Goulding M (2012) Neuron "Motor neurons that multitask."

Goulding M

[Neuron, 2012]

Animals use a form of sensory feedback termed proprioception to monitor their body position and modify the motor programs that control movement. In this issue of Neuron, Wen etal. (2012) provide evidence that a subset of motor neurons function as proprioceptors in C.elegans, where B-type motor neurons sense body curvature to control the bending movements that drive forward locomotion.

Smith, Jayson et al. (2021) International Worm Meeting "The SWI/SNF chromatin remodeling assemblies BAF and PBAF differentially regulate cell cycle exit and cellular invasion in vivo"

Chondhok Delos Reyes, Mana, Kratsios, Paschalis, Moore, Frances, Smith, Jayson, Martinez, Michael, Adikes, Rebecca, Zhang, Wan, Wen, Kailong, Xiao, Yutong, Kohrman, Abraham, Liu, Simeiyun, Matus, David, Palmisano, Nicholas, Bracht, Sydney, Parsan, Nithin, Medwig-Kinney, Taylor

[International Worm Meeting, 2021]

Chromatin remodeling complexes, such as the SWItching defective/Sucrose Non-Fermenting (SWI/SNF) ATP-dependent chromatin remodeling complex, coordinate metazoan development through broad regulation of chromatin accessibility and transcription, ensuring normal cell cycle control and cellular differentiation in a lineage-specific and temporally restricted manner. Mutations in the structural subunits of chromatin, such as histone subunits, and chromatin regulating factors (CRFs) are associated with a variety of diseases including cancer metastasis, which co-opts cellular invasion programs functioning in healthy cells during development. Here we utilize Caenorhabditis elegans anchor cell (AC) invasion as an in vivo model to identify the suite of chromatin agents and CRFs that promote cellular invasiveness. We demonstrate that the SWI/SNF ATP-dependent chromatin remodeling complex is a critical regulator of AC invasion, with pleiotropic effects on both G0 cell cycle arrest and activation of invasive machinery. Using targeted protein degradation and RNA interference (RNAi), we show that SWI/SNF contributes to AC invasion in a dose-dependent fashion, with lower levels of activity in the AC corresponding to aberrant cell cycle entry and increased loss of invasion. Specifically, we implicate the SWI/SNF BAF assembly in the regulation of the cell cycle, whereas our data suggests that the SWI/SNF PBAF assembly promotes AC attachment to the basement membrane (BM) and promotes the activation of the invasive machinery. Together these findings demonstrate that the SWI/SNF complex is necessary for two essential components of AC invasion: arresting cell cycle progression and remodeling the BM. The work here provides valuable single-cell mechanistic insight into how the SWI/SNF assemblies differentially contribute to cellular invasion and how SWI/SNF subunit-specific disruptions may contribute to tumorigeneses and cancer metastasis.

Antebi A et al. (1996) East Coast Worm Meeting "daf-12 Coordinates Multiple Developmental Events"

Hedgecock EM, Antebi A

[East Coast Worm Meeting, 1996]

In the nematode, developmental events within or between tissues are precisely coordinated. The DAF-12 nuclear hormone receptor plays multiple roles in synchronizing development. As a heterochronic regulator, it instructs stage specific programs in both gonad and soma. In the dauer pathway, it selects dauer or continuous development in response to growth conditions. Gonadal, somatic and dauer functions are genetically separable, suggesting a complex locus, and alleles can be grouped into six idealized classes. In collaboration with Don Riddle, Pam Larsen and Wen Hui Yeh, we have begun a molecular analysis of alleles to correlate structure with function. So far, we have found a sharp clustering of alleles which selectively disrupt dauer formation within the zinc fingers of the receptor. A unifying hypothesis is that a hormone, acting through DAF-12 and related receptors, coordinates events in gonad and some, as well as dauer development. We suggest a simple model in which the commitments or starts to each developmental stage are synchronized by a hormonal pulse available to all tissues. Moreover, we propose that the starts to each developmental stage lie between the molts, as judged by new cuticle synthesis in the hypodermic and transitions in the migratory behavior of gonadal leader cells. These "parastages" may more accurately reflect the actual functional boundaries of developmental stages.

Kim, Jinmahn et al. (2019) International Worm Meeting "Decoding head neural circuit underlying rhythmic forward movement in C. elegans."

Pyo, Seondong, Kim, Kyuhyung, Yeon, Jihye, Kim, Jongrae, Park, Cheon-Gyu, Kim, Jinmahn, Suh, Byung-Chang

[International Worm Meeting, 2019]

Forward locomotion of C. elegans is a rhythmic behavior which is initiated by contraction and relaxation of head muscles. However, the neuronal and molecular mechanisms in which to generate and maintain forward movement are not fully understood. Previously, cholinergic B-type and GABAergic D-type motor neurons process proprioceptive signals and regulate activity of body muscles during forward movement (Wen et al., 2012). To investigate the neural circuit underlying head movement, we analyzed neural connectome data and found that the two cholinergic SMB and SMD neurons innervate the head muscles and connect to the RME GABAergic neurons. When we genetically ablated SMB or SMD using recCaspase system, the SMD ablated worms displayed poor forward but normal backward movement. While the SMB ablated worms move normally, they exhibit increased wave width of sinusoidal waveform. We then activated SMD or SMB via optogenetic manipulation and found that transgenic animals expressing ReaChR (red-activatable ChR) in SMD or SMB elicit immediate forward movement or increase of wave width, respectively, upon light exposure. Additionally, to identify the molecules that regulate forward movement, we examined expression pattern of 29 TRP and DEG/ENaC channels and found that unc-8 DEG/ENaC channel gene is expressed in SMB. unc-8 mutant animals fail to maintain wave form during forward movement. Furthermore, expression of UNC-8 in HEK293T cells generates outward currents upon mechanical deformation in a heterologous system. Currently, we are investigating function of the SMB, SMD and RME neurons and their circuit mechanisms in regulation of forward movement.

de Vries CJ et al. (1998) European Worm Meeting "A cytosolic dynein heavy chain is required for sensory neuron structure and function."

de Vries CJ, Wicks SR, Plasterk RHA

[European Worm Meeting, 1998]

We have developed two new assays of nematode chemotaxis (see abstract Stephen Wicks). The first gene identified and cloned using these assays was a cytosolic isoform (1B subfamily) of the dynein heavy chain. Complementation studies show that this dynein heavy chain is the CHE-3 protein. Previously, this isoform of the dynein heavy chain was shown to be expressed during cilia outgrowth in sea urchins (Gibbons, 1994), and involved in the organisation of the Golgi-apparatus in non-ciliated human cell lines (Vaisberg, 1996). GFP expression studies indicate that che-3 is expressed exclusively in all ciliated sensory neurons in the worm. The highest levels of che-3 expression are correlated with outgrowth of cilia. To visualise the structure of ciliated endings we used two GFP markers of amphid and phasmid integrity (GPA-13::GFP and GPA-15::GFP, as integrated transgenes, gifts of Gert Jansen). These markers indicate that the amphid and phasmid cilia are malformed in the worm, and that the degree of disorganisation appears to increase as the animal ages. These results suggest that dynein heavy chain has a function in cilia outgrowth in C. elegans, but has no role in the organisation of the Golgi apparatus in the worm. Gibbons, B.H., Asai, D.J., Wen-Jing, Y., Hays, T.S., and Gibbons, I.R. (1994). Phylogeny and expression of axonemal and cytoplasmic dynein genes in sea urchins. Mol. Biol. Cell 5, 57-70. Vaisberg, E.A., Grissom, P.M., and McIntosh, J.R. (1996). Mammalian cells express three distinct dynein heavy chains that are localized to different cytoplasmic organelles. J. Cell Biol. 133, 831-842.

S Saeki et al. (1999) International C. elegans Meeting "Another form of associative learning in chemotactic behavior of C. elegans"

Y Iino, S Saeki, M Yamamoto

[International C. elegans Meeting, 1999]

An associative learning paradigm based on chemotactic behavior has previously been reported by van der Kooy's group (Wen et al ., 1997, Behav. Neurosci. 111:354-368). In this paradigm, chemotaxis to sodium ion and chloride ion were differentially conditioned by paired presentation of one of the ions with food, and the other without food. We have found another form of associative learning in chemotaxis. When worms were starved on plates including NaCl, their chemotaxis to NaCl was dramatically reduced. This conditioning required both presence of NaCl and absence of bacteria, indicating that it is not a mere adaptation or habituation. In contrast, decrease in chemotaxis to the volatile chemoattractant isoamylalcohol after continuous exposure to the same odorant (Colbert and Bargmann, 1995, Neuron. 14:803-812) occurred irrespective of the presence or absence of food. While chemotaxis to isoamylalcohol did not significantly change after conditioning with NaCl, chemotaxis to other water-soluble attractants also decreased. This suggests that altered response of a cell(s) that is specifically involved in chemotaxis to water-soluble chemoattractants is responsible for the behavioral change. Decrease in chemotaxis occurred slowly over 3-4 hours of conditioning and returned quickly to the original level when either of the conditioning stimulus, NaCl or starvation, was removed. Application of serotonin partially blocked this change in chemotaxis, consistent with the proposed function of this neurotransmitter in food signaling. We have isolated several mutants with reduced plasticity as assayed in this paradigm. This form of behavioral plasticity expands the opportunities in which one can study molecular and cellular mechanisms of learning using C. elegans .

Endo, Yuto et al. (2021) International Worm Meeting "Whole-brain imaging with neuronal identities to elucidate the mechanism of a sensory processing"

Miyachi, Miyu, Kimura, Kotaro, Wen, Chentao, Endo, Yuto

[International Worm Meeting, 2021]

A neural circuit in the brain processes sensory stimuli such as an odor to elicit a motor command. To understand the mechanism of such a sensory processing, a number of studies have sought to identify a neural circuit which processes a specific sensory stimulus (functional neural circuit). For identification of a functional neural circuit, it is required to conduct two types of experiments throughout the brain: 1) locating neurons that respond to the stimulus, and 2) identifying their cell types (cell-IDs) to estimate their connectivity based on anatomical connections. Locating stimulus-responsive neurons can be achieved by whole-brain calcium imaging, which record all neuronal activities throughout the brain. However, due to the lack of way to efficiently identifying cell-IDs, it has been difficult to identify a complete functional neural circuit with whole-brain imaging and cell identification. To overcome the limitation, the method for cell identification of all neurons, called NeuroPAL, was developed in C. elegans (Yemini et al., Cell, 2020). Together with the connectome information as well as the records of all neuronal activities, we are now able to estimate a functional neural circuit based on cell-IDs of stimulus-responsive neurons. To identify a complete functional neural circuit by integrating those techniques, we established a whole-brain imaging system combined with efficient cell identification system using NeuroPAL. This system consists of a 3D confocal microscopy, a multi-color imaging system, a microfluidic device, and a pipeline of an image analysis (Chronis et al., Nat. Meth., 2007; Wen et al., eLife, 2021). By using this system, we successfully recorded activities of most head neurons simultaneously with an information of each cell-ID. Now we are identifying a set of odor-responsive neurons using this system with stimulation by a repellent odor 2-nonanone (Kimura et al., J. Neurosci., 2010). This study aims to identify a complete functional neural circuit for specific sensory processing pathways and it may provide clues for how a sensory stimulus is processed in the whole of a neural circuit. We thank Ev Yemini and Oliver Hobert for the help on NeuroPAL.

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).

Valansi C et al. (1998) European Worm Meeting "DEVELOPMENTAL, GENETIC AND BIOCHEMICAL ANALYSES OF adm-1 AND adm-2 IN C.elegans"

Podbilewicz B, Valansi C, Lapidot Z, Broza R, Maroun M, Adir V, Shemer G

[European Worm Meeting, 1998]

ADM proteins in C. elegans are multidomain membrane receptors that contain A Disintegrin and Metalloprotease domains similar to snake venoms. The ADaM gene family includes fertilin involved in fertilization[1], meltrin-a that appears to be required for myotube formation[2], TACE, a TNF-a converting enzyme[3], KUZ involved in NOTCH signalling in Drosophila[4], and SUP-17 (ADM-3) that is related to KUZ[5]. The mutation sup-17(n316) acts as a suppressor of lin-12d and is the only known mutant of a member of the ADM family in C. elegans. Other members of this family may be involved in different cell-cell and cell-matrix interactions. ADM-1, was the first gene from this family found in C. elegans[6]. ADM-1 expression in cell membranes that participate in epithelial cell fusions and in sperm suggests that it can be involved in cell fusion events of developmental importance. adm-2 was mapped to chromosome X close to sem-1. We found that the cosmid C04A11 containing adm-2 did not rescue sem-1. The cellular localization of adm-1 products together with dsRNA interference experiments suggest that adm-1 and adm-2 can have roles in embryonic development. We are currently exploring the localization of adm-2 using a GFP reporter construct. It is known that the founder members of the ADAMs family (fertilins) form heterodimers after proteolytical processing. Thus, to investigate the processing and the putative biochemical and genetic, interactions between ADM-1, ADM-2 and other proteins we have used a monoclonal antibody against the cytoplasmic domain of ADM-1 to affinity purify and coimmunoprecitate interacting proteins. The processing of ADM-1 from a precursor to a mature form is followed using western blots, the amino termini of different bands will be sequenced and mass spectroscopy will be used to identify interacting proteins. 1.Blobel, C.P., et al. Nature 356, 248-252 (1992). 2.Yagami-Hiromasa, T., et al. Nature 377, 652-656 (1995). 3.Blobel, C. Cell 90, 589-592 (1997). 4.Rooke, J., Pan, D., Xu, T. & Rubin, G.M. Science 273, 1227-1231 (1996). 5.Wen, C., Metzstein, M.M. & Greenwald, I. Development 124, 4759-4767 (1997). 6.Podbilewicz, B. Mol. Biol. Cell 7, 1877-1893 (1996).

Alfred Tamayo et al. (2005) International Worm Meeting "Molecular identification of srf genes suggests a role in protein secretion"

Patricia Berninsone, Alfred Tamayo, Katie MacFarland

[International Worm Meeting, 2005]

In a mutagenic screen designed to select for animals with altered cuticle surface glycosylation, several mutants termed srf (surface) were isolated (1). These loss-of-function mutants display ectopic surface binding to the lectin Wheat Germ Agglutinin. Some of these srf mutants also have gross pleiotropic defects (uncoordinated movement, protruding vulva, abnormal egg laying, aberrant copulatory bursae and malformed gonads) (1). Therefore, the molecular events affected by these genes play important roles not only in expression of cuticle surface glycoconjugates, but also in the normal development of various organs and tissues.Prior genetic mapping located srf-4, srf-8 and srf-9 to specific intervals of LGV (1). We searched these intervals for ORFs encoding products with homology to known components of glycosylation and secretion pathways in other organisms, and tested these candidates by dsRNAi inactivation. Among these candidates, we have identified a family of proteins which when targeted by dsRNAi, generated animals that display phenotypes closely resembling those of the srf mutants. Direct sequencing of the corresponding genes in the srf mutant genomes revealed genetic lesions consistent with strong or complete loss-of function. This protein family has been implicated in ER to Golgi cargo selection, the fidelity of ER sorting mechanisms and the exclusion/inclusion of unfolded proteins in vesicles exiting the ER (2). Our finding supports the hypothesis that the underlying defect in these mutants affects protein secretion.We have found that inactivation of the putative srf genes by dsRNAi resulted in strong induction of hsp-4::gfp, a reporter construct of the mammalian ER chaperone BiP homolog, which is a target of the unfolded protein response (UPR) in yeast and mammals (3, 4). Such RNAi also caused embryonic lethality in a mutant background deficient in an ER molecular chaperone. Furthermore, srf-8 mutants are sensitive to treatments which cause accumulation of unfolded proteins in the ER. Our evidence suggests that mutations in these srf genes cause ER-stress, and that these genes may play a role in the secretion of cellular membrane proteins or extracellular matrix components important for normal development.(1)Link C. et al (1992) Genetics 131: 867-881 (2)Wen and Greenwald (1999) J Cell Biol 145: 1165-1175 (3)Shen X. et al (2001) Cell 107: 893-903 (4)Calfon M. et al (2001) Nature 415: 92-96