WormMine: Gene WBGene00004078

• WormBase Gene ID: WBGene00004078
• Gene Name: pos-1
• Sequence Name: F52E1.1
• Brief Description: pos-1 encodes a CCCH-type zinc-finger protein; during embryogenesis, maternally provided POS-1 is essential for proper fate specification of germ cells, intestine, pharynx, and hypodermis; POS-1's role in cell fate specification is likely as a translational regulator, as POS-1 is required, in posterior blastomeres, for positive regulation of apx-1 mRNA translation and negative regulation of glp-1 mRNA translation via direct binding to the spatial control region (SCR) in the glp-1 mRNA 3' UTR; in regulating mRNA translation, POS-1 interacts with SPN-4, an RNP-type RNA binding protein, that may function to negatively regulate POS-1 activity; POS-1 can also bind the mex-6 3'-UTR in vitro, although expression of a MEX-6 reporter fusion protein does not appear to be affected in pos-1 mutant animals; pos-1 mRNA is first detected in the gonads of L4 and adult animals, and is present uniformly in oocytes and newly fertilized embryos; during early embryonic divisions, pos-1 mRNA is present at higher levels in germline blastomeres until it disappears following the division of P4; POS-1 protein is first apparent at low levels in 1-cell embryos, with subsequent expression mirroring that of pos-1 mRNA: high levels in germline blastomeres until its disappearance after the P4 division; in the germline blastomeres P1, P2, P3, and P4, POS-1 colocalizes with cytoplasmic and perinuclear P granules.
• Organism: Caenorhabditis elegans
• Automated Description: Enables mRNA 3'-UTR binding activity; poly(U) RNA binding activity; and transcription corepressor activity. Involved in several processes, including cell fate specification; embryonic pattern specification; and negative regulation of transcription by RNA polymerase II. Located in P granule. Expressed in several structures, including Psub4; germ line; neurons; oocyte; and rectal gland cell. Human ortholog(s) of this gene implicated in breast cancer. Is an ortholog of human ZFP36 (ZFP36 ring finger protein); ZFP36L1 (ZFP36 ring finger protein like 1); and ZFP36L2 (ZFP36 ring finger protein like 2).
• Biotype: SO:0001217
• Genetic Position: V :1.40307 ±0.003599
• Length (nt): 1169

1 Organism

• Name: Caenorhabditis elegans
• Taxon Id: 6239

1 Synonyms

• Value: WBGene00004078

Genomics

1 Transcripts

WormMine ID	Sequence Name	Length (nt)	Chromosome Location
Transcript:F52E1.1.1	F52E1.1.1	1117	V: 8414086-8415254

Other

1 CDSs

WormMine ID	Sequence Name	Length (nt)	Chromosome Location
CDS:F52E1.1	F52E1.1	795	V: 8414094-8414492

46 RNAi Result

• WBRNAi00067038
• WBRNAi00067097
• WBRNAi00067141
• WBRNAi00067151
• WBRNAi00067542
• WBRNAi00047979
• WBRNAi00112036
• WBRNAi00091973
• WBRNAi00065357
• WBRNAi00083270
• WBRNAi00111038
• WBRNAi00112191
• WBRNAi00078970
• WBRNAi00078971
• WBRNAi00078969
• WBRNAi00093848
• WBRNAi00066186
• WBRNAi00111037
• WBRNAi00032614
• WBRNAi00022691
• WBRNAi00008828
• WBRNAi00025569
• WBRNAi00078956
• WBRNAi00078985
• WBRNAi00078987
• WBRNAi00078986
• WBRNAi00078989
• WBRNAi00078988
• WBRNAi00078991
• WBRNAi00078990

25 Allele

• gk963301
• gk964351
• gk962860
• gk964052
• gk241367
• gk241368
• gk776089
• gk744919
• gk340690
• gk369515
• gk723763
• gk433812
• gk356053
• zu363
• ne51
• zu454
• zu125
• gk826553
• gk508140
• gk549880
• gk519677
• gk358769
• zu148
• WBVar01460940
• zu175

1 Chromosome

• WormBase ID: V
• Organism: Caenorhabditis elegans
• Length (nt): 20924180

1 Chromosome Location

• Feature . Primary Identifier: WBGene00004078
• Start: 8414086
• End: 8415254
• 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_chrV_8415255..8415647
• Length (nt): 393
• Chromosome Location: V: 8415255-8415647
• Organism: Caenorhabditis elegans

264 Expression Clusters

Regulated By Treatment	Description	Algorithm	Primary Identifier
	Genes with expression altered >= 3-fold in dpy-10(e128) mutants.	Data across the wild type series was analyzed using the Significance analysis of Microarrays (SAM) algorithm (to calculate the False Discovery Rate (FDR)).	WBPaper00035873:dpy-10_regulated
	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
Osmotic stress	Transcripts that showed significantly altered expression with 500 mM salt (NaCl) vs 100 mM salt when food was present	DESeq(version 1.10.1), FDR < 0.05.	WBPaper00050726:OsmoticStress_regulated_Food
Bacteria infection: Enterococcus faecalis OG1RF. Exposure for 16 hours.	Transcripts that showed significantly decreased expression in N2 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_N2
	Proteins interacting with NHR-49-GFP according to co-IP and LC-MS.	N.A.	WBPaper00064071:NHR-49_interacting
	Transcripts expressed in the epithelial tissues surrounding the pharynx that includes the arcade and intestinal valve (AIV) cells, according to PAT-Seq analysis using Pbath-15-GFP-3XFLAG mRNA tagging.	Cufflinks FPKM value >=1.	WBPaper00050990:arcade_intestinal-valve_expressed
	Transcripts expressed in body muscle, according to PAT-Seq analysis using Pmyo-3-GFP-3XFLAG mRNA tagging.	Cufflinks FPKM value >=1.	WBPaper00050990:body-muscle_expressed
	Transcripts expressed in GABAergic neuron, according to PAT-Seq analysis using Punc-47-GFP-3XFLAG mRNA tagging.	Cufflinks FPKM value >=1.	WBPaper00050990:GABAergic-neuron_expressed
	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
	Transcripts expressed in NMDA neuron, according to PAT-Seq analysis using Pnmr-1-GFP-3XFLAG mRNA tagging.	Cufflinks FPKM value >=1.	WBPaper00050990:NMDA-neuron_expressed
	Transcripts expressed in pharynx, according to PAT-Seq analysis using Pmyo-2-GFP-3XFLAG mRNA tagging.	Cufflinks FPKM value >=1.	WBPaper00050990:pharynx_expressed
	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 decreased expression in day 3 adult hermaphrodite comparing to in L4 larva glp-1(e2141) animals.	Fold change > 2, FDR < 0.05	WBPaper00064088:Day-3-adult_vs_L4_downregulated_glp-1(e2141)
	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 diet: Escherichia coli HB101. Fed for 30 generations.	Transcripts that showed significantly decreased expression after fed by bacteria E. coli HB101 for 30 generations comparing to animals fed by E. coli OP50.	DESeq2 fold change > 2, p-value < 0.01.	WBPaper00061007:HB101_downregulated
Bacteria diet: Sphingomonas aquatilis Yellow. Fed for 30 generations.	Transcripts that showed significantly decreased expression after fed by bacteria Sphingomonas aquatilis (Yellow) for 30 generations comparing to animals fed by E. coli OP50.	DESeq2 fold change > 2, p-value < 0.01.	WBPaper00061007:S.aquatilis_downregulated
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 6h), according to RNAseq.	Cuffdiff, ajusted p-value < 0.01.	WBPaper00046497:B.thuringiensis_0.1mix_downregulated_6h
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 6h), according to RNAseq.	Cuffdiff, ajusted p-value < 0.01.	WBPaper00046497:B.thuringiensis_0.5mix_downregulated_6h
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 decreased expression in hsp-6(mg585) comparing to in N2 at L4 larva stage.	EdgeR, fold change > 2, FDR < 0.001.	WBPaper00056290:hsp-6(mg585)_downregulated
	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
	Strictly maternal class (SM): genes that are the subset of maternal genes that are not also classified as embryonic.	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_SM
	Transcripts that showed significantly increased expression in animals exposed to 400uM tamoxifen from L1 to L4 larva stage.	DEseq2, fold change > 2	WBPaper00064505:tamoxifen_upregulated
	Transcripts that showed significantly increased expression in alg-1(gk214), comparing to in N2.	DESeq2, Fold change > 1.5.	WBPaper00051404:alg-1(gk214)_upregulated
Heat Shock: 35C 4 hours at L4 larva stage.	Transcripts that showed significantly decreased expression after L4 larva N2 animals were heat stressed at 35C for 4 hours	DESeq2	WBPaper00057154:HeatShock_downregulated_mRNA

14 Expression Patterns

• Primary Identifier: Expr1031967
• Pattern: Tiling arrays expression graphs

• Primary Identifier: Expr8554
• Remark: New Symbol: tia-1. Picture: Fig. 1, Fig S1.
• Subcellular Localization: All P-body and stress granule GFP fusions localized to cytoplasmic foci. Some fusions appeared almost exclusively in foci (DCAP-1 and PATR-1), whereas others were also detected diffusely in the cytoplasm (CGH-1, LSM-1/-3, CCF-1, PAB-1, and TIA-1). DCAP-1, CGH-1, PATR-1, and CCF-1 fusions formed foci in both somatic and germline blastomeres. In contrast, LSM-1 and LSM-3 fusions only localized to foci in somatic blastomeres, and PAB-1 and TIA-1 fusions only localized to foci in germline blastomeres. In contrast, exosome GFP fusions were diffusely distributed in the cytoplasm and nuclei in all blastomeres and did not form distinct foci.

• Primary Identifier: Expr1151795
• Pattern: Developmental gene expression time-course. Raw data can be downloaded from ftp://caltech.wormbase.org/pub/wormbase/datasets-published/hashimshony2015

• Primary Identifier: Expr7578
• Remark: Clone: pUL#JS6B11
• Pattern: Expression is seen in the nerves of the head and weakly in the tail. There is also intermittent GFP expression in the anterior and posterior intestine and occasional faint expression in the rectal glands.

• Primary Identifier: Expr16337
• Pattern: Nine promoters (klp-19p, his-68p, W05F2.3p, spn-4p, pos-1p, Y75B12B.1p, puf-5p, mei-2p, and mesp-1p) produced GFP expression that was specific to the germline.

• Primary Identifier: Expr4116
• Remark: Curated by authors based on online in-situ hybridization database (Y. Kohara, personal communication; http://nematode.lab.nig.ac.jp).
• Pattern: Expressed in medial germline.

• Primary Identifier: Expr14423
• Pattern: body wall muscle

• Primary Identifier: Expr712
• Remark: This information was extracted from published material (Archana Sharma-Oates, Andrew Mounsey and Ian A. Hope).
• Pattern: First detected during first cell division. It is more abundant in the posterior half of the embryo. Uniform distribution in oocyte and newly fertilized embryo. At the 2-cell stage, there is higher level of expression observed in the germline blastomere P1 than in somatic blastomere. Initially present at similar levels in both daughters of P1 but persists at high levels only in the germline daughter P2. Asymmetrical pattern is seen at each of the subsequent divisions of germline blastomeres. After division of the final germline blastomere P4, pos-1 is not detected in either daughters. In L4 larvae, staining observed in the immature gonads and in adults staining is detected in the mature gonad.

• Primary Identifier: Expr713
• Remark: This information was extracted from published material (Archana Sharma-Oates, Andrew Mounsey and Ian A. Hope).
• Pattern: First detected at low levels in some 1-cell embryos. At the 2-cell stage higher level of expression detected predominantly in germline blastomere P1. Distribution of POS-1 protein is similar to distribution of mRNA after 2-cell stage when P1 divides. POS-1 protein is initially present at equal levels in both P1 daughters but persists at higher level only in germline daughter P2. After the division of the final germline blastomere P4, POS-1 is not detected in any cell. POS-1 shows strong, specific staining of granules within the cytoplasm of germline blastomeres. In double labeling experiments with an Ab specific for P granules determined that POS-1 is associated with cytoplasmic and perinuclear P granules. Although P granules is present in germline at all stages of embryonic and postembryonic development, POS-1 staining is only seen in P granules in germline blastomeres, P1, P2, P3 and P4. POS-1 gene is expressed maternally, POS-1 is cytoplasmic, P granule associated protein is present predominantly in germline blastomeres during early embryogenesis.
• Subcellular Localization: POS-1 is cytoplasmic.

• Primary Identifier: Expr9715
• Reporter Gene: We employed a transgene-based assay that tests the post-transcriptional control activity of 3' UTRs in vivo. In this assay, the GFP::H2B reporter fusion is placed upstream of the selected 3' UTR such that the entire fusion-GFP::H2B-3' UTR-is produced as a single transcript. Expression in the germline is achieved by using pie-1 promoter, which has been shown earlier to drive transgene expression in the germline.
• Pattern: The transgene containing pos-1 3' UTR expressed the GFP::H2B reporter strongly in oocytes, but not in mitotic or early pachytene regions.

• Primary Identifier: Expr11088
• Pattern: The RFP-fused antibody clearly detected the antigen and it appeared to be localized to the P-granules in the germline blastomers P3 and P4.

• Primary Identifier: Expr2015001
• 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: Expr1017711
• Pattern: Developmental gene expression time-course. Raw data can be downloaded from ftp://caltech.wormbase.org/pub/wormbase/datasets-published/levin2012

• Primary Identifier: Expr2033236
• 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).

22 GO Annotation

16 Homologues

1 Locations

• Feature . Primary Identifier: WBGene00004078
• Start: 8414086
• End: 8415254
• Strand: 1

22 Ontology Annotations

0 Regulates Expr Cluster

1 Sequence

• Length: 1169

1 Sequence Ontology Term

• Name: gene

4 Strains

• WBStrain00022471
• WBStrain00022478
• WBStrain00030276
• WBStrain00005744

1 Upstream Intergenic Region

• WormBase ID: intergenic_region_chrV_8413483..8414085
• Length (nt): 603
• Chromosome Location: V: 8413483-8414085
• Organism: Caenorhabditis elegans