Difference between revisions of "PMID:26412237"

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Also, it would be helpful to define exactly when gastrulation begins and ends in C. elegans.  Begins when two E daughters, Ea and Ep, start to ingress?  Ends at ventral cleft closure?
 
Also, it would be helpful to define exactly when gastrulation begins and ends in C. elegans.  Begins when two E daughters, Ea and Ep, start to ingress?  Ends at ventral cleft closure?
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|Figure 2
 
|Figure 2
 
| Arrested embryos (29 ± 1.8% of total; n = 940) segregated into three major classes. Class I embryos were arrested at late gastrulation prior to the formation of epidermal cells. Cells in these embryos appeared round and detached, suggesting severe weakening of cell-cell adhesion.  
 
| Arrested embryos (29 ± 1.8% of total; n = 940) segregated into three major classes. Class I embryos were arrested at late gastrulation prior to the formation of epidermal cells. Cells in these embryos appeared round and detached, suggesting severe weakening of cell-cell adhesion.  

Revision as of 19:32, 13 October 2015

Figure in Paper Evidence Sentence(s) Gene or Protein WPO Annotation EQ Annotation GO Annotation Comments
Figure S1 ULP-2, a member of the Ulp2-like branch of SUMO proteases (Mukhopadhyay and Dasso, 2007) shares 17% amino acid similarity with the mammalian SUMO proteases SENP6 and SENP7 (Figure S1). ULP-2 n/a n/a MF - GO:0016929 SUMO-specific protease activity

BP - GO:0016926 protein desumoylation EC = ISS with human SENP6

Note that WB and UniProtKB both only represent the larger isoform right now.
Figure 1A-C, 1D and 1E RT-PCR of embryonic mRNA identified two ulp-2 isoforms; ulp-2a, which is expressed in both the nucleus and cytosol, and the shorter isoform ulp-2b, which is expressed solely in the cytosol (Figures 1D and 1E). UPL-2 n/a n/a CC - GO:0005634 nucleus

CC - GO:0005829 cytosol

EC = IDA

Note that WB and UniProtKB both only represent the larger isoform right now.
Figure 2, Figure S2 Embryos in which ulp-2 expression was silenced by RNAi or gene mutation—ulp-2(tv380), which we generated by the CRISPR/Cas9 system (Friedland et al., 2013)—were arrested (29% and 63.4% embryonic arrest, respectively) during a developmental window from late gastrulation through epidermal morphogenesis. ulp-2 BP - GO:0009792 embryo development ending in birth or egg hatching

EC = IMP

Note that BP - GO:0009790 embryo development is included in the 'do not manually annotate' subset of GO terms
Figure 2, Figure S2 Arrested embryos were segregated into three major classes: (I) late gastrulation failure, (II) cleft/enclosure failure, and (III) elongation failure (Figure 2; Figure S2; Movies S1, S2, S3 and S4). ulp-2 BP - GO:0007369 gastrulation

BP - GO:0010172 embryonic body morphogenesis

BP - GO:0016331 morphogenesis of embryonic epithelium

EC = IMP

Currently, there are not specific GO BP terms for late gastrulation, ventral cleft closure, ventral enclosure, embryonic and/or epidermal elongation.
Figure 2 Figure 2. ULP-2 KD Causes Dorsal Intercalation, Ventral Cleft Closure, and Epidermal Enclosure Defects in ulp-2(RNAi) Embryos ulp-2 BP - GO:0010172 embryonic body morphogenesis

BP - GO:0016331 morphogenesis of embryonic epithelium

EC = IMP

There is no specific GO BP term for dorsal intercalation.

Also, it would be helpful to define exactly when gastrulation begins and ends in C. elegans. Begins when two E daughters, Ea and Ep, start to ingress? Ends at ventral cleft closure?

Figure 2 Arrested embryos (29 ± 1.8% of total; n = 940) segregated into three major classes. Class I embryos were arrested at late gastrulation prior to the formation of epidermal cells. Cells in these embryos appeared round and detached, suggesting severe weakening of cell-cell adhesion. ulp-2 BP - GO:0007369 gastrulation

BP - GO:0070587 regulation of cell-cell adhesion involved in gastrulation

EC = IMP

Is the annotation to GO:0070587 too interpretive? Do later experiments provide more evidence for this interpretation?



Existing GO Terms

GO:0007369 gastrulation

GO:0003381 epithelial cell morphogenesis involved in gastrulation

GO:0070587 regulation of cell-cell adhesion involved in gastrulation

GO:0016331 morphogenesis of embryonic epithelium

GO:0010172 embryonic body morphogenesis

GO:1904696 protein localization to cell-cell adherens junctions

GO:1904704 positive regulation of protein localization to cell-cell adherens junctions

GO:0016926 protein desumoylation

GO:0034334 adherens junction maintenance

GO:0071260 cellular response to mechanical stimulus


Possible New GO Terms

GO:new? ventral cleft closure?

GO:new? ventral epidermal enclosure?

GO:new? dorsal intercalation?

GO:new? embryonic elongation?

GO:new? regulation of cell-cell adhesion involved in morphogenesis of embryonic epithelium?

GO:new? positive regulation of protein localization to cell-cell adherens junctions via protein desumoylation?


Chris' allele-phenotype EQ-PATO annotations

anatomical structure morphogenesis (Figure 4A)

apical protein localization (Figure 6A-C)

developmental process (Figure 4B)

embryo development (Figure S2A,D, 3E, 4A)

embryo development, gastrulation (Figures 3A-3C, 3G, and 3H; Table S1; Movie S5)

gastrulation PATO: failure/non-functional (Figure S2A,D, 4A)

regulation of protein sumoylation (Figure 5F)


Chris' RNAi EQ-PATO annotations:

actin filament bundle assembly (Figure 7C-E)

apical protein localization (Figure 6)

body morphogenesis (Figure 4B, Movie S6)

cell morphogenesis (Figure 2E)

embryo development (Figure 2C,D,F, 4A, S2A,D)

digestive tract development (Figure S2F)

gastrulation (Figure 2C,S2D,F, 4A,B, Movie S6)

neuroblast migration (Figure S2E)

protein localization (Figure 6D)

regulation of protein sumoylation (Figure 5F)

catenin complex PATO: mislocalized (Figure 7A,B)

cell-cell contact zone (Figure 6D, S3D,E)