL-1 levels have been reduced (Figure 4). Lower levels of HBL-1 oppose L3 cell fates and also promote dauer formation, perhaps by regulating common targets with DAF-12. At the same time, a feedback loop between DAF-12 and let-7-family microRNAs is operating (Hammell et al. 2009), and LIN-42/Period modulates the dauer formation decision by opposing the activity of unliganded DAF-12 (Tennessen et al. 2010). This complex set of interactions may coordinate stage-specific cell fates with the dauer formation decision.

An efficient and sensitive method for preparing cDNA libraries from scarce biological samples


RNA (2011), 17:00–00. Published by Cold Spring Harbor Laboratory Press. Copyright _ 2011 RNA Society


Animals have evolved mechanisms to ensure the robustness of developmental outcomes to changing environments. MicroRNA expression may contribute to developmental robustness because microRNAs are key post-transcriptional regulators of developmental gene expression and can affect the expression of multiple target genes. Caenorhabditis elegans provides an excellent model to study developmental responses to environmental conditions. In favorable environments, C. elegans larvae develop rapidly and continuously through four larval stages. In contrast, in unfavorable conditions, larval development may be interrupted at either of two diapause stages: The L1 diapause occurs when embryos hatch in the absence of food, and the dauer diapause occurs after the second larval stage in response to environmental stimuli encountered during the first two larval stages. Dauer larvae are stress resistant and long lived, permitting survival in harsh conditions. When environmental conditions improve, dauer larvae re-enter development, and progress through two post-dauer larval stages to adulthood. Strikingly, all of these life history options (whether continuous or interrupted) involve an identical pattern and sequence of cell division and cell fates. To identify microRNAs with potential functions in buffering development in the context of C. elegans life history options, we used multiplex real-time PCR to assess the expression of 107 microRNAs throughout development in both continuous and interrupted life histories. We identified 17 microRNAs whose developmental profile of expression is affected by dauer life history and/or L1 diapause, compared to continuous development. Hence these microRNAs could function to regulate gene expression programs appropriate for different life history options in the developing worm.


FIGURE 1. Schematic representation of continuous and interrupted life history options. C. elegans larvae develop continuously through four larval stages in favorable environmental conditions, but can interrupt their development by entry to the stress-resistant L1 diapause or dauer diapause in unfavorable environmental conditions. (Red shading) Unfavorable or (blue shading) favorable environmental conditions sensed by larvae. These environmental conditions drive larvae to either continuous or diapause-interrupted life histories. (Dashed lines) Junctures where larvae may switch between diapauseinterrupted and continuous life history depending on the severity of the conditions encountered. Developmental stages at which miRNA levels were assessed in each life history: (blue) stages are within the continuous life history; (red) stages are within the dauer-interrupted life history. Developmentally equivalent stages were compared (Table 1); these are the red and blue stages at the same point along the vertical axis. (Orange) L1 diapause, which can lead to either continuous or dauer life histories, was compared to both embryos and continuously developing L1 larvae (Table 2).