WormMine: Gene WBGene00004101

• WormBase Gene ID: WBGene00004101
• Gene Name: hgrs-1
• Sequence Name: C07G1.5
• Brief Description: hgrs-1 encodes a VHS and FYVE zinc finger-domain containing protein that is the C. elegans ortholog of S. cerevisiae Vps27p and mammalian hepatocyte growth factor-regulated tyrosine kinase substrate (HGS); hgrs-1 activity is essential for molting and thus for proper larval development; consistent with its proposed role in the endocytic pathway, HGRS-1 is also required for proper trafficking of the LRP-1 low-density lipoprotein receptor-related protein 1 and for endosome maturation and regulation of autophagic vesicle accumulation; an HGRS-1::GFP fusion protein is widely expressed, but particularly enriched in epithelial cells; within cells, HGRS-1::GFP localizes to endosomal membranes; HGRS-1 and STAM-1 physically interact in vivo, forming the C. elegans ESCRT-0 complex; on early endosomes; in the context of the complex, both STAM-1 and HGRS-1 bind ubiquitin.
• Organism: Caenorhabditis elegans
• Automated Description: Enables ubiquitin binding activity. Involved in protein localization to non-motile cilium. Located in early endosome and endosome membrane. Part of ESCRT-0 complex. Expressed in several structures, including coelomocyte; excretory canal; hermaphrodite gonad; intestine; and vulva. Is an ortholog of human HGS (hepatocyte growth factor-regulated tyrosine kinase substrate).
• Biotype: SO:0001217
• Genetic Position: IV :3.6681 ±0.002259
• Length (nt): 4675

1 Organism

• Name: Caenorhabditis elegans
• Taxon Id: 6239

1 Synonyms

• Value: WBGene00004101

Genomics

3 Transcripts

WormMine ID	Sequence Name	Length (nt)	Chromosome Location
Transcript:C07G1.5.2	C07G1.5.2	2595	IV: 8201374-8206048
Transcript:C07G1.5.3	C07G1.5.3	2680	IV: 8201374-8205272
Transcript:C07G1.5.1	C07G1.5.1	2493	IV: 8201429-8205065

Other

1 CDSs

WormMine ID	Sequence Name	Length (nt)	Chromosome Location
CDS:C07G1.5	C07G1.5	2190	IV: 8201723-8201796

33 RNAi Result

• WBRNAi00008362
• WBRNAi00024499
• WBRNAi00078386
• WBRNAi00078470
• WBRNAi00068517
• WBRNAi00068516
• WBRNAi00068519
• WBRNAi00068518
• WBRNAi00068520
• WBRNAi00064506
• WBRNAi00064536
• WBRNAi00064621
• WBRNAi00064748
• WBRNAi00064844
• WBRNAi00068956
• WBRNAi00080721
• WBRNAi00090871
• WBRNAi00091173
• WBRNAi00091172
• WBRNAi00040016
• WBRNAi00087645
• WBRNAi00098080
• WBRNAi00099139
• WBRNAi00060663
• WBRNAi00060664
• WBRNAi00064388
• WBRNAi00060665
• WBRNAi00060666
• WBRNAi00078471
• WBRNAi00064728

59 Allele

• gk964278
• gk964500
• gk962765
• gk963722
• gk963417
• gk963416
• tm345
• WBVar02020957
• WBVar00190994
• WBVar01688018
• WBVar02057920
• gk369617
• gk748993
• gk332599
• gk631162
• WBVar01794892
• gk332181
• gk206857
• gk632790
• gk206858
• gk873095
• gk395228
• gk206856
• gk578392
• gk670409
• gk370304
• gk321864
• WBVar01833342
• gk933177
• gk651120

1 Chromosome

• WormBase ID: IV
• Organism: Caenorhabditis elegans
• Length (nt): 17493829

1 Chromosome Location

• Feature . Primary Identifier: WBGene00004101
• Start: 8201374
• End: 8206048
• 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_chrIV_8201234..8201373
• Length (nt): 140
• Chromosome Location: IV: 8201234-8201373
• Organism: Caenorhabditis elegans

115 Expression Clusters

Regulated By Treatment	Description	Algorithm	Primary Identifier
	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
	Genes that showed expression levels higher than the corresponding reference sample (embryonic 24hr reference).	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:all-neurons_L1-larva_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
	Proteins interacting with NHR-49-GFP according to co-IP and LC-MS.	N.A.	WBPaper00064071:NHR-49_interacting
	Transcripts expressed in hypodermis, according to PAT-Seq analysis using Pdpy-7-GFP-3XFLAG mRNA tagging.	Cufflinks FPKM value >=1.	WBPaper00050990:hypodermis_expressed
	Transcripts expressed in intestine, according to PAT-Seq analysis using Pges-1-GFP-3XFLAG mRNA tagging.	Cufflinks FPKM value >=1.	WBPaper00050990:intestine_expressed
	Maternal class (M): genes that are called present in at least one of the three PC6 replicates.	A modified Welch F statistic was used for ANOVA. For each gene, regressed error estimates were substituted for observed error estimates. The substitution is justified by the lack of consistency among the most and least variable genes at each time point. Regressed error estimates were abundance-dependent pooled error estimates that represented a median error estimate from a window of genes of similar abundance to the gene of interest. A randomization test was used to compute the probability Pg of the observed F statistic for gene g under the null hypothesis that developmental time had no effect on expression. P-values were not corrected for multiple testing.	[cgc5767]:expression_class_M
	Transcripts expressed in seam cells, according to PAT-Seq analysis using Pgrd-10-GFP-3XFLAG mRNA tagging.	Cufflinks FPKM value >=1.	WBPaper00050990:seam_expressed
	Transcripts that showed significantly increased expression in day 1 adult hermaphrodite comparing to in L4 larva fem-3(q20) animals.	Fold change > 2, FDR < 0.05	WBPaper00064088:Day-1-adult_vs_L4_upregulated_fem-3(q20)
	Transcripts that showed significantly increased expression in day 3 adult hermaphrodite comparing to in L4 larva fem-3(q20) animals.	Fold change > 2, FDR < 0.05	WBPaper00064088:Day-3-adult_vs_L4_upregulated_fem-3(q20)
Bacteria infection: Bacillus thuringiensis	mRNAs that showed significantly decreased expression after pathogenic bacteria Bacillus thuringiensis infections comparing to non pathogenic BT (BT247(1 to 10 mix) vs BT407 12h), according to RNAseq.	Cuffdiff, ajusted p-value < 0.01.	WBPaper00046497:B.thuringiensis_0.1mix_downregulated_12h
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 hrde-1(tm1200) animals, comparing to in N2, after growing at 25C for five generations (late generation).	CuffDiff2	WBPaper00051265:F4_hrde-1(tm1200)_upregulated
	Transcripts that showed significantly altered expression after 24 hour exposure to stavudine (d4T) starting at L1 lava stage.	DESeq	WBPaper00053302:stavudine_24h_regulated
	Transcripts that showed significantly decreased expression in dissected female germline comparing to in dissected male germline.	Log2 Fold change > 2 or <-1, p-value < 0.05.	WBPaper00053599:female_vs_male_downregulated
	Genes that showed expression levels higher than the corresponding reference sample (L2 all cell reference).	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_L2-larva_expressed
	Genes that showed expression levels higher than the corresponding reference sample (L2 all cell reference).	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:GABAergic-motor-neurons_L2-larva_expressed
	Genes that showed expression levels higher than the corresponding reference sample (L3/L4 all cell reference).	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:hypodermis_L3-L4-larva_expressed
	Transcripts that showed significantly decreased expression after animals were treated with 50uM Rifampicin and 250uM Allantoin from day 1 to day 3 adult hermaphradite.	DESeq2(v1.14.1), fold change > 2, p-value < 0.05	WBPaper00055354:Rifampicin-Allantoin_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
	Proteins identified in extracellular vesicle.	N.A.	WBPaper00062669:extracellular-vesicle_protein
	Transcripts that showed significantly increased expression after N2 animals were exposed to BL21 bacteria carrying pET28a-cry5B, comparing to animals exposed to BL21 control bacteria.	Differentially expressed genes were identified through fold change as well as P value calculated with t-test. The threshold set for up- and down-regulated genes was a fold change >= 2.0 and a P value <= 0.05.	WBPaper00065732:Cry5Ba_upregulated_N2
Bacteria infection: Enterococcus faecalis OG1RF. Exposure for 16 hours.	Transcripts that showed significantly decreased expression in hpx-2(dg047) after animals were exposed to E. faecalis OG1RF for 16 hours comparing to exposure to E. Coli OP50.	Cuffcompare and Cuffdiff	WBPaper00056090:E.faecalis_downregulated_hpx-2(dg047)
	Genes found to be regulated by low-copy overexpression of sir-2.1 with p < 0.014.	N.A.	WBPaper00026929:sir-2.1_overexpression_regulated
	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
	WT-Pico Pan-neural Depleted Genes, with genes found multiple times in a single dataset removed (without dups).	To identify differentially expressed transcripts, normalized intensity values from the pan-neural data sets were compared to a reference (from all larval cells) using Significance Analysis of Microarray software (SAM). A two class unpaired analysis of the data was performed to identify neuron-enriched genes. Pan-neural enriched transcripts in the IVT and WT-Pico-derived data set were defined as 1.5X elevated vs the reference at a False Discovery Rate (FDR) = 3%.	WBPaper00031532:Larva_Pan_Neuronal_Depleted
	Transcripts that showed significantly decreased 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)_downregulated
	Transcripts that showed significantly altered expression after 24 hour exposure to stavudine (FLT) starting at L1 lava stage.	DESeq	WBPaper00053302:alovudine_24h_regulated
	Transcripts that showed significantly increased expression in sftb-1(cer6) deletion homozygous comparing to to in N2 animals at L4 larva stage.	DESeq2, fold change > 2	WBPaper00058725:sftb-1(cer6)_upregulated

9 Expression Patterns

• Primary Identifier: Expr1031981
• Pattern: Tiling arrays expression graphs

• Primary Identifier: Expr7858
• Remark: Cevps-27 = C07G1.5 Immunohistochemical analyses with anti-CeVPS-27 antibodies (Figure 2AD,GJ) and observation of CeVPS-27::GFP transgenic worms (Figure 2E,F,K) revealed a similar expression pattern. Picture: Figure 2, Figure 3. Several arguments support the idea that CeVPS-27 localizes to endosomes. First, CeVPS-27-positive vesicles are not lysosomes as revealed by an absence of colocalization of CeVPS-27::GFP with the lysosomal marker lysotracker. Second, CeVPS-27 is localized in vesicles close to the plasma membrane in epithelial cells and in the coelomocytes, which are specialized in endocytosis of fluid and macromolecules from the body cavity. Finally, the inactivation of the homolog of the class E vps-23, which in yeast and mammals results in the formation of enlarged endosomes, induced the production of enlarged CeVPS-27-positive vesicles. Together, these data indicate that CeVPS-27 is localized at the endosomal membrane in C. elegans.
• Pattern: CeVPS-27 was detected ubiquitously, as early as in the 2-cell embryo and persisted throughout the embryonic and larval development and in adult animals. At mid-embryogenesis, when epithelialization proceeds, CeVPS-27-positive vesicles were preferentially enriched in hypodermal, pharyngeal and intestinal cells. The specificity of the signal was confirmed by its complete disappearance after inactivation of Cevps-27 by RNAi. During larval development and in adults, CeVPS-27 was expressed ubiquitously but remained more abundant in the intestine, the hypodermis, the pharynx and in the adult epithelial tissues; namely the uterus, the vulva, the spermatheca and the gonad. CeVPS-27 could also be found in the excretory canal, and the six scavenger cells called coelomocytes.
• Subcellular Localization: The protein was detected as a punctate pattern in the cytoplasm indicating a vesicular localization. At mid-embryogenesis, when epithelialization proceeds, CeVPS-27-positive vesicles were preferentially enriched in hypodermal, pharyngeal and intestinal cells, where they localized close to the apical membrane as revealed by the apical junction marker AJM-1. Later during morphogenesis, CeVPS-27-positive vesicles became more uniformly localized. Several arguments support the idea that CeVPS-27 localizes to endosomes (see Remark).

• Primary Identifier: Expr2012409
• 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: Expr1144091
• Pattern: Developmental gene expression time-course. Raw data can be downloaded from ftp://caltech.wormbase.org/pub/wormbase/datasets-published/hashimshony2015

• Primary Identifier: Expr2030645
• 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: Expr1018369
• Pattern: Developmental gene expression time-course. Raw data can be downloaded from ftp://caltech.wormbase.org/pub/wormbase/datasets-published/levin2012

• Primary Identifier: Expr14670
• Subcellular Localization: HGRS-1 localized to distinct regions of the early endosome, typically on the side of the endosome facing the interior of the cell.

• Primary Identifier: Expr3953
• Remark: Picture: Figures S7.
• Subcellular Localization: In cells that express Pced-1 hgrs-1::gfp or Pced-1 hgrs-1::mrfp1, the HGRS-1 fusion proteins were observed in the cytoplasm as puncta and patches. To determine if the puncta and patches represent endosomal compartments, authors first examined whether HGRS-1::GFP co-localized with fluorescent dye FM 4-64, which is endocytosed into cells and labels endocytic compartments. FM 4-64 introduced into adult C. elegans hermaphrodites by soaking displays a punctate localization pattern in the cytoplasm typical for endosomes and lysosomes. Authors incubated L4-stage worms expressing Pced-1 hgrs-1::gfp in a buffer containing FM 4-64 (160 uM) for 1 hr and observed co-localization of HGRS-1::GFP and FM 4-64 on a large number of puncta, indicating that HGRS-1 is associated with endocytic compartments.

• Primary Identifier: Expr16171
• Subcellular Localization: Using affinity-purified antibodies directed against Hrs and STAM, we confirmed that both proteins largely co-localize with the early endosomal marker EEA-1 in C. elegans embryos.

16 GO Annotation

4 Homologues

1 Locations

• Feature . Primary Identifier: WBGene00004101
• Start: 8201374
• End: 8206048
• Strand: -1

16 Ontology Annotations

0 Regulates Expr Cluster

1 Sequence

• Length: 4675

1 Sequence Ontology Term