Open Resources and Plasmid Tools For Studying C. elegans

Posted by Alyssa Cecchetelli on Jul 18, 2019 8:55:32 AM


The C. elegans community has always emphasised the need for open science and collaboration. The field already has comprehensive reference pages and curated databases for scientists including Wormbook, Wormatlas and Wormbase. And scientists have been continuously sharing their worm strains through the Caenorhabditis Genetics Center (CGC) which maintains and distributes the strains all over the world.

When I was at the 22nd International C. elegans meeting, I was again reminded of the extent that C. elegans researchers embrace open science and share resources and tools. That message was fully exemplified in Cori Bargmann’s keynote speech and in the workshops on CRISPR techniques and new tools for conditional expression and degradation. These workshops not only highlighted new tools but also included time for questions and a group discussion on the best strategies and protocols for different experiments. 

In this blog post I will highlight some of the other open resources discussed at the meeting, in addition to useful plasmids and toolkits available at Addgene. 

C elegans

C. elegans open resources

The C. elegans Neuronal Gene Expression Map & Network (CeNGEN)

The CeNGEN goal is to establish a comprehensive gene expression atlas of every C.elegans  neuron. Scientists are currently doing this using two approaches: single-cell RNA-sequencing to identify neuronal class and deep sequencing of neurons from each class to fully characterize the transcriptome. The first data release for CeNGEN is planned for August 15th, 2019. For more information about the aims and approach of CeNGEN, check out their publication.  

3’UTRome

The 3’UTRs of mRNA are important for post-transcriptional regulation in C. elegans. To study the role of 3’UTRs, the Arizona State University (ASU) Biodesign institute developed a 3’UTR database specifically for C. elegans. This database provides detailed information about C. elegans 3’UTRs structures, alternative polyadenylation for all protein coding mRNAs, and annotations extracted from other databases (Mangone et al., 2008). 

OpenWorm

OpenWorm is an open source project that is creating the “first virtual organism in a computer.” This project has produced various resources for the worm community that makes it easier to view and explore the worm. These resources include the open worm browser, which allows you to view the anatomy of worm layer by layer, the NeuroML C. elegans connectome, a model of the C.elegans neural network, and Sibernetic, a fluid mechanics simulator that can be used to simulate muscle tissue as it applies to C. elegans locomotion. To see the other resources included in OpenWorm, check out the OpenWorm website.

microPublication

microPublication is a unique publication for the worm community where one can publish brief novel findings. These results are normally one figure and can be negative and/or even replicated studies to show reproducible results. This a great resource for scientists to publish findings that don't fit into larger publications and would otherwise be lost in lab notebooks forever. microPublications are peer-reviewed and assigned a DOI that can be referenced. In addition the data published in microPublications is curated and added to other databases including wormbase and flybase. microPublication is run and maintained by members of the worm community but there are Drosophila and zebrafish articles published there as well.  

Worm Development Dynamics Database (WDDD)

The WDDD aims to acquire quantitative data on all the cell divisions of the C. elegans embryo when all essential embryonic genes are individually depleted via RNA interference (RNAi). Scientists monitor the effects of RNAi using four-dimensional contrast interference (DIC) microscopy and computer imaging processing. The combination of these methods provides unique opportunities to develop computational methods to better understand animal development (Kyoda et al., 2012). 

C. elegans plasmid tools at Addgene

In addition to the wealth of open resources described above, there were many plasmid tools presented at the C. elegans meeting. Here I’ll highlight a few toolkits that we have available at Addgene that were discussed primarily at the workshops on new resources and tools for the community.

Plasmids for the Auxin Inducible Degradation System (AID)

The Dernberg lab in 2015 adapted the AID system discovered in plants to conditionally deplete proteins of interest in C. elegans (Zhang et al., 2015). In this system a modified TIR-1 protein can degrade degron-tagged proteins in an auxin dependent manner. This system allows scientists to both spatially and temporally knock-down proteins of interest. 

Plasmids for cGAL and split cGAL systems

The Sternberg lab in 2016 created cGAL, a GAL-4 based bipartite expression system that can regulate gene expression in C.elegans. In this system a promoter controls the expression of a GAL-4 driver that can bind to activation sequences upstream of genes to stimulate expression (Wang et al., 2016). In 2018, the lab expanded on this tool by splitting cGAL4 in two and binding each half to a gp41-1-N-intein. Split inteins are protein domains that naturally “associate, self-excise, and covalently ligate their flanking peptides together (Wang et al., 2018).” With the split system, only cells that have both halves of cGAL can drive expression of your gene of interest. 

SapTrap Tool Kit for CRISPR Cas9 edits

At Addgene, we have the entire SapTrap toolkit from the Jorgensen lab. SapTrap is a reagent toolkit and plasmid assembly line for the creation of CRISPR targeting vectors that each contains a guide RNA and repair template of your choosing (Schwartz and Jorgensen, 2016). Using SapTrap, this CRISPR plasmid can be created in a single tube. You can also find additional SapTrap plasmids used for introducing point mutations that was published in a microPublication (Schwartz and Jorgensen, 2018). 

These are just some examples of worm resources and tools openly shared by the worm community. For additional resources about C. elegans and the plasmids we have at Addgene check out our worm expression resources page. This page is continuously curated as we continue to receive plasmids designed for the worm so check back frequently for what’s new and popular!


References

Hammarlund, Marc, et al. "The CeNGEN Project: The Complete Gene Expression Map of an Entire Nervous System." Neuron 99.3 (2018): 430-433. PubMed PMID: 30092212. PubMed Central PMCID: PMC6576255.

Kyoda, Koji, et al. "WDDD: worm developmental dynamics database." Nucleic acids research 41.D1 (2012): D732-D737. PubMed PMID: 23172286. PubMed Central PMCID: PMC3531189.

Mangone, Marco, et al. "UTRome. org: a platform for 3′ UTR biology in C. elegans." Nucleic acids research 36.suppl_1 (2007): D57-D62. PubMed PMID: 17986455. PubMed Central PMCID: PMC2238901.

Schwartz, Matthew L., and Erik M. Jorgensen. "SapTrap, a toolkit for high-throughput CRISPR/Cas9 gene modification in Caenorhabditis elegans." Genetics 202.4 (2016): 1277-1288. PubMed PMID: 26837755. PubMed Central PMCID: PMC4905529

Schwartz, M. L., & Jorgensen, E. M. "SapTrap vectors for introducing point mutations with unc- 119 + selection." MicroPublication 1 (2018): 2–3.

Wang, Han, et al. "cGAL, a temperature-robust GAL4–UAS system for Caenorhabditis elegans." Nature methods 14.2 (2017): 145. PubMed PMID: 27992408. PubMed Central PMCID: PMC5693259

Wang, Han, et al. "Split cGAL, an intersectional strategy using a split intein for refined spatiotemporal transgene control in Caenorhabditis elegans." Proceedings of the National Academy of Sciences 115.15 (2018): 3900-3905. PubMed PMID: 29581308. PubMed Central PMCID: PMC5899461

Zhang, Liangyu, et al. "The auxin-inducible degradation (AID) system enables versatile conditional protein depletion in C. elegans." Development 142.24 (2015): 4374-4384. PubMed PMID: 26552885. PubMed Central PMCID: PMC4689222.

Additional resources on the Addgene blog

Resources on Addgene.org

Topics: Open Science

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