WormMine: Gene WBGene00023404

• WormBase Gene ID: WBGene00023404
• Gene Name: plr-1
• Sequence Name: Y47D3B.11
• Brief Description: plr-1 encodes a transmembrane RING finger protein that is homologous to the mammalian transmembrane E3 ubiquitin ligases RNF43 and ZNRF3; PLR-1 negatively regulates Wnt pathway signaling by downregulating cell surface levels of the Wnt receptors CFZ-2, LIN-17, MIG-1, and MOM-5, as well as CAM-1 and LIN-18; plr-1 is expressed in a subset of head, ventral nerve cord, and tail neurons as well as in the excretory canal and tail epidermis; PLR-1 protein localizes primarily to endosomes.
• Organism: Caenorhabditis elegans
• Automated Description: Predicted to enable ubiquitin-protein transferase activity. Involved in negative regulation of Wnt signaling pathway. Located in Golgi apparatus; early endosome; and late endosome. Expressed in several structures, including egg-laying apparatus; enteric muscle; neurons; pharynx; and tail. Human ortholog(s) of this gene implicated in several diseases, including gastrointestinal system cancer (multiple); irritable bowel syndrome; and villous adenoma. Is an ortholog of human RNF43 (ring finger protein 43) and ZNRF3 (zinc and ring finger 3).
• Biotype: SO:0001217
• Genetic Position: III :9.70776±
• Length (nt): 6021

1 Organism

• Name: Caenorhabditis elegans
• Taxon Id: 6239

1 Synonyms

• Value: WBGene00023404

Genomics

1 Transcripts

WormMine ID	Sequence Name	Length (nt)	Chromosome Location
Transcript:Y47D3B.11.1	Y47D3B.11.1	1890	III: 11456877-11462897

Other

1 CDSs

WormMine ID	Sequence Name	Length (nt)	Chromosome Location
CDS:Y47D3B.11	Y47D3B.11	1464	III: 11456927-11457080

4 RNAi Result

• WBRNAi00094790
• WBRNAi00056768
• WBRNAi00037167
• WBRNAi00101325

101 Allele

• gk963887
• gk925309
• gk944767
• WBVar01269934
• tm2957
• WBVar02076791
• WBVar01723851
• WBVar01723852
• WBVar01723853
• WBVar01448800
• WBVar01448801
• gk955052
• WBVar02036305
• hd128
• hd129
• gk962365
• gk325233
• gk886634
• gk438435
• gk654840
• gk736559
• gk662753
• gk707700
• gk630613
• gk868918
• gk546073
• gk556240
• gk894636
• gk730835
• gk411267

1 Chromosome

• WormBase ID: III
• Organism: Caenorhabditis elegans
• Length (nt): 13783801

1 Chromosome Location

• Feature . Primary Identifier: WBGene00023404
• Start: 11456877
• End: 11462897
• Strand: 1

4 Data Sets

• WormBaseAcedbConverter
• GO Annotation data set
• C. elegans genomic annotations (GFF3 Gene)
• Panther orthologue and paralogue predictions

1 Downstream Intergenic Region

• WormBase ID: intergenic_region_chrIII_11462898..11463664
• Length (nt): 767
• Chromosome Location: III: 11462898-11463664
• Organism: Caenorhabditis elegans

101 Expression Clusters

Regulated By Treatment	Description	Algorithm	Primary Identifier
	Transcripts that showed significantly increased expression in L1 neural cells comparing to in adult neural cells.	DESeq2 (v1.18.1) fold change > 2, P-adj<0.05, using BenjaminiHochberg correction.	WBPaper00060811:L1_vs_adult_upregulated_neural
	Transcripts of coding genes that showed significantly decreased expression in muscle.	DESeq2 (version 1.24.0). Transcripts with a false-discovery rate adjusted p-value less than 0.05 were considered significantly differentially expressed.	WBPaper00062325:muscle_depleted_coding-RNA
	Transcripts expressed in neuronal cells, by analyzingfluorescence-activated cell sorted (FACS) neurons.	DESeq. False discovry rate (FDR) < 0.1.	WBPaper00048988:neuron_expressed
adult vs dauer larva	Transcripts that showed differential expression in adult vs dauer lava in N2 animals at 20C.	N.A.	WBPaper00050488:adult_vs_dauer_regulated_N2_20C
	Transcripts that showed significantly increased expression after animals were treated with 50uM Rifampicin from day 1 to day 3 adult hermaphradite.	DESeq2(v1.14.1), fold change > 2, p-value < 0.05	WBPaper00055354:Rifampicin_upregulated
	Transcripts that showed significantly higher expression in somatic gonad precursor cells (SGP) vs. head mesodermal cells (hmc).	DESeq2, fold change >= 2, FDR <= 0.01.	WBPaper00056826:SGP_biased
	Transcripts that showed significantly decreased expression in atfs-1(cmh15) (null allele) animals comparing to in N2 animals at L4 larva stage.	edgeR, fold change > 2, FDR < 0.05	WBPaper00060909:atfs-1(cmh15)_downregulated
	Transcripts that showed significantly increased expression in sin-3(tm1276) comparing to in N2.	DESeq2, fold change > 2, p-value < 0.01.	WBPaper00061203:sin-3(tm1276)_upregulated
Bacteria infection: Bacillus thuringiensis	mRNAs that showed significantly decreased expression after pathogenic bacteria Bacillus thuringiensis infections comparing to non pathogenic BT (BT247(1 to 2 mix) vs BT407 12h), according to RNAseq.	Cuffdiff, ajusted p-value < 0.01.	WBPaper00046497:B.thuringiensis_0.5mix_downregulated_12h
	Transcripts that showed significantly increased expression in aak-1(tm1944);aak-2(ok524) animals comparing to in N2.	DEseq 1.18.0, adjusted p-value < 0.05.	WBPaper00056471:aak-1(tm1944);aak-2(ok524)_upregulated
	Transcripts that showed significantly decreased expression in sin-3(tm1276) comparing to in N2 at early embryo when there were only 3 -5 eggs in the adult.	DESeq2, fold change > 2, adjusted p-value < 0.01	WBPaper00058598:sin-3(tm1276)_downregulated
Gamma irradiation 100 mGY per hour for 72 hours since L1 larva.	Transcripts that showed significantly increased expression after exposure to 100mGy per hour gamma irradiation from L1 to day 1 adult hermaphrodite stage.	DESeq2, FDR <= 0.05, log2 fold change >= 0.3 or <= -0.3.	WBPaper00058958:100mGy-irradiation-72h_upregulated
	Transcripts that showed significantly decreased expression after animals were treated with 100uM Rapamycin and 250uM Allantoin from day 1 to day 3 adult hermaphradite.	DESeq2(v1.14.1), fold change > 2, p-value < 0.05	WBPaper00055354:Rapamycin-Allantoin_downregulated
	Transcripts that showed significantly decreased expression in pfd-6(gk493446); daf-2(e1370) comparing to in daf-2(e1370).	Limma version 3.24.15. Fold change < 0.67 (p < 0.05).	WBPaper00055827:pfd-6(gk493446)_downregulated
	Genes that were not enriched in either spermatogenic fem-3(q96gf) nor oogenic fog-2(q71) gonads, according to RNAseq analysis.	To identify differentially expressed transcripts, authors used R/Bioconductor package DESeq.	WBPaper00045521:Gender_Neutral
	Transcripts that showed significantly increased expression in animals lacking P granules by RNAi experiments targeting pgl-1, pgl-3, glh-1 and glh-4, and unc-119-GFP(+), comparing to in control animals, at 2-day post L4 adult hermaphrodite stage.	DESeq2, Benjamini-Hochberg multiple hypothesis corrected p-value < 0.05 and fold change > 2.	WBPaper00050859:upregulated_P-granule(-)GFP(+)_vs_control_day2-adult
	Transcripts that showed significantly increased expression in animals lacking P granules by RNAi experiments targeting pgl-1, pgl-3, glh-1 and glh-4, and unc-119-GFP(-), comparing to in control animals, at 2-day post L4 adult hermaphrodite stage.	DESeq2, Benjamini-Hochberg multiple hypothesis corrected p-value < 0.05 and fold change > 2.	WBPaper00050859:upregulated_P-granule(-)GFP(-)_vs_control_day2-adult
	Genes significantly enriched in NSM neurons (isolated by FACS) versus the reference, according to tiling array analysis towards total RNA.	A linear model and moderated t-statistic were used to determine differentially expressed genes as implemented by the limma package (v3.21.4). Enriched list contains only genes significantly enriched in the NSM neurons versus the reference <=1.5X and <= 5% FDR.	WBPaper00045974:NSM_enriched_totalRNA_tiling
	Genes expressed in N2.	Expressed transcripts were identified on the basis of a Present call in 3 out of 4 N2 experiments as determined by Affymetrix MAS 5.0.	WBPaper00025141:N2_Expressed_Genes
	Transcripts that showed significantly increased expression in spr-1(ok2144) comparing to in N2.	DESeq2, fold change > 2, p-value < 0.01.	WBPaper00061203:spr-1(ok2144)_upregulated
	Transcripts that showed significantly decreased expression in bcf-1(ylf1) comparing to in N2 adult animals.	DESeq2	WBPaper00064933:bcf-1(ylf1)_downregulated_transcript
	Genes that showed significantly altered expression between N2 and npr-1(ur89) strains exposed to either the nematocidal B. thuringiensis B-18247, the pathogenic P. aeruginosa PA14, or the control E. coli OP50 for 12 or 24 hours.	Estimation of transcript abundance and significantly differentially expressed genes were identified by Cuffdiff using the quartile normalization method. Transcripts with a significant change between different conditions (adjusted p-value < 0.01 by the false discovery rate, FDR) were treated as signature for each comparison.	WBPaper00049498:npr-1(ur89)_regulated_3
	Genes upregulated in sma-2 L4 (3 arrays) or sma-4 L4 (1 array) vs. N2 L4.	FDR = 0%, SAM.	WBPaper00037682:sma-2_sma-4_upregulated
	Transcripts that showed significantly increased expression in jmjd-3.1p::jmjd-3.1 comparing to in N2.	DESeq2 Benjamini-Hochberg adjusted p-value < 0.05.	WBPaper00049545:jmjd-3.1(+)_upregulated
	Transcripts that showed significantly increased expression in rgef-1p::jmjd-1.2 comparing to in N2.	DESeq2 Benjamini-Hochberg adjusted p-value < 0.05.	WBPaper00049545:rgef-1p-jmjd-1.2(+)_upregulated
	Transcripts that showed significantly depleted expression in sensory neuron (labeled by iaIs25[Pgcy-37::GFP + unc-119(+)]) comparing to in whole worm.	Fold change > 2, p-value < 0.05.	WBPaper00060661:sensory-neuron_depleted
	Significantly downregulated genes from cyc-1(RNAi) microarrays using SAM algorithm with an FDR < 0.1 from adult-only chips.	SAM algorithm with an FDR < 0.1.	WBPaper00033065:cyc-1(RNAi)_downregulated
	Transcripts that showed significantly increased expression in lin-22(ot267) comparing to in N2 at L3 larva.	Differences in gene expression were then calculated using the negative binomial test in the DESeq package (FDR = 0.1).	WBPaper00053295:lin-22(ot267)_upregulated
	Genes significantly enriched (> 2x, FDR < 5%) in a particular cell-type versus a reference sample of all cells at the same stage.	A Mann-Whitney U test with an empirical background model and FDR correction for multiple testing was used to detect expressed transcripts (Benjamini and Hochberg 1995). Genes and TARs with an FDR <= 0.05 were reported as expressed above background. Authors detected differentially expressed transcripts using a method based on linear models. Genes and TARs were called differentially expressed if the FDR was <= 0.05 and the fold change (FC) >= 2.0. To more strictly correct for potential false-positives resulting from multiple sample comparisons, authors divided individual FDR estimates by the number of samplesor sample comparisons, respectively. This resulted in an adjusted FDR of 1.3 * 0.0001 for expression above background and of 7.4 * 0.0001 for differential expression. Authors called genes selectively enriched in a given tissue if they met the following requirements: (1) enriched expression in a given tissue (FDR <= 0.05 and FC >= 2.0), (2) fold change versus reference among the upper 40% of the positive FC range observed for this gene across all tissues, and (3) fold-change entropy among the lower 40% of the distribution observed for all genes.	WBPaper00037950:excretory-cell_larva_enriched
	Genes that showed flat mRNA expression level throughout the 16 hour time courses from L3 larva to young adult.	The following three lines of R code were used to perform the classification: increasing <-2*amplitude-PC1 < -1.7; oscillating <-!increasing & (amplitude > 0.55); flat <-!increasing & !oscillating; Note that the amplitude of a sinusoidal wave corresponds to only half the fold change between trough and peak.	WBPaper00044736:flat_dev_expression

9 Expression Patterns

• Primary Identifier: Expr1019703
• Pattern: Developmental gene expression time-course. Raw data can be downloaded from ftp://caltech.wormbase.org/pub/wormbase/datasets-published/levin2012

• Primary Identifier: Expr12085
• Pattern: plr-1::GFP expression became visible in late gastrulation stage embryos. Strongest expression was detected in many cells in the tail region and by comma stage the most prominent expression was seen in body wall muscle cells. In early larval stages expression was detectable in a number of different tissues including the major hypodermal cells, muscle and marginal cells of the pharynx, the intestine (strongest in the anteriormost and posteriormost cells) as well as the anal depressor and stomatointestinal muscle. In the nervous system GFP expression was visible in a few neurons in head ganglia, many ventral cord motor neurons and several neurons in the tail ganglia including the PDA neuron. Based on the lack of commissures the motor neurons are likely of the VA, VB, VC and/or AS class. Based on the number of cells the majority (or even all) of these classes express GFP. In general expression was strongest in the tail region throughout development. This also held true for the motor neurons in the ventral cord, where GFP was strongest in the posterior-most cells and barely detectable in anterior motor neurons. Expression is maintained throughout larval development. In later larval stages expression is also seen occasionally in the distal tip cell of the developing gonad, the vulva and uterine muscle cells and the VC4 and VC5 neurons flanking the vulva. Expression in AVG, HSN or CAN neurons was not detectable with this reporter construct, but was detected in a previous study in HSN and CAN using a longer genomic construct (Moffat et al., 2014, Expr11480).

• Primary Identifier: Expr12087
• Pattern: GFP expression is detectable in comma stage embryos with strongest expression in the tail region. The distinct subcellular localization makes it difficult to confirm cell identities, but overall expression is comparable to the plr-1::GFP promoter construct. Postembryonical GFP expression in the head region seems restricted to some neurons and the posterior region of the pharynx. Expression was not readily detectable in hypodermal or body wall muscle cells with this construct postembryonically. Expression of the PLR-1::GFP fusion protein, however, is detectable in the AVG neuron and also in the excretory cell. This suggests that the promoter construct lacks some control elements. Since the GFP expression of the fusion protein is significantly lower than the expression of the promoter construct, it is possible that low levels of expression in tissues and cells expressing the plr-1::GFP transcriptional reporter remain undetectable.

• Primary Identifier: Expr11480
• Pattern: plr-1 expression was observed in a subset of head, ventral nerve cord and tail neurons as well as in the excretory canal and tail epidermis. In particular, expression was observed in DB, NSM, RIF or RIG, PHC, CAN, HSN, and VC. Transient expression was detected in AVG during early larval development and late embryogenesis, which is when AVG differentiates. The mechanosensory neurons ALM, AVM, PLM and PVM respond to Wnts and do not express PLR-1.
• Subcellular Localization: When co-expressed in AVG, most PLR-1-mCherry puncta are colabeled with the late endosomal marker RME-8-GFP and some PLR-1-GFP vesicles are marked by the early endosomal reporter mRFP-EEA-1. A few PLR-1 vesicles are co-labeled with the Golgi marker MANS-YFP, but none are marked by the lysosomal reporter LMP-1-GFP. Thus, PLR-1 accumulates primarily in endosomes.

• Primary Identifier: Expr2014964
• Pattern: Single cell embryonic expression. Only cell types with an expression fraction of greater 0.2 of the maximum expressed fraction are labeled (Full data can be downloaded from http://caltech.wormbase.org/pub/wormbase/datasets-published/packer2019/). The colors represent the broad cell class to which the cell type has been assigned. The size of the point is proportional to the log2 of the numbers of cells in the dataset of that cell type. Interactive visualizations are available as a web app (https://cello.shinyapps.io/celegans/) and can also be installed as an R package (https://github.com/qinzhu/VisCello.celegans).

• Primary Identifier: Expr1035740
• Pattern: Tiling arrays expression graphs

• Primary Identifier: Expr1160223
• Pattern: Developmental gene expression time-course. Raw data can be downloaded from ftp://caltech.wormbase.org/pub/wormbase/datasets-published/hashimshony2015

• Primary Identifier: Expr2033199
• Pattern: Single cell embryonic expression. Only cell types with an expression fraction of greater 0.2 of the maximum expressed fraction are labeled (Full data can be downloaded from http://caltech.wormbase.org/pub/wormbase/datasets-published/packer2019/). The colors represent the broad cell class to which the cell type has been assigned. The size of the point is proportional to the log2 of the numbers of cells in the dataset of that cell type. Interactive visualizations are available as a web app (https://cello.shinyapps.io/celegans/) and can also be installed as an R package (https://github.com/qinzhu/VisCello.celegans).

• Primary Identifier: Expr12086
• Subcellular Localization: The GFP signal is concentrated in puncta spread throughout the cytoplasm mainly in the cell body, but also extends into neuronal processes. The punctate expression of PLR-1::GFP fusion protein suggests that PLR-1 is present in some endocytotic compartments. Recently PLR-1 has been shown to colocalize with endosomal markers (Moffat et al., 2014, Expr11480), suggesting that PLR-1 indeed enters the secretory pathway.

17 GO Annotation

7 Homologues

1 Locations

• Feature . Primary Identifier: WBGene00023404
• Start: 11456877
• End: 11462897
• Strand: 1

17 Ontology Annotations

0 Regulates Expr Cluster

1 Sequence

• Length: 6021

1 Sequence Ontology Term