Thomas M et al. (2010) Nat Struct Mol Biol "Desperately seeking microRNA targets."

Thomas M, Lieberman J, Lal A

[Nat Struct Mol Biol, 2010]

MicroRNAs (miRNAs) suppress gene expression by inhibiting translation, promoting mRNA decay or both. Each miRNA may regulate hundreds of genes to control the cell's response to developmental and other environmental cues. The best way to understand the function of a miRNA is to identify the genes that it regulates. Target gene identification is challenging because miRNAs bind to their target mRNAs by partial complementarity over a short sequence, suppression of an individual target gene is often small, and the rules of targeting are not completely understood. Here we review computational and experimental approaches to the identification of miRNA-regulated genes. The examination of changes in gene expression that occur when miRNA expression is altered and biochemical isolation of miRNA-associated transcripts complement target prediction algorithms. Bioinformatic analysis of over-represented pathways and nodes in protein-DNA interactomes formed from experimental candidate miRNA gene target lists can focus attention on biologically significant target genes.

Thomas M Ratliff et al. (2001) International C. elegans Meeting "A mutation affecting phasmid function and tail morphogenesis"

Thomas M Ratliff, Michael A Herman

[International C. elegans Meeting, 2001]

mh21 was isolated in a screen for mutations that cause phasmid dye-filling defects. The phasmids are a pair of bilateral sensory structures found in the C. elegans tail. Each phasmid is comprised of two neurons, a sheath cell, and two glial support cells, called socket cells, which serve to provide a pore for phasmid neurons to sense the outside environment. When animals are soaked in fluorescent dyes, such as DiO, the phasmid neurons fill with dye. Phasmid socket cells are derived from the posterior daughter of the first asymmetric division of the T blast cell, T.p. Despite a highly penetrant phasmid dye-filling defect, amphid dye-filling is normal in mh21 animals and most have phasmid socket cells. These observations suggest that either the phasmid sockets or phasmid neurons are rendered non-functional in mh21 animals. Expression of the srb-6::gfp phasmid neuron reporter was normal in mh21 animals, which indicates that mh21 phasmid socket cells are defective. The mh21 mutation is pleiotropic. mh21 animals display reduced fecundity, uncoordinated movement, constipation and an egg-laying defect. mh21 males have abnormal tail morphologies; sensory rays 3 and 4 are often fused and spicules are short or crumpled and fail to protract. The multiple defects caused by this mutation suggest that the gene identified by mh21 has several morphogenetic roles. mh21 has been physically mapped to a small region on LG IV by mapping breakpoints of non-complementing deficiencies relative to nearby polymorphisms. Transformation rescue has been achieved with a YAC clone found within the mh21 interval. Rescue experiments aimed at cloning mh21 are underway and their progress will be reported.

Thomas M Ratliff et al. (2002) Mid-west Worm Meeting "EGL-27 MTA-interacting proteins are components of the CCR4-NOT complex and synMuv B pathway"

Thomas M Ratliff, Michael A Herman, Duaa H Mohammad

[Mid-west Worm Meeting, 2002]

Mutations in egl-27 cause defects in cell migrations, cell fate specification, cell fusion and morphogenesis. The amino terminal region of EGL-27 is similiar to a human metastasis-associated factor (MTA), recently identified as a co-purifying member of a human complex having ATP-dependent nucleosome-remodeling and histone deacetylase (NURD) function. Other C. elegans homologs of human NURD components--specifically, let-418 Mi-2, lin-53 RbAp48 and hda-1 HDAC--have been shown to act as synthetic multivulva (synMuv) class B genes. The synMuv class B genes function redundantly with synMuv class A genes to antagonize Ras signaling-mediated vulval induction in the vulval precursor cells. Several class B synMuv members have been identified, including those similar to the human tumor suppressor, pRB, and its human binding partners, DP and E2F. Despite a ubiquitous nuclear expression pattern that overlaps with other NURD and synMuv B members, the apparently obscure role of EGL-27 MTA in vulval induction suggests a lack of functional conservation with its human counterpart. In an effort to better understand the function of EGL-27, a two-hybrid screen was performed in yeast (two-hybrid library kindly provided by Robert Barstead). Multiple library clones were retrieved that corresponded to the mep-1 locus and two genes having similarity to components of the highly conserved CCR4-NOT complex, Cenot-2 and Cenot-3. MEP-1 is a large C2H2 zinc-finger protein with two potential homologs in Drosophila. CeNOT-2 and CeNOT-3 contain a previously unidentified domain of similarity located near their respective carboxy termini. Bacterially-expressed GST::EGL-27 interacts in vitro with CeNOT-2 and CeNOT-3 fragments corresponding to the two-hybrid library clones, thus verifying the two-hybrid interactions.

Stern MJ et al. (1991) Development "A normally attractive cell interaction is repulsive in two C. elegans mesodermal cell migration mutants."

Stern MJ, Horvitz HR

[Development, 1991]

In wild-type Caenorhabditis elegans hermaphrodites, two bilaterally symmetric sex myoblasts (SMs) migrate anteriorly to flank the precise center of the gonad, where they divide to generate the muscles required for egg laying (J. E. Sulston and H. R. Horvitz (1977) Devl Biol. 56, 110-156). Although this migration is largely independent of the gonad, a signal from the gonad attracts the SMs to their precise final positions (J. H. Thomas, M. J. Stern and H. R. Horvitz (1990) Cell 62, 1041-1052). Here we show that mutations in either of two genes, egl-15 and egl-17, cause the premature termination of the migrations of the SMs. This incomplete migration is caused by the repulsion of the SMs by the same cells in the somatic gonad that are the source of the attractive signal in wild-type animals.

Tax FE et al. (1994) Worm Breeder's Gazette "Some Notes on Mapping Contigs Using Molecular Analysis of Deficiences"

Thomas JH, Tax FE

[Worm Breeder's Gazette, 1994]

Some notes on mapping contigs using molecular analysis of deficiencies Frans Tax and Jim Thomas, Dept. of Genetics, University of Washington, Seattle WA 98195

Thomas JH et al. (1994) Worm Breeder's Gazette "lin-36, a Class B Synthetic Multivulva Gene, Encodes a Novel Protein"

Thomas JH, Horvitz HR

[Worm Breeder's Gazette, 1994]

lin-36, a Class B Synthetic Multivulva Gene, Encodes a Novel Protein Jeffrey H. Thomas and H. Robert Horvitz, HHMI, Dept. Biology, MIT, Cambridge, MA 02139, USA

Burglin TR et al. (1993) Worm Breeder's Gazette "ceh-6 Expression and Generation of a Knock-Out"

Plasterk RHA, Ruvkun GB, Burglin TR

[Worm Breeder's Gazette, 1993]

ceh 6 expression and generation of a knock-out Thomas Burglin, Ron Plasterk*, Gary Ruvkun Dept. of Molecular Biology, Wellman 8, Massachusetts General Hospital, Boston, MA, 02114, USA, and *Netherlands Cancer Institute, Plesmanlaan 121, 1066CX Amsterdam, The Netherlands.

Reilly, Molly et al. MicroPubl Biol

Hobert, Oliver, Reilly, Molly

[MicroPubl Biol, 2020]

We have previously described the expression patterns of all but one of the 102 homeobox genes present in the C. elegans genome, using either fosmid-based reporter transgenes or CRISPR/Cas9-engineered gfp reporter alleles (Reilly et al., 2020). The last remaining homeobox gene for which we were initially not able to generate a reporter reagent for is ceh-84 (Reilly et al., 2020). As previously recognized by Thomas Brglin (Hench et al., 2015), ceh-84 codes for an unusual homeodomain protein with two divergent homeodomains (Fig.1D). It likely is a tandem duplicate of the ceh-85 gene, which has been classified as a pseudogene (Fig.1B). ceh-84 has no recognizable homologs in other Caenorhabditis species (Hench et al., 2015). Together with its duplicate, ceh-85, localizes to a large cluster of extensively duplicated genes on chromosome II, described by James Thomas (Thomas, 2006). Most of the duplicated genes code for MATH and BTB type proteins (Fig.1A). The entire cluster seems to be C. elegans-specific (Thomas, 2006) and, apart from a number of pseudogenes, it also contains the C. elegans-specific ceh-81, ceh-82 and ceh-83 homeobox genes (Fig.1A).

Wypijewska A et al. (2012) Biochemistry "7-methylguanosine diphosphate (m(7)GDP) is not hydrolyzed but strongly bound by decapping scavenger (DcpS) enzymes and potently inhibits their activity."

Wypijewska A, Darzynkiewicz E, Davis RE, Jemielity J, Bojarska E, Lukaszewicz M, Stepinski J

[Biochemistry, 2012]

Decapping scavenger (DcpS) enzymes catalyze the cleavage of a residual cap structure following 3' 5' mRNA decay. Some previous studies suggested that both m(7)GpppG and m(7)GDP were substrates for DcpS hydrolysis. Herein, we show that mononucleoside diphosphates, m(7)GDP (7-methylguanosine diphosphate) and m(3)(2,2,7)GDP (2,2,7-trimethylguanosine diphosphate), resulting from mRNA decapping by the Dcp1/2 complex in the 5' 3' mRNA decay, are not degraded by recombinant DcpS proteins (human, nematode, and yeast). Furthermore, whereas mononucleoside diphosphates (m(7)GDP and m(3)(2,2,7)GDP) are not hydrolyzed by DcpS, mononucleoside triphosphates (m(7)GTP and m(3)(2,2,7)GTP) are, demonstrating the importance of a triphosphate chain for DcpS hydrolytic activity. m(7)GTP and m(3)(2,2,7)GTP are cleaved at a slower rate than their corresponding dinucleotides (m(7)GpppG and m(3)(2,2,7)GpppG, respectively), indicating an involvement of the second nucleoside for efficient DcpS-mediated digestion. Although DcpS enzymes cannot hydrolyze m(7)GDP, they have a high binding affinity for m(7)GDP and m(7)GDP potently inhibits DcpS hydrolysis of m(7)GpppG, suggesting that m(7)GDP may function as an efficient DcpS inhibitor. Our data have important implications for the regulatory role of m(7)GDP in mRNA metabolic pathways due to its possible interactions with different cap-binding proteins, such as DcpS or eIF4E.

O'Connell EM et al. (2015) J Infect Dis "Targeting Filarial Abl-like Kinases: Orally Available, Food and Drug Administration-Approved Tyrosine Kinase Inhibitors Are Microfilaricidal and Macrofilaricidal."

Nutman TB, O'Connell EM, Bennuru S, Steel C, Dolan MA

[J Infect Dis, 2015]

BACKGROUND: Elimination of onchocerciasis and lymphatic filariasis is targeted for 2020. Given the coincident Loa loa infections in Central Africa and the potential for drug resistance development, the need for new microfilaricides and macrofilaricides has never been greater. With the genomes of L. loa, Onchocerca volvulus, Wuchereria bancrofti, and Brugia malayi available, new drug targets have been identified. METHODS: The effects of the tyrosine kinase inhibitors imatinib, nilotinib, and dasatinib on B. malayi adult males, adult females, L3 larvae, and microfilariae were assessed using a wide dose range (0-100 M) in vitro. RESULTS: For microfilariae, median inhibitory concentrations (IC50 values) on day 6 were 6.06 M for imatinib, 3.72 M for dasatinib, and 81.35 M for nilotinib; for L3 larvae, 11.27 M, 13.64 M, and 70.98 M, respectively; for adult males, 41.6 M, 3.87 M, and 68.22 M, respectively; and for adult females, 42.89 M, 9.8 M, and >100 M, respectively. Three-dimensional modeling suggests how these tyrosine kinase inhibitors bind and inhibit filarial protein activity. CONCLUSIONS: Given the safety of imatinib in humans, plans are underway for pilot clinical trials to assess its efficacy in patients with filarial infections.