(1991) International C. elegans Meeting "Regulators of Sex Determination and Dosage Compensation--- A Molecular Overview."

[International C. elegans Meeting, 1991]

[See Figure]

Blackwell TK et al. (2000) East Coast Worm Meeting "A conserved transcription motif suggesting functional parallels betweenC. elegans SKN-1 and Cap 'n' Collar-related bZIP proteins"

Walker AK, Blackwell TK, See R, Shi Y, An JH

[East Coast Worm Meeting, 2000]

In C. elegans embryogenesis, the maternal factor SKN-1 plays a pivital role in the specification of gut, some body wall muscle and pharynx. The acitivity of SKN-1 also requires mutliple inputs from transcriptional co-factor interactions as well as defined signal transduction pathways. To understand how SKN-1 responds to different blastomere enviroments and coordinates distinct developmental outcomes, we have begun to analyze SKN-1 structure and function. The SKN-1 DNA binding region is related to those of the Cap n Collar (CNC) family of basic leucine zipper (bZIP) proteins, which bind DNA as dimers, but SKN-1 is unique in that it binds DNA as a monomer. The similarity between SKN-1 and CNC proteins, such as NF-E2, NRF-1 and NRF-2, might simply reflect overlapping DNA binding strategies, but bZIP containing CNC proteins are not present in C. elegans, and no momermeric SKN-1 like protein has been identifed outside of nematodes. However, the involvement of CNC proteins, such as NRF-1, in endoderm and mesoderm development suggests that they may be close functional counterparts to SKN-1. With a cell culture assay, we have determined that SKN-1 induces transcription through three potent activation domains. The functional core of one of these domains is a short sequence motif, the DIDLID element, which is highly conserved in NRF-1 and NRF-2. The DIDLID element is important for SKN-1-driven transcription, suggesting that it is also likely to be significant in NRF proteins. In addition, SKN-1 binds to and activates transcription through the p300/CBP coactivator, supporting the genetic prediction that SKN-1 recruits the C. elegans p300/CBP ortholog, CBP-1. The role of CBP-1 in SKN-1 target gene activation is currently under investigation. The DIDLID element appears to act independently of p300/CBP, however, suggesting that it has a distinct conserved target. Thus, the evolutionary preservation of the DIDLID transcriptional element suggests that SKN-1 and NRF proteins interact with analogous co-factors, and may have preserved functional similarities despite diverging in their DNA binding domains.

Mello CC et al. (1995) International C. elegans Meeting "PIE-1 PROTEIN LOCALIZATION CORRELATES WITH THE GERM CELL FATE DURING EARLY C. ELEGANS EMBRYOGENESIS"

Zhang W, Lobel R, Priess JR, Schubert CM, Mello CC, Draper BW

[International C. elegans Meeting, 1995]

The maternally expressed gene pie-1 is required for germline specification in the early C. elegans embryo. In pie-1 single mutants and in all double mutant combinations analyzed, the germ cell precursors adopt somatic cell fates, in addition, pie-1 mutations exhibit a synthetic dominant maternal effect sterile phenotype in specific genetic backgrounds (see abstracts by Flanagan and Rocheleau). Recent findings suggest that pie-1 may suppress somatic development in the germ lineage by acting as a general transcriptional repressor (see abstracts by Batchelder and Seydoux).

Park, Jisoo et al. (2013) International Worm Meeting "Identification of mechanisms by which the expression of lim-4 homeodomain gene is regulated to specify the SMB motor neuron fate."

Kim, Kyuhyung, Yeon, Jihye, Park, Jisoo

[International Worm Meeting, 2013]

A cascade of transcriptional control confers neuron-specific morphologies and functions of individual neuronal cell types. The precise spatiotemporal regulation of transcription factors is essential for this neuronal differentiation and specification. However, the developmental mechanisms by which transcription factors are regulated to specify neuronal cell fate are not well known. We identified a lim-4 LIM homeodomain gene as a 'terminal selector' transcription factor (Hobert, 2008) that specifies the SMB motor neuron fate (See Jinmanh Kim's abstract). From the promoter analyses of the lim-4 gene, we identified several cis-regulatory sequences that are necessary for the expression of lim-4 in the SMB neurons. These sequences include a motif responsible for autoregulation of lim-4 in the SMB neurons (SMBDL/R and SMBVL/R). Interestingly, we also identified two other regulatory motifs that regulate the expression of lim-4 in the SMB dorsal (SMBDL/R) and SMB ventral (SMBVL/R) neurons, respectively, suggesting that the expression of lim-4 in SMB dorsal and ventral neurons is independently controlled. To explore the nature of differential expression of lim-4 in SMB, we are generating transgenic animals expressing GFP in the SMB dorsal neurons as well as mCherry in the SMB ventral neurons and performing mutant screens to identify upstream molecules, such as transcription factors. *Key words: SMB motor neurons, lim-4, terminal selector.

Rand JB et al. (2000) East Coast Worm Meeting "UNC-13 in the C. elegans Nervous System"

Kohn RE, Rand JB, McManus JR, Moulder GL, Duke A, Barstead RJ, Duerr JS

[East Coast Worm Meeting, 2000]

C. elegans unc-13 and its homologues in vertebrates and Drosophila are involved in neurotransmitter release. UNC-13 has several regions homologous to PKC regulatory domains; these domains confer it with calcium, phorbol ester and phospholipid binding properties (Maruyama and Brenner, PNAS 88, 1991). A 5.9kb transcript coding for a 200kDa protein was initially identified (now designated L-R for left and right regions). We have identified two additional types of transcripts. One transcript includes a 1kb novel exon (L-M-R, M for middle region) and another transcript lacks the 5' region included in the other two transcripts (M-R). All three transcripts are identical at the 3' end (R). C. elegans with mutations in the 5' end of the gene (L) alter two types of transcripts (L-R and L-M-R) resulting in an uncoordinated coily phenotype and resistance to the anti-cholinesterease, aldicarb. A 2.7kb deletion near the 3' end (R) (identified by Bob Barstead using PCR analysis) affects all unc-13 transcripts and results in a lethal phenotype. Antibodies recognizing the N-terminal region of UNC-13 (L) label synapses, but not synaptic vesicles, of most or all neurons; many mutations in L and R remove staining with this antibody. Supported by grants from the NIH and OCAST.

Yuji Kohara et al. (2001) International C. elegans Meeting "Developmental expression map of C.elegans genome"

Ikuko Sugiura, Masahiro Ito, Keiko Hirono, Yuji KOHARA, Michiko Serizawa, Tokie Oba, Takami Suzuki, Yohei Minakuchi, Kyoko Nakata, Masumi Obara, Mina Iwata, Tadasu SHIN-I, Yumiko Ueta

[International C. elegans Meeting, 2001]

We have been performing whole mount in situ hybridization using the cDNAs that have been classified in our EST project (See Thierry-Mieg et al.) as gene probes. Although there was a big delay in the project last year because we needed almost half a year to fix problems due to which our standard protocol suddenly didn't work, now we get the project back on the track and have finished some 7,600 genes. We have given minimal annotation to the in situ results; 10 stages for embryogenesis, 4 stages for larval-adult stage, on average 10 patterns (cell(s), tissue, region) per stage, 3 levels of relative intensity of signals per each pattern. Using the information, clustering analysis and extraction of consensus sequences in the upstream regulatory regions are in progress (see Ito et al.). Subsets of genes whose expression patterns are identical are being subjected to various analysis including RNAi, immunostaining and bioinformatic analysis (motif search, for example). This is a unique and powerful approach and, for example, we identified the function of proteasome in oocyte maturation and fertilization (see Hirono et al.). All the relevant data are integrated in NEXTDB and we are preparing to make them open by the worm meeting (See the demo by Shin-i et al.). In this report, we will show the content and the results of studies based on the database. Furthermore, we are planning "Annotation Relay" in which experts in various fields are invited to this lab by turns (a week or two per round and several people per round depending on the number of microscope) and look at the in situ slides on the microscope with the expert eyes to give more precise and deeper annotations to the in situ data than those we gave.

Marra MA et al. (1991) International C. elegans Meeting "CHARACTERIZATION OF THE COSMID C11 F2.II. FRAGMENT 'R' ENCODES A DECARBOXYLASE."

Clark DV, Prasad SS, Marra MA, Baillie DL

[International C. elegans Meeting, 1991]

We are attempting to identify and characterize all genes in the 100 kb interval between /et-56(1V) and unc-22(1V). Currently, we are focussing on the cosmid C1 1F2, which has been shown to rescue two alleles of let-56. This cosmid contains four Pst1 fragments we call P, Q, R, and S. The 18 kb fragment Q contains sequences homologous to the human Na+ / Ht antiporter (see other abstract Marra et al.). Immediately adjacent to this 18 kb fragment is the 8 kb fragment 'R'. Fragment R detects three messages on Northern blots. These messages are 1.9, 2.7 and 3.5 kilobases in length. The use of fragment R as a probe to screen B. Barstead's cDNA library in lambda ZAP resulted in the identification of a single positive clone out of approximately 300, 000 plaques screened. This clone was determined to be 1.9 kb in length. Sequence analysis of this clone revealed a long open reading frame of approximately 1940 nucleotides. Five hundred amino acids predicted from this long open reading frame were used to search the latest releases of the SWISS (rel.16) and translated EMBL(rel.25) databanks using the FASTA program of Pearson and Lipmann. Significant similarities to a variety of decarboxylases were detected, including rat and Drosophila melanogaster dopa decarboxylase, (40 % and 36% amino acid identity, respectively) and rat and human histidine decarboxylase (39% amino acid identity for both proteins). We are now sequencing genomic DNA from fragment R in order to elucidate the structure and function of this C. elegans decarboxylase-homologous gene. This work has been supported by an NSERC predoctoral scholarship to M.A.M. and an NSERC grant to D.L.B.

Birsoy, Bilge et al. (2009) International Worm Meeting "Right Way to Have Sex."

Bloss, Tim, Birsoy, Bilge, Rothman, Joel H., Downes, Joanna C., Choi, Shin Sik

[International Worm Meeting, 2009]

While the mechanism that breaks left-right (L-R) anatomical asymmetry (handedness) has been described in C. elegans, we have found that at least one additional mechanism must exist to establish other handedness cues that generates L-R differences in the deployment of alternative cell death pathways (see abstract from our lab by Choi et al.). To assess whether such a system might affect a behavior in the worm, we investigated whether male mating behavior exhibits L-R handedness. Upon recognizing a hermaphrodite, males initiate backward locomotion and continuously scan along the hermaphrodite''s body. When their tails reach either the head or tail of the hermaphrodite, males turn to maintain contact and then continue backward locomotion on the opposite side of the hermaphrodite. We found that this turning behavior shows a distinct right-handed bias: when individual males were allowed to mate with lin-2(e1309) vulvaless hermaphrodites, >70% of the turns when made over the hermaphrodites'' body (away from the agar surface) and >55% of turns when made under the hermaphrodites'' body (toward the agar surface) are right-handed. To determine whether this bias in turning direction correlated with L-R asymmetry in the male mating structure, which results from stochastic EGL-1-dependent loss of sensory rays (Choi et al. abstract), we examined the turning bias in egl-1(n1084n3082) mutants. We were surprised to find that, although wild-type males lack rays more frequently on the right, the right-hand turning bias is actually increased in the egl-1 mutant, in which no rays are lost and therefore rays are always symmetrically arranged. Thus, the intrinsic turning bias is even more apparent in males with symmetric mating structures. To assess whether this L-R behavioral bias is dependent on anatomical handedness, we analyzed gpa-16(it143) mutants in which the L-R asymmetry of the internal organs is reversed as a result of the reversal in the early embryonic symmetry break. Males with reversed anatomical asymmetry showed a virtually identical right hand bias in turning, demonstrating that a handedness-determining system that is independent of the previously described L-R symmetry breaking event must control this behavior. These findings raise the possibility that, analogous to brain laterality in humans, functionally L-R asymmetry in the C. elegans motor nervous system may be independent of anatomical handedness.

Zhou, Yiwen et al. (2017) International Worm Meeting "Stereospecific bioactivity of the eicosanoid 17,18-epoxyeicosatetraenoic acid on the pharyngeal pumping of Caenorhabditis elegans."

Zhou, Yiwen, Menzel, Ralph

[International Worm Meeting, 2017]

17,18-epoxyeicosatetraenic acid (17,18-EEQ), the most abundant cytochrome P450 (CYP)-eicosanoid in C. elegans, is a potential signaling molecule in the regulation of pharyngeal pumping activity. Here we tested the hypothesis that stereo-discrimination of this chiral molecule may hint the existence of a receptor in the pharyngeal muscle and/or neuronal cells. We analyzed the effect of short-term incubation in both well fed and starved condition and found that the stereoisomer 17(R),18(S)-EEQ, clearly rescued impairments of pharyngeal pumping in D-6 fatty acid desaturase mutant strain fat-3(wa22). After treatment with the 17(S),18(R)-EEQ stereoisomer, however, we found no effect on pumping activity. In addition, we will analyze the total endogenous eicosanoid stereoisomer content of C. elegans by chiral LC/MS-MS to see whether or not only specific stereoisomers are endogenous resources. 17(R),18(S)-EEQ was more active in ceeh-1(ok3153) mutant background in comparison to other stains. We suspect that ceeh-1(ok3153), failing to produce a functional active soluble hydrolase (sEH), is unable to efficiently catalyze the hydrolysis of 17,18-EEQ to the corresponding diol (17,18-DHEQ), which we found correlated with a loss of function of this signaling molecule. 17,18-DHEQ treatment was inactive in a C. elegans' pumping assay.

O'Neil NJ et al. (1996) West Coast Worm Meeting "SYSTEMATIC HIGH RESOLUTION MAPPING OF ESSENTIAL GENES IN THE sDf125 REGION BY TRANSGENIC RESCUE."

Kuervers LM, Baillie DL, Vatcher GP, O'Neil NJ

[West Coast Worm Meeting, 1996]

We have demonstrated that transgenic rescue is an effective method for high resolution mapping of essential genes. Our lab is constructing a map of essential genes on LGIII left. We have divided the left end of the central cluster into manageable regions which are defined by overlapping deficiencies and duplications. These regions are determined physically by PCR testing the deficiencies to determine endpoints (see N.Franz et al. abstract, this meeting). Into these regions, we have mapped a set of EMS induced lethals and maternal effect lethals. (see abstracts by H. Stewart et al. and G. Vatcher and D. Baillie, this meeting). One such region is defined by sDf125 and sDp8. This region spans 340 000 base pairs and is completely covered by nine cosmids. Within this region there are 75 putative genes predicted by Genefinder. We have used a sytematic approach to rescue essential genes within the sDf125 region with transgenic cosmids from the library created by J. Schein, D. Janke and The Ha as part of a CGAT grant to Ann Rose and David Baillie (see abstracts by J.Schein et al. and D. Janke et al., this meeting) To date this method has proven very successful. At least 8 genes have been completely rescued in this region by this approach. These transgenic rescues map these genes to 40 kB (one cosmid) resolution as opposed to the 340 kB resolution of the deficiency and duplication data. This is almost a ten-fold increase in resolution and reduces the number of ORFs which may be responsible for the gene function. The next step will be the subcloning of cosmids with which we have rescued essential genes. This will directly corellate the lethal or maternal effect lethal phenotype to the appropriate ORF. We have already begun the subcloning of cosmid C05D11 (see G.Vatcher and D.Baillie abstract, this meeting). This project is funded by a CGAT grant to Ann Rose and David Baillie.