GExplore 1.4: An expanded web interface for queries on<i>Caenorhabditis elegans</i>protein and gene function

Hutter, Harald; Suh, Jinkyo

doi:10.1080/21624054.2016.1234659

Cited by 34 publications

(45 citation statements)

References 20 publications

(16 reference statements)

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“…Under these conditions, worms completed their development normally and exhibited no overt morphological defects. We chose one tubulin alpha tba-2 and one tubulin beta tbb-2, as these genes have been reported to be highly expressed in the epidermis (Cao et al, 2017;Hutter and Suh, 2016). In young adult tba-2(RNAi) or tbb-2(RNAi) worms, EB1::GFP comets were no longer visible suggesting that MT dynamics had been severely compromised ( Fig.…”

Section: Tba-2 or Tbb-2 Inactivation Results In Abrogation Of Eb1 Dynmentioning

confidence: 99%

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Microtubule plus-end dynamics link wound repair to the innate immune response

Taffoni

Omi

Huber

et al. 2019

Preprint

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As a first line of defence against the environment, the epidermis protect animals from infection and physical damage. In C. elegans, wounding the epidermal epithelium triggers both an immune reaction and a repair response. Exactly how these are controlled, and the degree to which they are inter-connected remains unclear. To address these questions, we established a simple system for simultaneously inflicting precise laser wounds and imaging at high spatial and temporal resolution. We show that in C. elegans, wounding provokes a rapid sealing of the plasma membrane, involving reorganisation of phosphatidylinositol 4,5bisphosphate domains. This is followed by a radial recruitment at the wound site of EBP-2/EB1, a protein that binds the plus ends of microtubules. EB1 recruitment is accompanied by a reorganisation of microtubules, required for the subsequent recruitment of actin and wound closure. It is also required for the directed trafficking towards the site of injury of the key signalling protein SNF-12. In the absence of SNF-12 recruitment, there is an abrogation of the immune response. Our results suggest that microtubule dynamics coordinate the cytoskeletal changes required for wound repair and the concomitant activation of the innate immune response.

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Section: Tba-2 or Tbb-2 Inactivation Results In Abrogation Of Eb1 Dynmentioning

confidence: 99%

“…The RNAi bacterial clones were obtained from the Ahringer library (Kamath et al, 2003) or Vidal library (Rual et al, 2004) and sequenced to confirm their identity using CloneMapper (Thakur et al, 2014…”

Section: Rnaimentioning

confidence: 99%

Microtubule plus-end dynamics link wound repair to the innate immune response

Taffoni

Omi

Huber

et al. 2019

Preprint

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“…Thus, our results suggest two possibilities: (i) a nuclear function of ancestral IκBs has emerged in an NF-κB-free scenario and has primarily been maintained by BCL3 in mammals, whereas IκBα has functionally diverged to inhibit NF-κB, maintaining (Camacho, et al, 2009). Data for (A) and (B) were retrieved from GExplore 1.4 (www.genome.sfu.ca/gexplore) (Hutter and Suh, 2016). representation of the nfki-1 and ikb-1 mutants used in the study.…”

Section: Discussionmentioning

confidence: 99%

“…We searched in public transcriptomic datasets for the expression patterns of nfki-1 and ikb-1 in different tissues and developmental stages. Temporal series of RNA-sequencing (RNA-seq) during C. elegans embryonic development showed that nfki-1 and ikb-1 are expressed in late embryos, coinciding with morphogenesis and final differentiation of embryonic cells, and at all larval 6 stages with elevated expression at dauer stage, which is acquired in starvation conditions (Boeck, et al, 2016;Hutter and Suh, 2016;Gerstein, et al, 2010) ( Figure S2A). A dataset of Single cell Combinatorial Indexing RNAseq (sci-RNAseq) at L2 stage shows that nfki-1 expression is rather ubiquitous in somatic cells but enriched in neuronal cells, whereas ikb-1 is mainly restricted to muscle cells ( Figure 1E) (Cao et al, 2017;Hutter and Suh, 2016).…”

Section: Nfki-1 and Ikb-1 Are The Homologs Of Mammalian Iκbs And Dispmentioning

confidence: 99%

Ancestral function of Inhibitors-of-kappaB regulatesCaenorhabditis elegansdevelopment

Brena

Bertran

Porta-de-la-Riva

et al. 2020

Preprint

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Mammalian IκB proteins (IκBs) exert their main function as negative regulators of NF-κB, a central signaling pathway controlling immunity and inflammation. An alternative chromatin role for IκBs has been shown to affect stemness and cell differentiation. However, the involvement of NF-κB in this function has not been excluded. NFKI-1 and IKB-1 are IκB homologs in Caenorhabditis elegans, which lacks NF-κB nuclear effectors. We found that nfki-1 and ikb-1 mutants display developmental defects that phenocopy mutations in Polycomb and UTX-1 histone demethylase, suggesting a role for C. elegans IκBs in chromatin regulation. Further supporting this possibility (i) we detected NFKI-1 in the nucleus of cells; (ii) NFKI-1 and IKB-1 bind to histones and Polycomb proteins, (iii) and associate with chromatin in vivo, and (iv) mutations in nfki-1 and ikb-1 alter chromatin marks. Based on these results, we propose that ancestral IκB inhibitors modulate Polycomb activity at specific gene subsets with an impact on development.

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“…Unconnected proteins are not shown. Proteins that display maximum transcript expression levels (using data from a stage‐specific RNA‐seq gene expression dataset, see Supporting Information, Table 4) in the stage we determined the protein to be specifically expressed are highlighted in bold, red text.…”

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confidence: 71%

Proteomic Characterization of Caenorhabditis elegans Larval Development

et al. 2017

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The nematode Caenorhabditis elegans is widely used as a model organism to study cell and developmental biology. Quantitative proteomics of C. elegans is still in its infancy and, so far, most studies have been performed on adult worm samples. Here, we used quantitative mass spectrometry to characterize protein level changes across the four larval developmental stages (L1-L4) of C. elegans. In total, we identified 4130 proteins, and quantified 1541 proteins that were present across all four stages in three biological replicates from independent experiments. Using hierarchical clustering and functional ontological analyses, we identified 21 clusters containing proteins with similar protein profiles across the four stages, and highlighted the most overrepresented biological functions in each of these protein clusters. In addition, we used the dataset to identify putative larval stage-specific proteins in each individual developmental stage, as well as in the early and late developmental stages. In summary, this dataset provides system-wide analysis of protein level changes across the four C. elegans larval developmental stages, which serves as a useful resource for the C. elegans research community. MS data were deposited in ProteomeXchange (http://proteomecentral.proteomexchange.org) via the PRIDE partner repository with the primary accession identifier PXD006676.

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GExplore 1.4: An expanded web interface for queries onCaenorhabditis elegansprotein and gene function

Cited by 34 publications

References 20 publications

Microtubule plus-end dynamics link wound repair to the innate immune response

Microtubule plus-end dynamics link wound repair to the innate immune response

Ancestral function of Inhibitors-of-kappaB regulatesCaenorhabditis elegansdevelopment

Proteomic Characterization of Caenorhabditis elegans Larval Development

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