WormMine: Gene WBGene00004027

• WormBase Gene ID: WBGene00004027
• Gene Name: pie-1
• Sequence Name: Y49E10.14
• Brief Description: pie-1 encodes a C-x8-C-x5-C-x3-H-type zinc-finger protein; maternally provided PIE-1 is essential for germline cell fate determination, as it functions as a repressor of RNA polymerase II-dependent gene expression in the developing germ line; PIE-1 localization, initially uniform and then concentrated in the posterior germ cell lineages, is regulated by other maternally supplied gene products including PAR-1, MEX-5, and MEX-6.
• Organism: Caenorhabditis elegans
• Automated Description: Predicted to enable mRNA 3'-UTR binding activity. Involved in several processes, including embryonic pattern specification; formation of primary germ layer; and negative regulation of nitrogen compound metabolic process. Located in several cellular components, including P granule; centrosome; and cytosol. Expressed in germ line; head muscle; and nerve ring.
• Biotype: SO:0001217
• Genetic Position: III :17.7453 ±0.045821
• Length (nt): 2303

1 Organism

• Name: Caenorhabditis elegans
• Taxon Id: 6239

1 Synonyms

• Value: WBGene00004027

Genomics

2 Transcripts

WormMine ID	Sequence Name	Length (nt)	Chromosome Location
Transcript:Y49E10.14a.1	Y49E10.14a.1	1116	III: 12426893-12429195
Transcript:Y49E10.14b.1	Y49E10.14b.1	375	III: 12428713-12429087

Other

2 CDSs

WormMine ID	Sequence Name	Length (nt)	Chromosome Location
CDS:Y49E10.14b	Y49E10.14b	375	III: 12428713-12429087
CDS:Y49E10.14a	Y49E10.14a	1008	III: 12426893-12427177

65 RNAi Result

• WBRNAi00095794
• WBRNAi00082745
• WBRNAi00082744
• WBRNAi00106571
• WBRNAi00009359
• WBRNAi00067109
• WBRNAi00067132
• WBRNAi00067192
• WBRNAi00067201
• WBRNAi00067572
• WBRNAi00115799
• WBRNAi00057006
• WBRNAi00087573
• WBRNAi00006812
• WBRNAi00007158
• WBRNAi00077644
• WBRNAi00101758
• WBRNAi00101757
• WBRNAi00087575
• WBRNAi00087574
• WBRNAi00079052
• WBRNAi00026785
• WBRNAi00084325
• WBRNAi00077659
• WBRNAi00101759
• WBRNAi00101766
• WBRNAi00101769
• WBRNAi00057007
• WBRNAi00101745
• WBRNAi00079042

78 Allele

• gk963887
• gk964363
• gk964364
• gk188365
• gk188364
• gk188366
• gk188368
• gk188367
• gk188369
• WBVar00181567
• t1682
• gk944998
• gk963527
• WBVar01509224
• WBVar01832615
• WBVar01832614
• WBVar01793541
• WBVar01793540
• WBVar01793539
• WBVar01793538
• WBVar01509212
• WBVar01509213
• WBVar01509210
• WBVar02085569
• WBVar01509211
• WBVar01920061
• zu127
• WBVar01509208
• WBVar01920062
• WBVar01509209

1 Chromosome

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

1 Chromosome Location

• Feature . Primary Identifier: WBGene00004027
• Start: 12426893
• End: 12429195
• Strand: 1

4 Data Sets

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

0 Downstream Intergenic Region

155 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 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 decreased expression in AGP22 [nhr-49(nr2041)I;glp-1(e2141)III] comparing to in CF1903 [glp-1(e2144)III] at Day 2 adults.	Fold change > 2, p Value of < 0.05 and a false discovery rate (FDR) of < 0.05.	WBPaper00061530:nhr-49(e2144)_downregulated
	mRNAs that showed decreased expression in 1 cell mebryo comparing to in oocyte, according to RNAseq analysis.	Gaussian error propagation. As cutoff for the up-regulated genes authors used log2 fold change > 1 and P < 0.05 and as cutoff for the down-regulated genes authors used log2 fold change < -1 and P < 0.05.	WBPaper00045420:fertilization_downregulated_transcript
	Proteins interacting with NHR-49-GFP according to co-IP and LC-MS.	N.A.	WBPaper00064071:NHR-49_interacting
	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 hypodermis, according to PAT-Seq analysis using Pdpy-7-GFP-3XFLAG mRNA tagging.	Cufflinks FPKM value >=1.	WBPaper00050990:hypodermis_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 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
	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
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
	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
	mRNAs that showed differential expression in activated AAK-2(uthIs202[aak-2 (intron 1)::aak-2(aa1-aa321)::Tomato::unc-54 3'UTR + rol-6(su1006)]), activiated CRTC-1 (uthEx222[crtc-1p::crtc-1 cDNA (S76S, S179A)::tdTomato::unc-54 3'UTR + rol-6(su1006)]), or AAK-2;CRTC-1 comparing to in N2.	Genes were tested for differential expression between each mutant strain and wild-type using edgeRs glm method. Briefly, negative binomial models were fitted and dispersion estimates obtained. These were then used to calculate average levels of change between conditions and determine differential expression, using the generalized linear model likelihood ratio test. For each comparison, genes with less than 5 CPM were filtered and those with at least 50% change and False Discovery Rate (FDR) of 1% or less were considered differentially expressed.	WBPaper00046499:AMPK_regulated
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
	Transcripts that showed significantly altered expression after 24 hour exposure to stavudine (d4T) starting at L1 lava stage.	DESeq	WBPaper00053302:stavudine_24h_regulated
	Genes down regulated by mir-243(n4759).	RNAs that changed at least 2-fold with a probability of p > 0.05 in three biological replicates were considered differentially regulated between wild-type and mir-243.	WBPaper00036130:mir-243_down_regulated
	Genes with increased RNA expression after 24 hours rotenone treatment	EdgeR provides statistical routines for determining differential expression in digital gene expression data using a model based on the negative binomial distribution. The resulting p-values were adjusted using the Benjamini and Hochbergs approach for controlling the false discovery rate (FDR). Transcripts with an adjusted p-value smaller 0.05 were assigned as differentially expressed.	WBPaper00044426:rotenone_24h_upregulated
	Transcripts that showed significantly decreased expression in tetraploid N2 comparing to diploid N2 animals at L4 larva stage.	DESeq2 R package (1.20.0), fold change > 2, and FDR < 0.05.	WBPaper00066110:tetraploid_vs_diploid_downregulated
	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:dopaminergic-neurons_L3-L4-larva_expressed
	Transcripts that showed significantly increased expression in ilc-17.1(syb5296) comparing to in N2 animals at L4 larva stage.	DESeq2, fold change > 2, FDR < 0.05.	WBPaper00066594:ilc-17.1(syb5296)_upregulated
	Transcripts that showed significantly decreased 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_downregulated
	Transcripts that showed altered expression from P0 to F2 generation animals after N2 parental generation were treated with antimycin, but not in damt-1(gk961032) P0 to F2 animals after the parenal generaton were treated with antimycin.	N.A.	WBPaper00055862:antimycin_damt-1(gk961032)_regulated
	Transcripts that showed significantly decreased expression in nhl-2(ok818) comparing to in N2 at 25C.	EdgeR, FDR < 0.05, fold change < 0.5.	WBPaper00055971:nhl-2(ok818)_25C_upregulated
	Transcripts that showed decreased expression in hlh-11(ko1) knockout strain comparing to in wild type background.	DESeq2, FDR < 0.05	WBPaper00060683:hlh-11(ko1)_downregulated
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 significantely Up-regulated by GRO-seq in csr-1 hypomorph vs. N2 using DESeq p < 0.05.	DESeq package with an FDR of < 0.05.	WBPaper00045050:csr-1(hypomorph)_upregulated
	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
	TGF- Dauer pathway adult transcriptional targets. Results obtained by comparing the microarray results of the dauer-constitutive mutants daf-7(e1372), daf-7(m62), and daf-1(m40) with dauer-defective mutants daf-3(mgDf90), daf-5(e1386), and daf-7(e1372);daf-3(mgDf90) double mutants at the permissive temperature, 20C, on the first day of adulthood.	SAM	WBPaper00031040:TGF-beta_adult_downregulated

17 Expression Patterns

• Primary Identifier: Expr4258
• Subcellular Localization: In wild-type embryos, PIE-1 is enriched in posterior cytoplasm before the completion of P0 mitosis and segregated to the posterior daughter P1 after the first mitosis.

• Primary Identifier: Expr1031929
• Pattern: Tiling arrays expression graphs

• Primary Identifier: Expr7723
• Remark: Clone: pUL#JRH7F9
• Pattern: Strongest expression is seen in embryos. There is weak ubiquitous expression in the early embryo, strong expression in anterior and lateral regions in comma and late stage embryos. Post embryonically expression is seen only to L2 in several nerves in the nerve ring. There is also weak expression in head muscles.

• Primary Identifier: Expr7952
• Remark: Picture: Figure 5.
• Subcellular Localization: Wild-type PIE-1 accumulates in numerous fine nuclear foci.

• Primary Identifier: Expr7326
• Pattern: Click the movie links below for interactive 4D movies of a fluorescence reporter. http://glowormnotes.blogspot.com/2009/11/pie-1ph-gfp-transcriptional-fusion.html

• Primary Identifier: Expr8530
• Remark: Picture: Figure 1.
• Subcellular Localization: GFP::PIE-1 becomes enriched in the posterior, on and around punctate structures known as P granules, which are RNA-rich components of the germplasm. Although GFP::PIE-1 also becomes enriched in pronuclei, the nuclear localization of PIE-1 has been shown to have little effect on cytoplasmic enrichment. Posterior fluorescence intensity reached a plateau value approximately three times the initial prefertilization level, whereas anterior fluorescence intensity decreased to approximately half its initial value. Overall fluorescence intensity in the zygote increased slightly during the first cell division, suggesting a low level of expression throughout the first division.

• Primary Identifier: Expr574
• Remark: early embryo(author) = blastula embryo(curator).
• Pattern: PIE-1 protein is localized to the posterior of the zygote and continues to be observed in the germ line P1 through P4 and Z2 and Z3, but not in somatic blastomeres.
• Subcellular Localization: PIE-1 is associated with P granules in germline blastomere cytoplasm. At mitosis, PIE-1 accumulates around the centrosomes of the spindle and PIE-1 decreases in the cytoplasm. PIE-1 staining remains only in the germline blastomeres after division. After P4 divides, PIE-1 persists in both Z2 and Z3 centrosomes.

• Primary Identifier: Expr575
• Remark: early embryo(author) = blastula embryo(curator).
• Pattern: In oocytes,1-cell and 2-cell stage embryos, pie-1 mRNA is distributed uniformly. After the 4-cell stage, pie-1 mRNA was lost from somatic blastomeres and remained in the germ lineage. PIE-1 protein was first detected in maturing oocytes, where it is uniformly distributed. PIE-1 level increase during the one cell stage. PIE-1 protein also exists in P1, P2 P3, P4, Z2 and Z3. In P4, PIE-1 is found equally in the P4 daughters (Z2 and Z3) in contrast to earlier divisions in which PIE-1 is localized to the posterior cytoplasm and posterior centrosomes during mitosis.
• Subcellular Localization: A subset of PIE-1 molecules are associated with P granules, but there is a diffuse cytoplasmic component of PIE-1 staining in contrast to the punctate P granule pattern. PIE-1 protein is cytoplasmic until the 2-cell stage, after which it is increasingly nuclear. PIE-1 protein distribution in P0, P1, P2 and P3 follows a similar pattern: initially uniform cytoplasmic distribution, followed by asymmetric cytoplasmic localization at the time of P granule migration, and asymmetric cytoplasmic and centralsomal localizations during mitosis.

• Primary Identifier: Expr1078
• Remark: This fusion is functional, as it can rescue the embryonic lethality of a pie-1(0) mutant. In all 14 lines examined, GFP fluorescence in the adult germline and in embryos was observed in a pattern identical to that reported for PIE-1 using immunolocalization.
• Pattern: Expressed in blastula embryos, not detailed description on the expression in later stages.
• Subcellular Localization: In embryos, PIE-1:GFP was found predominantly in the cytoplasm and nuclei of germline blastomeres. In the cytoplasm, PIE-1:GFP was present both diffusely throughout the cytosol and at higher concentration on P granules. PIE-1:GFP also appeared to associate with discrete foci in nuclei. The identity of these foci is not known. In oocytes and newly fertilized embryos, PIE-1:GFP was present uniformly throughout the cytoplasm. In the late 1-cell stage after the pronuclei have formed, PIE-1:GFP levels began to decrease in the anterior and increase in the posterior. By pronuclear meeting, PIE-1:GFP was found predominantly in the posterior. During mitosis, PIE-1:GFP also accumulated on both centrosomes with higher levels on the posterior centrosome. As a result of this asymmetric enrichment, most of the PIE-1:GFP was inherited by the posterior blastomere P1 during the first cleavage. In P1, P2, and P3, PIE-1:GFP distribution followed a sequence similar to that observed in the zygote, with the exception that PIE-1:GFP became increasingly more nuclear during each interphase. Before each cell division, PIE-1:GFP in the cytoplasm decreased on the side of the cell destined for the next somatic blastomere. At the start of mitosis, PIE-1:GFP disappeared from the nucleoplasm and became associated with centrosomes at both ends of the newly formed spindle. As mitosis progressed, PIE-1:GFP levels in the cytoplasm continued to decrease on the somatic side of the cell; concomitantly PIE-1:GFP levels decreased on the centrosome destined for the somatic daughter and increased on the centrosome destined for the germline daughter. After cytokinesis, most PIE-1:GFP was found in the germline daughter with only low levels left in the somatic daughter (e.g., EMS in the 4-cell stage). PIE-1:GFP fluorescence diminished progressively in that cell and was not detected in its progeny.

• Primary Identifier: Expr2463
• Subcellular Localization: PIE-1:GFP and GFP:MEX-5 were initially uniformly distributed throughout the cytoplasm and began to increase (PIE-1) or decrease (MEX-5) in the posterior cytoplasm soon after the appearance of a smooth zone near the paternal pronucleus. The fusion proteins also appeared to decrease (PIE-1) or increase (MEX-5) at the opposite end of the embryo. Maximal asymmetry was reached by pseudocleavage with PIE-1:GFP enriched in the posterior and GFP:MEX-5 enriched in the anterior. For both fusions, localization was not absolute, with some GFP fluorescence remaining in the opposite domain. GFP:MEX-6 behaved essentially like GFP:MEX-5. PIE-1:GFP, GFP:MEX-5 and GFP:MEX-6 all accumulated on granules in germline blastomeres.

• Primary Identifier: Expr2014919
• 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: Expr1027155
• Pattern: Developmental gene expression time-course. Raw data can be downloaded from ftp://caltech.wormbase.org/pub/wormbase/datasets-published/levin2012

• Primary Identifier: Expr1170086
• Pattern: Time-lapse fluorescence microscopy was performed, including DIC for morphology. Gene expression patterns were summarized in 4 manners: Average over time, Average over time and at different positions along the anterior-posterior (AP) axis, a voxelized representation over time, and on individual cells overlaid from a reference coordinate dataset (https://doi.org/10.1016/j.ydbio.2009.06.014). The analysis was done with a pipeline based on the multi-purpose image analysis software Endrov (https://doi.org/10.1038/nmeth.2478), which further is needed to browse the raw recording data. Thumbnail movies were also generated, using maximum Z projection for the 3D fluorescence channel. Raw recordings available in the Endrov OST-file format are available at https://www.ebi.ac.uk/biostudies/studies/S-BIAD191?query=S-BIAD191

• Primary Identifier: Chronogram1328
• Remark: Original chronogram file: chronogram.2574.xml
• Reporter Gene: [Y49E10.14:gfp] transcriptional fusion.

• Primary Identifier: Chronogram1329
• Remark: Original chronogram file: chronogram.2575.xml
• Reporter Gene: [Y49E10.14:gfp] transcriptional fusion.

• Primary Identifier: Expr2033154
• 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: Expr1160452
• Pattern: Developmental gene expression time-course. Raw data can be downloaded from ftp://caltech.wormbase.org/pub/wormbase/datasets-published/hashimshony2015

31 GO Annotation

16 Homologues

1 Locations

• Feature . Primary Identifier: WBGene00004027
• Start: 12426893
• End: 12429195
• Strand: 1

31 Ontology Annotations

2 Regulates Expr Cluster

Regulated By Treatment	Description	Algorithm	Primary Identifier
	Transcripts that showed significantly increased expression in pie-1(ne4443[PIE-1-Degron-GFP])	DESeq2. Differentially expressed genes were defined as twofold change and adjusted p-value less than 0.05.	WBPaper00061478:pie-1(ne4433)_upregulated
	Transcripts that showed significantly increased expression in pie-1(ne4303[PIE-1(K68R)])	DESeq2. Differentially expressed genes were defined as twofold change and adjusted p-value less than 0.05.	WBPaper00061478:pie-1(ne4303)_upregulated

1 Sequence

• Length: 2303

1 Sequence Ontology Term