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WormBase Tree Display for Variation: WBVar00143205

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Name Class

WBVar00143205NamePublic_namee428
Other_nameCE26205:p.Gln394Ter
Y59A8B.1a.1:c.1180C>T
HGVSgCHROMOSOME_V:g.17945749G>A
Sequence_detailsSMapS_parentSequenceY59A8B
Flanking_sequencesacgtcatccacggactcactggagcatatgagaggaagagaaagaagcaacaggagactg
Mapping_targetY59A8B
Type_of_mutationSubstitutionctPaper_evidenceWBPaper00006355
SeqStatusSequenced
Variation_typeAllele
OriginSpeciesCaenorhabditis elegans
Strain (18)
LaboratoryCB
StatusLive
AffectsGeneWBGene00001080
TranscriptY59A8B.1a.1VEP_consequencestop_gained
VEP_impactHIGH
HGVScY59A8B.1a.1:c.1180C>T
HGVSpCE26205:p.Gln394Ter
cDNA_position1345
CDS_position1180
Protein_position394
Exon_number7/13
Codon_changeCag/Tag
Amino_acid_changeQ/*
InteractorWBInteraction000052180
WBInteraction000052432
WBInteraction000501500
Genetics (2)
DescriptionPhenotypeWBPhenotype:0000006Paper_evidenceWBPaper00001077
Curator_confirmedWBPerson712
RemarkSlightly Egl.Paper_evidenceWBPaper00001077
Curator_confirmedWBPerson712
WBPhenotype:0000062Person_evidenceWBPerson261
Curator_confirmedWBPerson712
Remarklethal to 2A;3XPerson_evidenceWBPerson261
Curator_confirmedWBPerson712
WBPhenotype:0000066Paper_evidenceWBPaper00001077
Curator_confirmedWBPerson712
Remark85% XX viable.Paper_evidenceWBPaper00001077
Curator_confirmedWBPerson712
WBPhenotype:0000135Person_evidenceWBPerson261
Curator_confirmedWBPerson712
RemarkSome X chromosome transcript levels elevated, in both XX and XO.Person_evidenceWBPerson261
Curator_confirmedWBPerson712
WBPhenotype:0000136Paper_evidenceWBPaper00001011
Curator_confirmedWBPerson712
RemarkmRNA levels of lin-14 are elevated ~1.9 foldPaper_evidenceWBPaper00001011
Curator_confirmedWBPerson712
EQ_annotationsLife_stageWBls:0000024PATO:0000460Paper_evidenceWBPaper00001011
Curator_confirmedWBPerson712
Phenotype_assayTreatmentRNA preparations were made from staged L1 animals and mRNA levels were normalized against act-1 mRNA levels.Paper_evidenceWBPaper00001011
Curator_confirmedWBPerson712
WBPhenotype:0000583Paper_evidenceWBPaper00001077
WBPaper00000666
WBPaper00001011
Person_evidenceWBPerson261
Curator_confirmedWBPerson712
RemarkXX animals are Dumpy; XO animals are not Dumpy.Paper_evidenceWBPaper00000666
Curator_confirmedWBPerson712
XX animals are dumpy.Paper_evidenceWBPaper00001011
Curator_confirmedWBPerson712
weak dumpy (XX); non-dumpy (XO), easy to score as adult, not easy to score as L1.Person_evidenceWBPerson261
Curator_confirmedWBPerson712
RecessivePaper_evidenceWBPaper00000666
Curator_confirmedWBPerson712
EQ_annotationsLife_stageWBls:0000057PATO:0000460Person_evidenceWBPerson261
Curator_confirmedWBPerson712
Phenotype_assayGenotypeher-1(e1520) him-5 lin-14(n179)Paper_evidenceWBPaper00001011
Curator_confirmedWBPerson712
Ease_of_scoringES3_Easy_to_scorePerson_evidenceWBPerson261
Curator_confirmedWBPerson712
WBPhenotype:0000717Paper_evidenceWBPaper00048953
Curator_confirmedWBPerson2987
Remark"To test if the expression changes seen in dpy-21(e428) and set-4(n4600) mutants are due to transcription, we performed AMA-1 (RNA Pol II large subunit) ChIP-seq analysis. Average RNA Pol II enrichment across the transcription start and end sites showed a 3' accumulation that was also noted in the GRO-seq analysis for C. elegans genes (Fig 5G) [43]. RNA Pol II on the X chromosome promoters increased relative to autosomes in dpy-21(e428) mutant (Fig 5G). In the set-4(n4600) mutant (Fig 5G), there was a subtle shift in RNA Pol II levels between the X and autosomes, suggesting that the effect of set-4 is also at the level of transcription. These results do not exclude post-transcriptional effects contributing to increased X expression in the dpy-21(e428) and set-4(n4600) mutants, but do suggest that dpy21 and set-4 act at the level of transcription."Paper_evidenceWBPaper00048953
Curator_confirmedWBPerson2987
WBPhenotype:0000718Paper_evidenceWBPaper00001011
WBPaper00048953
Curator_confirmedWBPerson712
WBPerson2987
RemarkAs determined by the penetrance of the lin-14(n179) mutant phenotype, based on the [# mutant seam cell nuclei (undivided seam cell nuclei + nuclei that generated precocious alae)/ total # seam cell nuclei] animals after the L3 molt.Paper_evidenceWBPaper00001011
Curator_confirmedWBPerson712
"In mixed embryos and L3, dpy-21(e428) mutation also caused X chromosome derepression (Fig 3F). In early embryos, dpy-21(e428) had a relatively less X-specific effect compared to dpy-27(y56). In dpy-21(e428) early embryos, 72% of X and 58% of autosomal genes were significantly upregulated."Paper_evidenceWBPaper00048953
Curator_confirmedWBPerson2987
"The effect of dpy-21(e428) on X chromosome expression was more specific in the later stage worms. Clustering and heatmap analysis of gene expression changes showed that dpy-21 (e428) caused both increased and decreased expression from the X chromosomes in early embryos, whereas majority of the X chromosomal genes were derepressed in comma stage embryos and L3s (S4C Fig)."Paper_evidenceWBPaper00048953
Curator_confirmedWBPerson2987
"H4K20me1 reduction due to set-1 or dpy-21 null mutation led to a significant increase in X chromosome expression compared to autosomes in L3 larvae (Fig 5C). We observed a small but significant increase in X expression compared to autosomes in the set-4(n4600) mutant L3 (Fig 5C) and mixed stage embryos (Fig 5D). Expression of previously defined dosage compensated genes [11,23,42] were increased in dpy-21(e428), set-1(tm1821), but not as much in set-4 (n4600) mutant (Fig 5E). To test if a subset of X chromosomal genes were responsible for the effect seen in the set-4(n4600) mutant (Fig 5C), we plotted the distribution of expression ratios on the X and autosomes (Fig 5F). This indicated a slight shift between X and autosomes, suggesting that set-4(n4600) has a subtle effect across all genes, rather than a large effect on a subset of X chromosomal genes."Paper_evidenceWBPaper00048953
Curator_confirmedWBPerson2987
"To understand the role of dpy-21 in the DCC, we compared gene expression changes in dpy-27 RNAi, dpy-21(e428), set-1(tm1821) and set-4(n4600) mutant L3 larvae by clustering differential expression ratios on the X chromosome and autosomes (Fig 6A). We note that while the effect of dpy-27 RNAi and dpy-21(e428) were generally similar on the X, genes in several clusters were affected differently between dpy-27 RNAi and dpy-21 (e428). We performed gene ontology (GO) analyses comparing enriched functions in each cluster compared to the whole genome (Fig 6B). Interestingly, the effect of dpy-27 RNAi and dpy-21(e428) on clusters enriched for cuticle genes were opposite, yet both mutations result in a dumpy phenotype."Paper_evidenceWBPaper00048953
Curator_confirmedWBPerson2987
Phenotype_assayTreatmentNomarski optics were used to follow the fates of the midbody seam cell nuclei of L3 animals raised at 24C.Paper_evidenceWBPaper00001011
Curator_confirmedWBPerson712
Temperature24Paper_evidenceWBPaper00001011
Curator_confirmedWBPerson712
Genotypelin-14(n179)Paper_evidenceWBPaper00001011
Curator_confirmedWBPerson712
WBPhenotype:0001348Paper_evidenceWBPaper00046016
Curator_confirmedWBPerson557
RemarkDecreased X chromosome compaction leading to enlarged X chromosomes.Paper_evidenceWBPaper00046016
Curator_confirmedWBPerson557
WBPhenotype:0001361Paper_evidenceWBPaper00046016
Curator_confirmedWBPerson557
RemarkDecreased X chromosome compaction leading to enlarged X chromosomes.Paper_evidenceWBPaper00046016
Curator_confirmedWBPerson557
WBPhenotype:0001581Paper_evidenceWBPaper00001011
Curator_confirmedWBPerson712
RemarkAnimals have 31%(n=40) mutant seam cell nuclei, similar to XXX lin-14 animals (26% n=25) and less mutant than XX lin-14 animals (77% n=40).Paper_evidenceWBPaper00001011
Curator_confirmedWBPerson712
EQ_annotationsAnatomy_termWBbt:0006913PATO:0000460Paper_evidenceWBPaper00001011
Curator_confirmedWBPerson712
Life_stageWBls:0000035PATO:0000460Paper_evidenceWBPaper00001011
Curator_confirmedWBPerson712
Phenotype_assayTreatmentNomarski optics were used to follow the fates of the midbody seam cell nuclei of L3 animals raised at 24C.Paper_evidenceWBPaper00001011
Curator_confirmedWBPerson712
Temperature24Paper_evidenceWBPaper00001011
Curator_confirmedWBPerson712
Genotypelin-14(n179)Paper_evidenceWBPaper00001011
Curator_confirmedWBPerson712
WBPhenotype:0001582Paper_evidenceWBPaper00001011
Curator_confirmedWBPerson712
RemarkXO lin-14(n179) males display significantly more lin-14 seam cell defects than lin-14 animals alone but similar to levels observed for lin-14/Df animals. Similar results were observed for e428/e459 (data not shown).Paper_evidenceWBPaper00001011
Curator_confirmedWBPerson712
EQ_annotationsLife_stageWBls:0000056PATO:0000460Paper_evidenceWBPaper00001011
Curator_confirmedWBPerson712
Phenotype_assayTemperature20Paper_evidenceWBPaper00001011
Curator_confirmedWBPerson712
Genotypelin-14(n179) or her-1(e1520) him-5 lin-14(n179)Paper_evidenceWBPaper00001011
Curator_confirmedWBPerson712
WBPhenotype:0001583Paper_evidenceWBPaper00001011
Curator_confirmedWBPerson712
RemarkXXX and XXXX progeny are lethal.Paper_evidenceWBPaper00001011
Curator_confirmedWBPerson712
WBPhenotype:0002078Paper_evidenceWBPaper00048953
Curator_confirmedWBPerson2987
Remark"We analyzed genome-wide expression changes that occur in dpy-21(e428), set-1(tm1821) and set-4(n4600) null mutants [18,19]. Set-1 null mutant is maternal effect sterile, and RNAi knockdown of set-1 leads to germline deficient adults, thus we could not isolate embryos. Therefore, we collected set-1(tm1821) homozygous and heterozygous L3 larvae (see Material and Methods). Western blot analysis in whole-larval extracts showed expected changes in H4K20me1 (Fig 5B) [18,19]. H4K20me1 reduced in dpy-21(e428), increased in set-4(n4600), and was eliminated in set-1(tm1821)."Paper_evidenceWBPaper00048953
Curator_confirmedWBPerson2987
Phenotype_not_observedWBPhenotype:0000065Paper_evidenceWBPaper00001077
Curator_confirmedWBPerson712
WBPhenotype:0000520Paper_evidenceWBPaper00000666
Curator_confirmedWBPerson712
RemarkXO males are morphologically indistinguishable from wild type males.Paper_evidenceWBPaper00000666
Curator_confirmedWBPerson712
RecessivePaper_evidenceWBPaper00000666
Curator_confirmedWBPerson712
EQ_annotationsLife_stageWBls:0000056PATO:0000460Paper_evidenceWBPaper00000666
Curator_confirmedWBPerson712
WBPhenotype:0000648Paper_evidenceWBPaper00000666
Curator_confirmedWBPerson712
RemarkXO males are not mating deficient relative to wild type males in fertility measurements.Paper_evidenceWBPaper00000666
Curator_confirmedWBPerson712
RecessivePaper_evidenceWBPaper00000666
Curator_confirmedWBPerson712
EQ_annotationsLife_stageWBls:0000056PATO:0000460Paper_evidenceWBPaper00000666
Curator_confirmedWBPerson712
Reference (13)
RemarkThe molecular changes given above for this allele were previously attributed to allele y428, owing to a published typo.Person_evidenceWBPerson421
MethodSubstitution_allele