Smith SJ (1978) Nature "The structural gene for myosin: a close look."

Smith SJ

[Nature, 1978]

The humble soild nematode Caenorhabditis elegans has proved a useful tool for the extension of the study of gene-protein relationships from prokaryotic to eukaryotic organisms. A variety of uncoordinated (unc) mutants can be isolated by their behavioral characteristics, and electron micrographs show that such mutations are associated with disorganisation of muscle structure. One such mutant of the unc-54 gene (e675) has a normal amount of myosin but the number of thick filaments (myosin-containing...

Heather Van Epps et al. (2007) International Worm Meeting "SYDN-1, a novel protein, regulates synapse stabilization and axon branching."

Yishi Jin, Ya Dai, Heather Van Epps

[International Worm Meeting, 2007]

We are interested in identifying new molecular players in synapse development. Many synapse development mutants display only subtle behavioral effects. This is likely due to redundancy of gene effects in synapse development. We reason that additional synapse development genes may be identified using a selective genetic background. We conducted a recessive enhancer screen in the rpm-1 mutant background, and isolated the sydn-1 (for Syd enhancer) mutant. Homozygous sydn-1 mutant animals display mild movement defects. Using a panel of synaptic reporter genes for the D type motor neurons, we observed abnormal synaptic vesicle pools and endosome compartments in sydn-1 mutants. Double mutants of sydn-1 with several synapse development mutants, e.g. rpm-1, syd-2, exhibit enhanced behavior and synaptic phenotypes. In particular, in these double mutants, excess axon branching in motor neurons and touch neurons frequently appeared near synapse sites. We mapped and cloned the sydn-1 gene. The sydn-1(ju541) mutation contains a 1kb deletion of Y39G10AR.17, which removes approximately 200bp of the promoter and approximately half of the 63kDa protein. Neuronal expression of Y39G10AR.17 rescues the behavior and neuronal phenotypes of the sydn-1 mutant. The enhanced phenotypes of sydn-1 with known synapse development genes suggest that sydn-1 defines a novel synapse development pathway. Live imaging studies in other organisms have shown that synapse formation stabilizes axon patterning(1-3). However, the molecular mechanism is poorly understood. Our phenotypic studies suggest that SYDN-1 may play a role in inhibiting axon branching or facilitating axon pruning via synapse stabilization. SYDN-1 protein has a Pro-rich domain, which is often present in proteins that regulate the actin cytoskeleton. To explore the molecular mechanism of the Sydn-1 phenotype we have conducted a suppressor screen and have isolated nine sydn-1 suppressors. Initial genetic analysis suggests that these suppressor mutations belong to at least two non-complementation groups. Dissecting the sydn-1 pathway will reveal new insights into synapse stabilization and axon branching. 1.Meyer MP and Smith SJ Neurosci. 2006 Mar 29;26(13):3604-14 2.Javaherian A and Cline HT Neuron. 2005 Feb 17;45(4):505-12 3.Ruthazer ES, Li J, Cline HT.J Neurosci. 2006 Mar 29;26(13):3594-603.

Rosenberg R (1978) Worm Breeder's Gazette

Rosenberg R

[Worm Breeder's Gazette, 1978]

All eyes are on the newest fashion trend, the Dumpy Look . Pace setting designer I.M. Worm s androgynous wardrobe is all the rage in Paris. Bianca Jagger quips, Tres, tres - Women s Wear Daily writes, Elegans personified - Patti Smith thinks, The punks won t buy it and Craig Russell says, It fits right in with my act . A product of Mutant Isolation, Inc.

Kravtsov, V. et al. (2013) International Worm Meeting "The effects of aging on dendritic plasticity and PVD-FLP branch coexistence."

Podbilewicz, B., Oren-Suissa, M., Kravtsov, V.

[International Worm Meeting, 2013]

Self-avoidance, tiling and coexistence are the main mechanisms that enable the best dendritic coverage. C. elegans undergoes aging-associated changes that ultimately lead to decreased functionality of the organism, including its neurological functions. Recent research has shown that the nervous system of C. elegans undergoes changes and alterations during aging including dendritic morphology (Tank et al., 2011). We study dendritic plasticity, aging and spatial dendritic organization of two highly arborized mechanoreceptors in C. elegans, PVD and FLP (Oren-Suissa et al., 2010). PVD dendrites of L4s and young adults show regenerative ability following dendrotomy (laser induced severing of dendrites). Our working hypothesis is that in older ages this ability to regenerate is compromised. Previous studies and our preliminary results indicate that PVD and FLP do not overlap in larval stages (Smith et al., 2010). In addition, dendrites within each bilateral PVD do not overlap through a self-avoidance mechanism (Smith et al., 2012). We found that (1) the coverage fields of the PVD and FLP overlap in adult worms, which indicates coexistence and not tiling. This overlap increases as the worm ages. (2) PVDs show aberrant arborization at the age of 9 days of adulthood. (3) Dramatic increase in self-avoidance defects as animals age. In humans many neurodegenerative diseases as well as generalized cognitive decline are associated with age, aberrant arborization or both (e.g. autism and Alzheimer's disease). However our understanding of how these disorders are triggered and aggravated is scarce. Our research provides an insight into the aging and regeneration process of individual neurons. Oren-Suissa, M., et al. (2010). Science 328, 1285-1288. Smith, C.J. et al. (2010). Developmental Biology 345, 18-33. Smith, C.J., et al. (2012). Nature Neuroscience 15, 731-737. Tank, E.M.H. et al. (2011). Journal of Neuroscience 31, 9279-9288.

Cassada RC et al. (1980) Worm Breeder's Gazette "initial characterization of ts embryonic defective (emb) mutants (Goettingen set)."

Culotti MR, Cassada RC, Von Ehrenstein G, Isnenghi E

[Worm Breeder's Gazette, 1980]

[See Figure 1] Already published allelism: Wood et al., 1980: b117=b189; b246 = let- 2.Miwa et al., 1980: hc57 = hc62; hc61 = hc67. Our global complementation results: g1 = g4; g16 = g65 = hc61 = hc67; g36 = hc65; g23 = g34 = hc70 = b117 = b189; g37 = b246 = let-2; b84 = hc66; g14 = g43; g57 = b1O. From frequency of multiple alleles we estimate 200-400 genes essential for embryogenesis. Mapping is in progress. We are also doing tsp's, R + H Tests, and cellular defects ( Isnenghi, Cassada, Radnia, Schierenberg, K. Smith, v. Ehrenstein).

Pourkarimi, Ehsan et al. (2015) International Worm Meeting "Epigenetic program of DNA replication."

Whitehouse, Iestyn, Pourkarimi, Ehsan, Bellush, James

[International Worm Meeting, 2015]

In eukaryotes, multiple replication origins initiate DNA synthesis bidirectionally. Half of the genome is duplicated discontinuously on the lagging strand in the form of Okazaki Fragments (OFs). Previously we have purified and sequenced OFs from S. cerevisiae, and have demonstrated their utility in mapping genome wide DNA replication patterns (1,2). Despite many years of research, the precise location efficiency and abundance of replication origins in metazoa remains elusive. Here we capture and sequence OFs from C. elegans and generate a genome wide map of DNA replication.We use a DNA ligation compromised genetic background and purify single stranded OFs from developing embryos. Aligning sequence reads of OFs to the C. elegans genome reveals a characteristic strand bias at specific sites that are approximately 50-100 Kb apart. The complementary enrichment of Okazaki fragments to either the Watson or Crick strands is the hallmark of a replication origin. Additionally we have found that origins of replication in C. elegans are correlated with transcriptionally active regions of chromatin. Using the histone modification data set of modENCODE we found a strong association between replication start sites and acetylation of Histone H3 lysine 27 (H3K27ac). Acetylation of H3K27 is a chromatin mark characteristic of gene enhancer elements. Finally, we show that a partial depletion of CBP/P300 the sole histone H3 acetyltransferase (HAT) responsible for H3K27 acetylation has a profound effect on DNA replication. Our data indicate that the DNA replication program is likely plastic and is matched with the transcriptional program. Ultimately our data show, both DNA replication and gene transcription are likely regulated by similar epigenetic processes. 1. Intrinsic coupling of lagging-strand synthesis to chromatin assemblyDuncan J. Smith& Iestyn Whitehouse. Nature, 20122. Quantitative, genome-wide analysis of eukaryotic replication initiation and termination.McGuffee SR, Smith DJ, Whitehouse I. Mol Cell, 2013.

Bo S et al. (2019) J Theor Biol "Potential relations between post-spliced introns and mature mRNAs in the Caenorhabditis elegans genome."

Zhao X, Li H, Bao T, Zhang Q, Lu Z, Bo S

[J Theor Biol, 2019]

There are potential interactions between introns and their corresponding coding sequences (CDSs) in ribosomal protein genes that have been proposed by our group and the interactions are achieved by sequence matches between the two kinds of sequences. Here, the optimal matching relations between mature mRNAs and their corresponding introns in Caenorhabditis elegans (C.elegans) were investigated by improved Smith-Waterman local alignment software. Our results showed that the remarkably matched regions appear in the untranslated regions (UTRs) of mRNAs, especially in the 3' UTR. The optimal matched segments (OMSs) are highly organized segments. In addition, the optimal matching relations were analysed between mature mRNAs and other introns. The matching strengths in the UTRs are clearly lower than those in their corresponding introns. Our studies indicate that there are potential interactions between mature mRNAs and their corresponding introns and the post-spliced introns should have other novel functions in the gene expression process.

Cohn DH et al. (2003) Am J Hum Genet "Mental retardation and abnormal skeletal development (Dyggve-Melchior-Clausen dysplasia) due to mutations in a novel, evolutionarily conserved gene."

Ehtesham N, Shanske A, Cohn DH, Krakow D, Powell BR, Rimoin DL, Unger S, Reinker K

[Am J Hum Genet, 2003]

Dyggve-Melchior-Clausen dysplasia (DMC) and Smith-McCort dysplasia (SMC) are similar, rare autosomal recessive osteochondrodysplasias. The radiographic features and cartilage histology in DMC and SMC are identical. However, patients with DMC exhibit significant developmental delay and mental retardation, the major features that distinguish the two conditions. Linkage studies localized the SMC and DMC disease genes to chromosome 18q12-21.1, providing evidence suggesting that they are allelic disorders. Sequence analysis of the coding exons of the FLJ90130 gene, a highly evolutionarily conserved gene within the recombination interval defined in the linkage study, identified mutations in SMC and DMC patients. The affected individuals in two consanguinous DMC families were homozygous for a stop codon mutation and a frameshift mutation, respectively, demonstrating that DMC represents the FLJ90130-null phenotype. The data confirm the hypothesis that SMC and DMC are allelic disorders and identify a gene necessary for normal skeletal development and brain function.

Michael A Beer (2005) International Worm Meeting "Systematic genome-wide identification of transcriptional cis-regulatory logic in C. elegans."

Michael A Beer

[International Worm Meeting, 2005]

We have developed a systematic approach for inferring cis-regulatory logic from whole-genome microarray expression data.[1] This approach identifies local DNA sequence elements and the combinatorial and positional constraints that determine their context-dependent role in transcriptional regulation. We use a Bayesian probabilistic framework that relates general DNA sequence features to mRNA expression patterns. By breaking the expression data into training and test sets of genes, we are able to evaluate the predictive accuracy of our inferred Bayesian network. Applied to S. cerevisiae, our inferred combinatorial regulatory rules correctly predict expression patterns for most of the genes. Applied to microarray data from C. elegans[2], we identify novel regulatory elements and combinatorial rules that control the phased temporal expression of transcription factors, histones, and germline specific genes during embryonic and larval development. While many of the DNA elements we find in S. cerevisiae are known transcription factor binding sites, the vast majority of the DNA elements we find in C. elegans and the inferred regulatory rules are novel, and provide focused mechanistic hypotheses for experimental validation. Successful DNA element detection is a limiting factor in our ability to infer predictive combinatorial rules, and the larger regulatory regions in C. elegans make this more challenging than in yeast. Here we extend our previous algorithm to explicitly use conservation of regulatory regions in C. briggsae to focus the search for DNA elements. In addition, we expand the range of regulatory programs we identify by applying to more diverse microarray datasets.[3] 1. Beer MA and Tavazoie S. Cell 117, 185-198 (2004). 2. Baugh LR, Hill AA, Slonim DK, Brown EL, and Hunter, CP. Development 130, 889-900 (2003); Hill AA, Hunter CP, Tsung BT, Tucker-Kellogg G, and Brown EL. Science 290, 809812 (2000). 3. Baugh LR, Hill AA, Claggett JM, Hill-Harfe K, Wen JC, Slonim DK, Brown EL, and Hunter, CP. Development 132, 1843-1854 (2005); Murphy CT, McCarroll SA, Bargmann CI, Fraser A, Kamath RS, Ahringer J, Li H, and Kenyon C. Nature 424 277-283 (2003); Reinke V, Smith HE, Nance J, Wang J, Van Doren C, Begley R, Jones SJ, Davis EB, Scherer S, Ward S, and Kim SK. Mol Cell 6 605-616 (2000).

Lee DG et al. (1997) International C. elegans Meeting "THE EXPRESSION PATTERN OF CALETICULIN, A HIGH AFFINITY CALCIUM BINDING PROTEIN"

Ahnn JH, Lee DG

[International C. elegans Meeting, 1997]

In C. elegans, a homologue of mammalian calreticulins was cloned and sequenced (M. Smith, DNA seq. 2: 235-40). This gene is composed of three exons and two introns and encodes a protein of 395 amino acid residues including an N-terminal signal sequence. The C-terminus contains an ER retention signal HDEL preceded by a polyacidic region similar to the mammalian calreticulins. Especially, the sequence displays 61% homology to mouse calreticulin, increasing up to 82% in the proline-rich region. This gene was designated as crt-1 and mapped to the left end of chromosome V of the physical map. To observe the expression pattern of calreticulin in some tissues of C. elegans, we are currently constructing a genomic clone fused with GFP reporter, which will be injected into an animal to obtain transgenic lines. At the same time, a cDNA clone obtained by PCR will be used for over expression in E. coli to produce antibodies.