Christopher M. Hammell

nhl-2 modulates microRNA activity in Caenorhabditis elegans

TRIM-NHL proteins represent a large class of metazoan proteins implicated in development and disease. We demonstrate that a C. elegans TRIM-NHL protein, NHL-2, functions as a cofactor for the microRNA-induced silencing complex (miRISC) and thereby enhances the posttranscriptional repression of several genetically verified microRNA targets, including hbl-1 and let-60/Ras (by the let-7 family of microRNAs) and cog-1 (by the lsy-6 microRNA). NHL-2 is localized to cytoplasmic P-bodies and physically associates with the P-body protein CGH-1 and the core miRISC components ALG-1/2 and AIN-1. nhl-2 and cgh-1 mutations compromise the repression of microRNA targets in vivo but do not affect microRNA biogenesis, indicating a role for an NHL-2:CGH-1 complex in the effector phase of miRISC activity. We propose that the NHL-2:CGH-1 complex functions in association with mature miRISC to modulate the efficacy of microRNA:target interactions in response to physiological and developmental signals, thereby ensuring the robustness of genetic regulatory pathways regulated by microRNAs.

Coupling of Termination, 3 Processing, and mRNA Export

ABSTRACT In a screen to identify genes required for mRNA export in Saccharomyces cerevisiae, we isolated an allele of poly(A) polymerase (PAP1) and novel alleles encoding several other 3′ processing factors. Many newly isolated and some previously described mutants (rna14-48, rna14-49, rna14-64, rna15-58, and pcf11-1 strains) are defective in polymerase II (Pol II) termination but, interestingly, retain the ability to polyadenylate these improperly processed transcripts at the nonpermissive temperature. Deletion of the cis-acting sequences required to couple 3′ processing and termination also produces transcripts that fail to exit the nucleus, suggesting that all of these processes (cleavage, termination, and export) are coupled. We also find that several but not all mRNA export mutants produce improperly 3′ processed transcripts at the nonpermissive temperature. 3′ maturation defects in mRNA export mutants include improper Pol II termination and/or the previously characterized hyperpolyadenylation of transcripts. Importantly, not all mRNA export mutants have defects in 3′ processing. The similarity of the phenotypes of some mRNA export mutants and 3′ processing mutants indicates that some factors from each process may mechanistically interact to couple mRNA processing and export. Consistent with this assumption, we present evidence that Xpo1p interacts in vivo with several 3′ processing factors and that the addition of recombinant Xpo1p to in vitro processing reaction mixtures stimulates 3′ maturation. Of the core 3′ processing factors tested (Rna14p, Rna15p, Pcf11p, Hrp1p, Fip1p, and Cft1p), only Hrp1p shuttles. Overexpression of Rat8p/Dbp5p suppresses both 3′ processing and mRNA export defects found in xpo1-1 cells.

A feedback circuit involving let-7-family miRNAs and DAF-12 integrates environmental signals and developmental timing in Caenorhabditis elegans

Animal development is remarkably robust; cell fates are specified with spatial and temporal precision despite physiological and environmental contingencies. Favorable conditions cause Caenorhabditis elegans to develop rapidly through four larval stages (L1–L4) to the reproductive adult. In unfavorable conditions, L2 larvae can enter the developmentally quiescent, stress-resistant dauer larva stage, enabling them to survive for prolonged periods before completing development. A specific progression of cell division and differentiation events occurs with fidelity during the larval stages, regardless of whether an animal undergoes continuous or dauer-interrupted development. The temporal patterning of developmental events is controlled by the heterochronic genes, whose products include microRNAs (miRNAs) and regulatory proteins. One of these proteins, the DAF-12 nuclear hormone receptor, modulates the transcription of certain let-7-family miRNAs, and also mediates the choice between the continuous vs. dauer-interrupted life history. Here, we report a complex feedback loop between DAF-12 and the let-7-family miRNAs involving both the repression of DAF-12 by let-7-family miRNAs and the ligand-modulated transcriptional activation and repression of the let-7-Fam miRNAs by DAF-12. We propose that this feedback loop functions to ensure robustness of cell fate decisions and to coordinate cell fate with developmental arrest.

Nucleocytoplasmic transport: Driving and directing transport

Nucleocytoplasmic transport involves assembly and movement across the nuclear envelope of cargo-receptor complexes that interact with the small GTPase Ran. The asymmetric distribution of Ran regulator proteins, RanGAP1 and RCC1, provides the driving force and directionality for nuclear transport.

The microRNA-argonaute complex A platform for mRNA modulation

With the cloning the lin-4 gene in 1993, the possibility of an approximately 21-nucleotide RNA functioning as a regulatory molecule intrigued a relatively small number of scientists. This idea appeared to be a peculiarity of C. elegans as it was not until seven years later that the second, more conserved small RNA, let-7 was cloned. A spate of papers in 2000 and 2001 revealed that the underlying properties of the lin-4 and let-7 genes were a common facet of animal genomes and the absolute number and potential of this new class of gene products requires us to integrate them with other aspects of gene expression and evolution1-3. A wealth of information has accumulated in the intervening years that outline, in general, how these small RNAs are expressed and processed into a functional form. Contemporaneous to these studies, experiments also identified a cadre of evolutionarily conserved proteins, the Argonautes (Agos) that directly associate with and are required for microRNA function. Computational and experimental methods have led the identification of many functional mRNA targets. In the last few years, a significant body of work has focused on resolving two key issues: How do microRNAs function in particular genetic contexts (i.e. as “molecular switches” or “fine-tuners” of gene expression) and secondly, what facet/s of mRNA metabolism do microRNAs modulate in their role/s as a regulatory molecule? The primary objective here is not to comprehensively compare the competing models of microRNA function (as have several, recent reviews have4-6) but to frame a potential solution to these two fundamental questions by suggesting that the core microRNA-Ribonucleic-Protein Complex (microRNP), composed of the microRNA and an Ago protein, functions as a highly modifiable scaffold that associates with specific mRNAs via the bound microRNA and facilitates the localized activity of a variety of accessory proteins. The resulting composite mechanism could account for the apparent complexities of measuring microRNA activity and furthermore, accommodate the broad levels of regulation observed in vivo.

Analysis of RNA export

Publisher Summary Nucleocytoplasmic transport plays a critical role in the expression of genetic information in eukaryotic cells. All RNAs except those encoded by the mitochondrial genome are synthesized in the nucleus, but most of these RNAs must be exported to the cytoplasm where they function in protein synthesis. The application of fluorescence in situ hybridization (FISH) to detect RNA in yeast has been critical for the analysis of RNA export. This technique is capable of providing information about the subcellular distribution of both total mRNA and individual mRNA species. Although not as quantitative as fractionation, FISH analysis also provides information about the distribution of RNA within the cytoplasmic and nuclear compartments. Because different mRNA molecules can have distinct subcellular distributions, it is sometimes useful to detect the location of specific mRNA species and—at the same time—the location of total mRNA. The ability to localize simultaneously both RNA and protein has also increased the understanding of RNA export. Finally, FISH analysis can be harnessed as a screen for mutants defective for RNA export or for distribution of a specific mRNA to its particular subcellular location.

Mutations in Conserved Residues of the C. elegans microRNA Argonaute ALG-1 Identify Separable Functions in ALG-1 miRISC Loading and Target Repression

microRNAs function in diverse developmental and physiological processes by regulating target gene expression at the post-transcriptional level. ALG-1 is one of two Caenorhabditis elegans Argonautes (ALG-1 and ALG-2) that together are essential for microRNA biogenesis and function. Here, we report the identification of novel antimorphic (anti) alleles of ALG-1 as suppressors of lin-28(lf) precocious developmental phenotypes. The alg-1(anti) mutations broadly impair the function of many microRNAs and cause dosage-dependent phenotypes that are more severe than the complete loss of ALG-1. ALG-1(anti) mutant proteins are competent for promoting Dicer cleavage of microRNA precursors and for associating with and stabilizing microRNAs. However, our results suggest that ALG-1(anti) proteins may sequester microRNAs in immature and functionally deficient microRNA Induced Silencing Complexes (miRISCs), and hence compete with ALG-2 for access to functional microRNAs. Immunoprecipitation experiments show that ALG-1(anti) proteins display an increased association with Dicer and a decreased association with AIN-1/GW182. These findings suggest that alg-1(anti) mutations impair the ability of ALG-1 miRISC to execute a transition from Dicer-associated microRNA processing to AIN-1/GW182 associated effector function, and indicate an active role for ALG/Argonaute in mediating this transition.

LIN-42, the Caenorhabditis elegans PERIOD homolog, Negatively Regulates MicroRNA Transcription

During C. elegans development, microRNAs (miRNAs) function as molecular switches that define temporal gene expression and cell lineage patterns in a dosage-dependent manner. It is critical, therefore, that the expression of miRNAs be tightly regulated so that target mRNA expression is properly controlled. The molecular mechanisms that function to optimize or control miRNA levels during development are unknown. Here we find that mutations in lin-42, the C. elegans homolog of the circadian-related period gene, suppress multiple dosage-dependent miRNA phenotypes including those involved in developmental timing and neuronal cell fate determination. Analysis of mature miRNA levels in lin-42 mutants indicates that lin-42 functions to attenuate miRNA expression. Through the analysis of transcriptional reporters, we show that the upstream cis-acting regulatory regions of several miRNA genes are sufficient to promote highly dynamic transcription that is coupled to the molting cycles of post-embryonic development. Immunoprecipitation of LIN-42 complexes indicates that LIN-42 binds the putative cis-regulatory regions of both non-coding and protein-coding genes and likely plays a role in regulating their transcription. Consistent with this hypothesis, analysis of miRNA transcriptional reporters in lin-42 mutants indicates that lin-42 regulates miRNA transcription. Surprisingly, strong loss-of-function mutations in lin-42 do not abolish the oscillatory expression patterns of lin-4 and let-7 transcription but lead to increased expression of these genes. We propose that lin-42 functions to negatively regulate the transcriptional output of multiple miRNAs and mRNAs and therefore coordinates the expression levels of genes that dictate temporal cell fate with other regulatory programs that promote rhythmic gene expression.

A genome-wide RNAi screen identifies factors required for distinct stages of C. elegans piRNA biogenesis

In animals, piRNAs and their associated Piwi proteins guard germ cell genomes against mobile genetic elements via an RNAi-like mechanism. In Caenorhabditis elegans, 21U-RNAs comprise the piRNA class, and these collaborate with 22G RNAs via unclear mechanisms to discriminate self from nonself and selectively and heritably silence the latter. Recent work indicates that 21U-RNAs are post-transcriptional processing products of individual transcription units that produce ∼ 26-nucleotide capped precursors. However, nothing is known of how the expression of precursors is controlled or how primary transcripts give rise to mature small RNAs. We conducted a genome-wide RNAi screen to identify components of the 21U biogenesis machinery. Screening by direct, quantitative PCR (qPCR)-based measurements of mature 21U-RNA levels, we identified 22 genes important for 21U-RNA production, termed TOFUs (Twenty-One-u Fouled Ups). We also identified seven genes that normally repress 21U production. By measuring mature 21U-RNA and precursor levels for the seven strongest hits from the screen, we assigned factors to discrete stages of 21U-RNA production. Our work identifies for the first time factors separately required for the transcription of 21U precursors and the processing of these precursors into mature 21U-RNAs, thereby providing a resource for studying the biogenesis of this important small RNA class.

Inducing RNAi in C. elegans by Feeding with dsRNA-expressing E. coli

Owing to the relative ease and high-throughput nature of ingestion-mediated RNAi, the feeding of engineered Escherichia coli to wild-type and mutant Caenorhabditis elegans has developed into the most productive and common method to probe the functions of C. elegans genes. This protocol includes two variations of RNAi by feeding: one in which L1 larvae are fed dsRNA-expressing E. coli in liquid culture (commonly used to score effects of RNAi on postembryonic larval development) and another involving feeding of late larval- or adult-staged animals on standard solid medium culture plates.