Marisa Foehr et al. (2007) International Worm Meeting "Dorsoventral patterning of the postembryonic mesoderm requires both LIN-12/Notch and TGF-beta signaling."

Marisa Foehr, Jun Liu

[International Worm Meeting, 2007]

The C. elegans post-embryonic mesodermal lineage arises from a single precursor cell, the M mesoblast, which will diversify to generate distinct dorsal and ventral cell types. The dorsal daughter of M gives rise to a subset of body wall muscles and two non-muscle coelomocytes, whereas the ventral daughter of M gives rise to two sex myoblasts in addition to a subset of body wall muscles. Mutations in the C. elegans Schnurri homolog sma-9 cause ventralization of the M lineage. We have previously shown that SMA-9 antagonizes the Sma/Mab TGF-beta signaling pathway to promote dorsal M lineage fates (Foehr et al., 2006). Interestingly, loss-of-function mutations in the Notch receptor homolog lin-12 cause dorsalization of the M lineage (Greenwald et al., 1983), an exact opposite phenotype of sma-9 mutants. We have found that while LIN-12 protein is present in both the dorsal and ventral M lineage cells, the ligands for LIN-12, LAG-2 and APX-1, are asymmetrically localized in cells adjacent to ventral M-derived cells, and they function redundantly in promoting ventral M lineage fates. To investigate how LIN-12/Notch signaling interacts with SMA-9 and the Sma/Mab TGF-beta pathway in regulating M lineage patterning, we generated double and triple mutant combinations among lin-12, sma-9 and dbl-1 (the ligand for the Sma/Mab TGF-beta pathway) and examined their M lineage phenotypes. Our results suggest that the LIN-12/Notch pathway and the Sma/Mab TGF-beta pathway function independently in regulating dorsoventral patterning of the M lineage, with LIN-12/Notch required for ventral M lineage fates, and SMA-9 antagonism of TGF-beta signaling required for dorsal M lineage fates. Our work provides a model for how combined Notch and TGF-beta signaling regulates the developmental potential of two equipotent cells along the dorsoventral axis.

Nirav Amin et al. (2008) Development & Evolution Meeting "Systematic analysis of transcription factors important in C. elegans postembryonic mesodermal development"

Zach Via, Jun Liu, Nirav Amin

[Development & Evolution Meeting, 2008]

The C. elegans postembryonic mesodermal lineage, the M lineage, is a powerful model system to study mesodermal patterning and cell fate specification at single cell resolution. The M lineage arises from a single pluripotent cell, the M mesoblast, during embryogenesis. In hermaphrodites, the M cell undergoes a series of postembryonic cell divisions to produce 18 cells: 14 body wall muscles (BWMs), 2 coelomocytes (CCs), and 2 sex myoblasts (SMs). We and others have previously identified a handful of transcription factors important for the proper development of this lineage. In order to identify additional transcription factors that play a role in the M lineage, we have generated a feeding RNAi library that targets a majority of the predicted transcription factors encoded in the C. elegans genome and conducted an RNAi screen using cell type-specific GFP reporters in the M lineage. From this screen, we identified a novel set of 32 transcription factors that, upon RNAi knockdown, give reproducible phenotypes in the M lineage. Among these 32 transcription factors, four are important for patterning and fate specification of the early M lineage, while the rest appear to play a role in fate decisions in the SM lineage. We have primarily focused on let-381, which encodes a forkhead transcription factor that is essential for C. elegans development. let-381(RNAi) causes a dorsal to ventral fate transformation in the M lineage. We have found that a let-381::gfp translational fusion is expressed in the dorsal M lineage. Previous studies from our lab have shown that SMA-9, the Sma/Mab TGF-beta and LIN-12/Notch signaling pathways are involved in dorsal/ventral patterning of the M lineage. We are currently investigating the relationship between let-381 and these pathways.

Yuan Jiang et al. (2004) East Coast Worm Meeting "MLS-2, an HMX class homeodomain protein essential for mesodermal patterning and cell fate specification"

Jun Kelly Liu, Yuan Jiang

[East Coast Worm Meeting, 2004]

We are interested in understanding mesodermal patterning and fate specification by studying the C. elegans postembryonic mesodermal lineage, the M lineage. The M lineage is derived from a single precursor cell, the M mesoblast, and gives rise to six cell types: striated bodywall muscles (BWMs), nonmuscle coelomocytes (CCs), and four classes of non-striated sex muscles which are descendants of the sex myoblasts (SMs). We are studying the function of the mls-2 (mesodermal lineage specification) gene in M lineage patterning and fate specification. The mls-2(cc615) mutation causes randomization of division planes in the M lineage, and subsequent fate transformation of CCs and BWMs to SMs. In addition, cc615mutants have defects in SM migration and show some larval and adult lethality. We have cloned the wild type mls-2 gene (C39E6.4). mls-2 encodes a homeodomain protein that belongs to the HMX family of homeodomain proteins that are also present in sea urchin, Drosophila and vertebrates., We examined the expression pattern of mls-2 using both functional mls-2::gfp fusion construct and affinity purified anti-MLS-2 antibodies. We found that the MLS-2 protein is localized in nuclei of early M lineage cells and a subset of head neurons. Furthermore, mls-2 expression in the M lineage and the head neurons appears to require distinct cis-acting elements. Overexpression of mls-2 in the early M lineage where mls-2 is normally expressed caused a variety of defects in the M lineage. Forced expression of mls-2 in the later M lineage such as in SMs where mls-2 is not normally expressed resulted in extra rounds of divisions of SMs. This suggests that mls-2 may have multiple roles in the M lineage and that MLS-2 protein level is critical for the correct patterning of the M lineage. The M lineage defects of mls-2(cc615) are very similar to those of mab-5, hlh-1, egl-27 and egl-20 mutants. We are currently carrying out molecular and genetic epistasis experiments to investigate the relationship between mls-2 and those factors.

Nirav Amin et al. (2008) Development & Evolution Meeting "The Six2 homeodomain protein CEH-34 functions downstream of Wnt signaling for proper fate specification in the postembryonic mesoderm"

Jun Liu, Sung-Eun Lim, Tania Jaber, Nirav Amin

[Development & Evolution Meeting, 2008]

We are using the C. elegans postembryonic mesodermal lineage, the M lineage, as a model to study mesodermal patterning and cell fate specification. The M lineage arises from a single pluripotent cell, the M mesoblast, during embryogenesis. In hermaphrodites, the M cell first undergoes a dorsal-ventral division and then a left-right division to produce four cells located in four quadrants of the L1 larva. These four cells subsequently undergo two to three more rounds of cell divisions along the anterior-posterior axis to produce 18 cells: 14 body wall muscles (BWMs), 2 coelomocytes (CCs), and 2 sex myoblasts (SMs). In particular, M.dlp and M.drp each give rise to an anterior CC and a posterior BWM. In an RNAi screen for transcription factors important for proper M lineage development, we identified the Six2 homeodomain factor ceh-34 for its requirement in the proper specification of M-derived CC fates. ceh-34(RNAi) results in a fate transformation of the anterior CC to its posterior sister cell, the BWM. We have generated translational ceh-34::gfp fusions and found that in the M lineage, ceh-34 is specifically expressed in the CC precursor cells. To understand the mechanisms underlying the asymmetric expression pattern of ceh-34, we determined the roles of the Wnt/beta-catenin asymmetry pathway in the M lineage because this pathway has been shown to regulate other asymmetric cell fates along the anterior-posterior axis. We have found that during both of the anterior-posterior cell divisions in the early M lineage, the TCF homolog POP-1 is enriched in the anterior daughters while the beta-catenin homolog SYS-1 is enriched in the posterior daughters. Furthermore, sys-1(q544) loss-of-function mutants have extra M lineage-derived CCs, while pop-1(RNAi) leads to a loss of M-derived CCs. We showed that ceh-34(RNAi) is epistatic to sys-1(q544) mutations and that ceh-34::gfp is ectopically expressed in the M lineage in sys-1(RNAi) animals but reduced in pop-1(RNAi) animals. These observations suggest that ceh-34 functions downstream of pop-1 and sys-1 in the M lineage. We are currently testing if POP-1 and SYS-1 directly regulate the asymmetric expression of ceh-34 in M lineage development.

Anita U Rao et al. (2007) International Worm Meeting "Genetic Dissection of Heme Pathways in C. elegans."

Brian Le, Iqbal Hamza, Anita U Rao

[International Worm Meeting, 2007]

Heme serves as a cofactor for a number of proteins involved in key metabolic processes. In eukaryotes, heme synthesis occurs in the mitochondria by an evolutionarily conserved multi-step pathway. Hemes are hydrophobic and thus insoluble in the aqueous environment of the cell. Moreover, free heme is cytotoxic because of peroxidase activity. We therefore hypothesize that intracellular pathways exist for trafficking of heme from the site of synthesis in the mitochondria to various cellular destinations. However, identification of these heme transport pathways has been difficult because heme synthesis is regulated by multiple effectors and is tightly coordinated with apo-protein synthesis. We have previously shown that C. elegans and related helminths do not make heme albeit requiring exogenous heme for normal metabolic processes. Importantly, C. elegans show a biphasic response for heme; worms are growth-arrested at 1.5 <font face=symbol>m</font>M and at 800 <font face=symbol>m</font>M heme. These results suggest that although worms are obligate heme auxotrophs they are likely to have all the pathways for heme utilization beyond the point of heme synthesis. To identify pathways for heme transport in C. elegans, we exploited their biphasic response to heme by screening for mutants that could survive heme toxicity. We screened 300,000 haploid genomes and isolated 13 mutants at 800 <font face=symbol>m</font>M heme in liquid axenic medium. Based on the mutants growth profile in medium containing low and high heme, we categorized the mutants into three broad phenoclusters: class A, class B and class C. Class A mutants grew robustly under low and high (800 and 1000<font face=symbol>m</font>M) heme, Class B mutants grew exceptionally well under low heme, moderately well at 800 <font face=symbol>m</font>M heme, and not at all at 1000 <font face=symbol>m</font>M heme, and Class C mutants grow moderately well under high heme (800<font face=symbol>m</font>M), but exhibit normal growth under low heme. The mutants were further sub-clustered by using gallium protoporphyrin (GaPP), a toxic heme analog. Complementation analyses revealed that these 13 mutants fall into five complementation groups. Genetic mapping by recombination localized the mutants from each complementation group to chromosome III. We are now producing a high resolution map to define a genetic interval and pinpoint the exact nature of the molecular lesion in these mutants.

J Liu et al. (1999) International C. elegans Meeting "Hox factors and other components in patterning of embryonic and postembryonic myogenic lineages"

J Liu, AZ Fire

[International C. elegans Meeting, 1999]

Bodywall muscles are derived from four of the embryonic founder cells as well as the postembryonic M blast cell. We are studying patterning of both the embryonic and postembryonic muscles in order to understand how myogenic cell fates are specified during development. As an entry point to study muscle patterning during embryonic development, we characterized enhancer elements from the hlh-1 regulatory region that are able to drive reporter expression in muscle precursors of the MS, D and C lineages. Analyses of these elements suggested regulatory roles of the Hox genes and the hlh-1 gene itself. These analyses also suggested regulatory mechanisms involving unknown bZIP, bHLH and novel transcription factors. We are currently in the process of genetically identifying these factors. The postembryonic M lineage provides an alternative model to study myogenic fate specification. The M lineage gives rise to 14 bodywall muscles, 2 coelomocytes and 16 sex muscles. A number of genes had previously been identified to function in patterning the M lineage, including the Hox gene mab-5 and the bHLH transcription factor twist (1, 2, 3). The role of the Hox factors in patterning the M lineage has been something of a mystery: mab-5 is expressed during the entire M lineage, but mab-5 mutants cause only limited lineage transformation. We will describe a series of experiments indicating a more central role for the Hox genes in activating twist and specifying the M lineage. We found that lin-39 mab-5 double mutants fail to activate twist and completely lack products of the M lineage. Expression (either ectopic or in a normal pattern) of either Hox gene is sufficient to activate twist expression. However, twist activation is not sufficient for specification of the M lineage. Current efforts are directed towards identification of other factors involved in specifying the M lineage. 1. Kenyon, C. (1986), Cell 46: 477-487 2. Harfe B. D., Vaz Gomes A., Kenyon C., Liu J., Krause M., Fire A. (1998) Genes & Dev. 12: 2623-2635 3. A. Corsi, S. Kostas, E. Jorgensen, A. Fire, and M. Krause (poster)

Yuan Jiang et al. (2006) Development & Evolution Meeting "CEH-20 regulates the expression of mls-2 in the postembryonic mesoderm"

Yuan Jiang, Jun Liu

[Development & Evolution Meeting, 2006]

mls-2 encodes a HMX homeodomain protein that plays critical roles in the C. elegans postembryonic mesodermal lineage, the M lineage. mls-2 is expressed in the M lineage as well as a few other cell types, such as several pairs of head neurons including ASK and AIM. To uncover mechanisms involved in regulating the expression of mls-2, we generated a series of promoter deletions and identified an M lineage enhancer (position -2221 to -2076) that is required for mls-2 expression in the M lineage. We further identified several essential elements within this M enhancer. Among these elements are two putative Exd/Abd-B binding sites that are conserved in C. briggsae. We have found that mls-2 expression in the M lineage is dependent on the C.elegans Exd/Pbx homolog CEH-20. We are currently testing whether CEH-20 directly binds to the mls-2 promoter and whether CEH-20 regulates mls-2 expression through acting together with the Abd-B class Hox proteins, EGL-5/PHP-3/NOB-1, and the Hth/Meis homolog, UNC-62.

Spica, Patrick et al. (2015) International Worm Meeting "The Effects of Wrapping NGM Culture Plates with Parafilm M® on the Growth and Development of Caenorhabditis elegans."

Scanga, Sara, Spica, Patrick, Shinn-Thomas, Jessica, Klempic, Emra

[International Worm Meeting, 2015]

Parafilm M&reg; is a thin thermoplastic used to seal a variety of containers in scientific laboratories. It is commonly used to seal Nematode Growth Media (NGM) culture plates to prevent microbial contamination and media dehydration. However, the effects on C. elegans of wrapping culture plates with Parafilm M&reg; during experiments are unknown. Parafilm M&reg; may limit gas exchange between the external and culture environment, potentially affecting the biology and life history of C. elegans, including its larval growth rate, viability, fecundity, lifespan, and behavior. In particular, wrapping culture plates with Parafilm M&reg; may produce a hypoxic (low oxygen) environment compared to plates with no Parafilm M&reg; (normoxic). Anoxic (no oxygen) and hypoxic conditions have been shown to change the metabolism, development, and longevity of C. elegans.Our research aims to determine the effects of wrapping NGM culture plates with Parafilm M&reg; on C. elegans. We hypothesized that worms cultured on plates wrapped in Parafilm M&reg; would exhibit a slower rate of larval growth and increased mortality compared to worms grown in normoxic conditions. Synchronized L1 worms were individually transferred to culture plates and incubated within an anoxic environment, hypoxic environment, normoxic environment, or wrapped one time with Parafilm M&reg;. BD GasPaks&trade; were used to create anoxic and hypoxic environments, and normoxic culture conditions consisted of unsealed plates. Larval growth rate and mortality were measured 5 times over 48 hours. We found no significant difference in the growth rate between worms cultured in normoxic conditions and on plates wrapped with Parafilm M&reg;. However, the growth rate between worms cultured on plates wrapped with Parafilm M&reg; and worms in anoxic and hypoxic conditions was significantly higher. Mortality was significantly higher in worms cultured in anoxic conditions, but was not significantly different among the other three environmental conditions. Our data suggest that wrapping C. elegans culture plates one time with Parafilm M&reg; does not affect the larval growth rate or viability. Future studies will focus on additional biological and life history metrics, such as fecundity and lifespan, to verify that wrapping with Parafilm M&reg; has no unexpected effects on the outcomes of C. elegans studies.

Jun Liu et al. (2001) International C. elegans Meeting "Mesodermal cell fate specification in the postembryonic M lineage"

Jun Liu, Andrew Fire

[International C. elegans Meeting, 2001]

We are interested in understanding how mesodermal cell fates are specified. The postembryonic mesodermal lineage, the M lineage, provides a valuable system for these studies. During postembryonic development, the single blast cell M divides characteristically and reproducibly to generate 14 striated bodywall muscles, 16 non-striated sex muscles (vulval and uterine muscles), and two non-muscle cells (coelomocytes). Previous work from our lab and others has shown that correct patterning of the M lineage involves both lineage specific intrinsic factors and cell-cell signaling. We are interested in identifying and characterizing the functions of these factors in M lineage fate specification. At the start of the M lineage, two Hox cluster genes lin-39 and mab-5 , as well as their cofactor, a homeodomain protein CEH-20 specify cellular identity and myogenic potential of M. We have found an overlapping function for lin-39 and mab-5 in diversification of different cell fates within the lineage, and have shown that the C. elegans twist ortholog hlh-8 is a direct target of these factors in the M lineage. Using gfp-based mutagenesis screens, we have isolated 26 additional mutants that have defects in M lineage patterning (12 of them came from a screen carried out by Judy Yanowitz in the lab). Three of these mutants turned out to be allelic to sma-9 , and showed intriguing genetic interactions with lin-12(0) . We are in the process of characterizing these and other mutants isolated from the screens.

Cha, S. et al. (2015) International Worm Meeting "An annotated genome of the root-knot nematode, Meloidogyne chitwoodi."

Cha, S., Bird, D.

[International Worm Meeting, 2015]

Plant-parasitic nematodes are responsible for annual crop losses in excess of USD123 billion worldwide. Most important are the root-knot nematodes (RKN: Meloidogyne spp.), which establish an intimate association with their host. As a genus, Meloidogyne has a host-range that spans the tracheophyta, although individual isolates are more restricted. In cool climates, M. hapla and M. chitwoodi predominate and are a significant problem on potato in Europe and the US. Because of its genetic tractability, we selected M. hapla for sequencing, and an annotated public release (HapPep1) was made in 2008 (Opperman et al., 2008). Since then we have undertaken on-going curation, and the current release (HapPep5) includes ~2xE9 RNA-Seq reads (Guo et al., 2014). We have also sequenced two additional strains of M. hapla (VW8 and LM) but they have not yet been released. Because M. hapla and M. chitwoodi are sympatric, they presumably have similar gene compliments. To test this, we sequenced the M. chitwoodi genome.Genomic DNA was isolated from nematodes collected in a potato field in Washington State, and confirmed by Axel Elling to be M. chitwoodi. Using an Illumina MiSeq II we obtained 20,079,197 short (~300 bp) paired-end reads. The assembly parameters were empirically optimized, and 4,735 contigs assembled; N50 is 82 kbp. The longest is ~758 kbp with coverage of 33 reads per bp. Average coverage genome-wide is 289 reads. At the protein level, CEGMA identified 245 (98.79%) of the core proteins, pointing to near 100% genome coverage. When CEGMA proteins as a query were blasted against the assembled contigs as a database, it was observed that one protein had hits with more than two contigs. Using CEGMA (and other) proteins, as well as M. chitwoodi ESTs, we trained AUGUSTUS for gene prediction. GO categorization was performed using InterProScan. Analysis of these data is in progress, with an emphasis on genes encoding replicas of plant peptide hormones (xenomones). Because of a potential role in speciation of the closely-related parasites, we have, in collaboration with David Lunt (University of Hull), examined the numbers and distribution of transposable elements: not surprising, M. chitwoodi is much more similar to M. hapla than it is to M. incognita.Operman et al., 2008. Proc Nat Acad Sci 105: 14802 -14807.Guo et al. 2014. Worm 3:e29158.