Thomas F Duchaine et al. (2002) East Coast Worm Meeting "Does heritable interference induced by dsRNA involve transcriptional silencing in C. elegans?"

Darryl Conte Jr, Craig C Mello, Thomas F Duchaine

[East Coast Worm Meeting, 2002]

In C. elegans, exposure to dsRNA triggers potent and specific genetic interference. Remarkably, interference can be transmitted to the progeny of exposed animals as well as to later generations. This spectacular and yet poorly explored phenomenon implies the transmission of an epigenetic determinant from the intestine of an exposed animal to its germline, and subsequently to the germline of its progeny. Although the transmitted agent has not been identified, siRNAs are likely candidates to be the inherited agent, since they are directly implicated in targeted destruction of mRNA during RNAi. Targeting two different germline-expressed genes, we have examined the transmission of interference, the steady state level of the targeted mRNA, and the accumulation of siRNA for several generations following exposure to dsRNA. In our hands, interference persisted until the F4 generation. Although the level of mRNA was dramatically reduced in F1 through F3 generations relative to control animals, the steady-state accumulation of mRNA later regained its original level. As postulated above, siRNAs were detected in the F1 larvae of exposed animals, indicating that siRNAs are indeed inherited. However, siRNAs were not detected in F1 adults or later generations, suggesting that the targeted degradation of mRNA mediated by siRNAs may not be solely responsible for long-term silencing. In lieu of these findings, one explanation for the long-term inheritance of interference is that RNA interference is coupled to transcriptional silencing in the germline of C. elegans. We are currently examining the transcriptional activity of the targeted germline genes to address this possibility.

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).

Sawh, Ahilya et al. (2015) International Worm Meeting "Regulation of DCR-1-dependent RNAi pathways through DCR-1 phosphorylation."

Duchaine, Thomas, Wohlschlegel, James, Lewis, Alexandra, Sawh, Ahilya

[International Worm Meeting, 2015]

RNA interference (RNAi) pathways are directed by small (18-22nt) non-coding RNAs and orchestrate a variety of evolutionarily-conserved gene-silencing programs. The type III RNase protein Dicer is at the center of most of these pathways, including responses triggered by exogenous sources of long double-stranded RNA (exoRNAi). Other pathways, such as microRNA-mediated silencing and endoRNAi are triggered by endogenous loci, and control developmental and homeotic events. Dicer's role is crucial and three-fold: it cleaves long dsRNA precursors into smaller RNAs that direct silencing events, it loads the small RNAs into Argonaute proteins to form an active RNA-induced silencing complex (RISC), and it acts as a scaffold for several protein co-factors required for substrate recognition and processing. In C. elegans, Dicer (DCR-1) is essential in three small-RNA mediated silencing mechanisms including exoRNAi and ERI endoRNAi, two RNAi pathways that compete for downstream effectors. DCR-1 is part of distinct multi-protein complexes in each of these RNAi pathways: RDE complex in exoRNAi and ERIC in ERI endoRNAi.We discovered and validated several phosphorylated determinants of DCR-1 in the C. elegans. Particular attention was placed on a cluster of phosphorylated sites between the PAZ and RNase III domains, one of which could implicate AMPK signaling. Recent crystal structures of human Dicer have shown that this region could be involved in recognition of dsRNA substrates. We thus hypothesized that phosphorylation in this cluster could impair substrate recognition, or alter its specificity.To study the effect of DCR-1 phosphorylation on the three DCR-1-dependent RNAi pathways in C. elegans, transgenic strains were engineered expressing phosphorylation-deficient, and phosphorylation-mimetic mutants of DCR-1 in this cluster of sites. Functional analysis on these strains revealed that phosphorylation-deficient mutants display an impaired exoRNAi response, and severe developmental defects. Phosphorylation-deficient DCR-1 mutants also enhance interaction with ERI-endoRNAi DCR-1 cofactors. Taken together, these results support a model wherein DCR-1 phosphorylation may promote its shift from the ERIC to the RDE complex. Post-translational regulation of Dicer and RNAi pathways are largely unexplored and could potentially be incredibly impactful in light of their crucial roles in development and disease. The present study will shed light on how RNAi pathways integrate signals through phosphorylation signaling cascades.

Tissenbaum HA et al. (1995) International C. elegans Meeting "GENETIC AND MOLECULAR ANALYSIS OF daf-2 AND daf-16."

Gottlieb S, Lee L, Tissenbaum HA, Ruvkun GB, Lam F

[International C. elegans Meeting, 1995]

We have been studying the genetic interactions between the genes daf-2, daf-23 and daf-16 (Gottlieb and Ruvkun 1994). These genes either act in a branch separate from the daf-11/daf-21 and daf-7 group of the genetic epistasis pathway for dauer formation or further downstream in the pathway ( Riddle et al. 1981; Vowels and Thomas 1992; Thomas et al. 1993; Gottlieb and Ruvkun 1994). Molecular analysis of daf-2, daf-16 as well as daf-23 (see abstract by Morris et al. this meeting) will help to elucidate function (e.g. neurons vs. target tissues) as well as shed light on the complex genetic interactions of these genes.

Sulston JE et al. (1992) Nature "The C. elegans genome sequencing project: a beginning."

Wilson RK, Metzstein MM, Ainscough R, Waterston RH, Coulson AR, Craxton M, Thomas K, Dear S, Qiu L, Staden R, Berks M, Halloran N, Thierry-Mieg J, Hillier L, Sulston JE, Du Z, Durbin RM, Hawkins TL, Green P

[Nature, 1992]

The long-term goal of this project is the elucidation of the complete sequence of the Caenorhabditis elegans genome. During the first year methods have been developed and a strategy implemented that is amenable to large-scale sequencing. The three cosmids sequenced in this initial phase are surprisingly rich in genes, many of which have mammalian homologues.AD - MRC Laboratory of Molecular Biology, Cambridge, UK.FAU - Sulston, JAU - Sulston JFAU - Du, ZAU - Du ZFAU - Thomas, KAU - Thomas KFAU - Wilson, RAU - Wilson RFAU - Hillier, LAU - Hillier LFAU - Staden, RAU - Staden RFAU - Halloran, NAU - Halloran NFAU - Green, PAU - Green PFAU - Thierry-Mieg, JAU - Thierry-Mieg JFAU - Qiu, LAU - Qiu LAU - et al.LA - engPT - Journal ArticleCY - ENGLANDTA - NatureJID - 0410462RN - 0 (Cosmids)SB - IM

Weifeng Gu et al. (2007) International Worm Meeting "Analysis of a novel DRH-3 dependent RNA in C. elegans."

Craig C. Mello, Weifeng Gu, Darryl Jr. Conte, Chun-Chieh G. Chen

[International Worm Meeting, 2007]

RNAi is highly conserved in a variety of organisms including worms, fruit flies, plants, and mammals. RNAi related mechanisms are involved in developmental gene regulation, heterochromatin formation and antivirus defense. Previously, Duchaine et al1 from our lab identified a number of Dicer interacting proteins including DRH-3, a DExH-box RNA helicase. DRH-3 is required for RNAi, transgene silencing, and chromosome segregation. Worms depleted of DRH-3 fail to accumulate several small RNAs including endogenous siRNA, tiny noncoding RNAs, and X cluster RNAs. We have recently identified a few temperature-sensitive alleles of drh-3. At non-permissive temperature, these mutants not only exhibit all the phenotypes previously observed with a deletion strain, but also exhibit a high incidence of males and a mutator phenotype. Interestingly, drh-3 mutants and the deletion strain also lack a novel class of ~22nt small RNA with a 5 triphosphate. Unlike X cluster RNAs, tncRNAs and endogenous siRNAs, the ~22nt RNA is not sensitive to the depletion of Dicer, ERGO-1 or RRF-3. We cloned and sequenced several thousand cDNAs corresponding to these ~22nt RNAs, and found ~40% are complementary to mRNA and anther ~40% map to intergenic regions. Currently, we are investigating the roles of this novel RNA in gene regulation and chromatin remodeling. 1 Duchaine et al. Cell 124, 343-354, 2006. .

(2024) Development "The people behind the papers - Thomas Mullan and Richard Poole."

[Development, 2024]

Asymmetric cell divisions can produce daughter cells of different sizes, but it is unclear whether unequal cell cleavage is important for cell fate decisions. A new paper in Development explores the role of unequal cleavages in Caenorhabditis elegans embryos. To learn more about the story behind the paper, we caught up with first author Thomas Mullan and corresponding author Richard Poole, Associate Professor of Developmental Biology at University College London, UK.