WormMine: Gene WBGene00019629

• WormBase Gene ID: WBGene00019629
• Gene Name: cid-1
• Sequence Name: K10D2.3
• Brief Description: cid-1 (also known as pup-1) encodes a template-independent poly(U)polymerase with 3'' end RNA substrates, orthologous to human ZCCHC6 andZCCHC11, and paralogous to PUP-2; CID-1 prevents larvae from growing toadulthood in media containing hydroxyurea (HU, a drug that stallsreplication forks) and represses HSP-4 expression; CID-1 is required forgonadogenesis, embryonic and vulval development, normally rapid growth,and normally short lifespan; CID-1, like HSP-4, is expressed inpostmitotic intestinal cells; by orthology with Cid1p in fission yeast,CID-1 is predicted to act in a DNA synthesis-to-mitosis checkpoint; incid-1(rf35::Tc4) mutants or cid-1(RNAi) animals grow from L1 larvae toadulthood despite the presence of HU, are abnormally resistant to lethalheat shock, overexpress hsp-4::GFP, have protruding vulvae, haveabnormally short and thick gonads with fewer germ cells than normal,produce disorganized embryos, grow slowly, and have abnormally longlifespans; CID-1 and its eukaryotic homologs are distantly related tothe GLD-2 family of poly(A) polymerases.
• Organism: Caenorhabditis elegans
• Automated Description: Enables RNA uridylyltransferase activity. Involved in RNA 3' uridylation. Located in P granule; condensed nuclear chromosome; and perinuclear region of cytoplasm. Expressed in germ line and intestine. Human ortholog(s) of this gene implicated in breast cancer and liver benign neoplasm. Is an ortholog of human TUT4 (terminal uridylyl transferase 4) and TUT7 (terminal uridylyl transferase 7).
• Biotype: SO:0001217
• Genetic Position: III :-2.03559 ±0.001456
• Length (nt): 6586

1 Organism

• Name: Caenorhabditis elegans
• Taxon Id: 6239

1 Synonyms

• Value: WBGene00019629

Genomics

1 Transcripts

WormMine ID	Sequence Name	Length (nt)	Chromosome Location
Transcript:K10D2.3.1	K10D2.3.1	4802	III: 5173922-5180507

Other

1 CDSs

WormMine ID	Sequence Name	Length (nt)	Chromosome Location
CDS:K10D2.3	K10D2.3	4278	III: 5173992-5174073

9 RNAi Result

• WBRNAi00034256
• WBRNAi00067548
• WBRNAi00050524
• WBRNAi00016976
• WBRNAi00069457
• WBRNAi00005089
• WBRNAi00062042
• WBRNAi00087773
• WBRNAi00001835

79 Allele

• rf34
• WBVar01263464
• tm936
• WBVar01541732
• WBVar01541733
• h10899
• h16314
• tm1021
• snx675
• gk955023
• snx2536
• snx4371
• gg519
• WBVar01416014
• gk174168
• gk174167
• gk174170
• gk174169
• WBVar02053264
• gk174176
• WBVar02085388
• gk174175
• gk174178
• gk174177
• gk174172
• gk174171
• gk174174
• gk174173
• gk856870
• gk674509

1 Chromosome

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

1 Chromosome Location

• Feature . Primary Identifier: WBGene00019629
• Start: 5173922
• End: 5180507
• 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_5180508..5180664
• Length (nt): 157
• Chromosome Location: III: 5180508-5180664
• Organism: Caenorhabditis elegans

109 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
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 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 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)
	Transcripts that showed significantly increased expression in xrep-4(lax137).	DESeq2. Genes were selected if their p value < 0.01.	WBPaper00066062:xrep-4(lax137)_upregulated
Temprature shift to 28C for 24 hours.	Transcripts that showed significantly decreased expression after animals were exposed to 28C temperature for 24 hours.	Differentially expressed genes wereidentified using DESeq (v.1.18.0) by normalizing readsbased on the negative binomial distribution method andcomparing each HS timepoint to the 0-h control.	WBPaper00061341:28C_24h_downregulated
	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
	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
	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 decreased expression in the neurons of bcat-1(RNAi) animals at 5-days post L4 adult hermaphrodite stage, comparing to animals injected with empty vector.	DESeq2. FDR < 0.05.	WBPaper00060459:bcat-1(RNAi)_downregulated
	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)
	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
	Germline-intrinsic transcripts.	Comparisons were made between genotypes by subtracting the mean log value of one ratio from another, and the significance of the difference was evaluated using Student t-test for two populations. For the fem-3(gf) versus fem-1(lf) direct comparison, authors performed the same analysis, except they used a Students t-test for one population. Author chose a combination of a twofold difference with a t value exceeding 99% confidence (P < 0.01), because these criteria allowed the inclusion of essentially all genes that had previously been identified as germline-enriched in a wt/glp-4 hermaphrodite comparison. Additionally, requiring a twofold difference reduced false positives, as the number of genes with two-fold difference and a P<0.01 only included ~100 genes more than with P < 0.001, and almost all genes showed germline expression by in situ hybridization.	[cgc6390]:intrinsic
	Transcripts unqiuely expressed in intestine, according to PAT-Seq analysis using Pges-1-GFP-3XFLAG mRNA tagging.	Cufflinks FPKM value >=1.	WBPaper00050990:intestine_enriched
	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
	Genes with significantly decreased expression in eat-2(ad465) comparing to N2.	The criteria for differential gene regulation included a greater than 1.5-fold change in expression compared to wild-type, a false discovery rate less than 0.05, and greater than 10 reads when normalized to the base mean. Statistical analysis and drawing of plots was performed in R using the bioconductor package Deseq (Anders, Huber 2010) and R function gplots.	WBPaper00044037:eat-2_downregulated
	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 increased expression in sur-5p::jmjd-1.2 comparing to in N2.	DESeq2 Benjamini-Hochberg adjusted p-value < 0.05.	WBPaper00049545:sur-5p-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
	Embryonic class (E): genes that significantly increase in abundance at some point during embryogenesis.	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_E
	Transcripts enriched in germline by comparing dissected germline tissue with dissected intestine tissue, both injected with empty RNAi vector.	Genes were determined germline-enriched if the lowest expression value (log2(FPKM+1)) observed in the germline empty vector samples was at least 2-fold higher than the highest expression value observed in the intestine empty vector samples.	WBPaper00051039:germline_enriched
Bacteria infection: Xenorhabdus nematophila	Caenorhabditis elegans Genes with expression levels changed significantly after treatment of Xenorhabdus nematophila.	Differential expression were calculated by empirical eBayes method using eBayes function. P_value <= 0.01 and log2 fold change > 1 were used to call differentially expressed genes in all datasets.	WBPaper00041606:CE_X.nematophila_regulated

15 Expression Patterns

• Primary Identifier: Expr8815
• Remark: Picture: Figure 2.
• Pattern: On whole mounts, clear staining of the gonad arms was visible and no other expression patterns were detected. Closer inspection on extruded gonads showed cid-1/cde-1 mRNA throughout the entire gonad, without clear localization to a specific region.

• Primary Identifier: Expr8817
• Remark: Picture: Figure 2.
• Subcellular Localization: CDE-1 was detected throughout the female germline cytoplasm, where it was enriched in the perinuclear region. However, CDE-1 did not display the clear granular structure that is commonly observed for the P granule marker, PGL-1 at this stage. In the sperm-producing germlines of both males and L4 stage hermaphrodites, bright granules were found in close proximity to the condensing DNA of maturating sperm. In embryos, CDE-1 was detected in perinuclear granules in the P-cell lineage, mainly colocalizing with PGL-1. In addition, staining could be detected on the outer edges of condensing chromosomes at prometaphase. This staining became more intense on the spindle-facing sides of the metaphase plate and remained detectable through anaphase. Parallel experiments in cde-1 mutant animals did not show the patterns described above, indicating that the observed signals reflect true CDE-1 localization. Specific intestinal staining as previously reported based on a transgenic approach (see Expr3928) could not be detected.

• Primary Identifier: Expr8816
• Remark: Picture: Figure 2.
• Pattern: Northern blot analysis showed that the cid-1/cde-1 signal was drastically decreased in the glp-4(bn2) mutant, which lacks a germline compared to wild-type worms, confirming its germline localization.

• Primary Identifier: Expr3928
• Reporter Gene: [cid-1::gfp] translational fusion.
• Pattern: Expressed in the postmitotic intestinal cells during development and adulthood,

• Primary Identifier: Expr14768
• Pattern: PUP-1 and PUP-2 are expressed throughout the developing germline.

• Primary Identifier: Expr15898
• Pattern: CDE-1 was expressed in the germline cells at all developmental stages.

• Primary Identifier: Expr2010010
• 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: Expr2028251
• 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: Expr1038477
• Pattern: Tiling arrays expression graphs

• Primary Identifier: Expr1154234
• Pattern: Developmental gene expression time-course. Raw data can be downloaded from ftp://caltech.wormbase.org/pub/wormbase/datasets-published/hashimshony2015

• Primary Identifier: Expr1026020
• Pattern: Developmental gene expression time-course. Raw data can be downloaded from ftp://caltech.wormbase.org/pub/wormbase/datasets-published/levin2012

• Primary Identifier: Expr14770
• Subcellular Localization: In embryonic germ cell precursors and larval germ cells, PUP-1 signal was primarily associated with perinuclear granules. At these stages, PUP-2 was diffusely distributed in the cytoplasm and weakly colocalized with PUP-1 perinuclear granules. Strikingly, the PUP-2 distribution shifted during development, becoming less prominently associated with perinuclear foci as larval development proceeded.

• Primary Identifier: Expr14772
• Subcellular Localization: In the adult germline, perinuclear PUP-1 foci (P granules) were visible throughout the proliferative and meiotic regions. In maturing oocytes, these foci were distributed in the cytoplasm. Overall, this localization pattern resembles P granules and is similar to expression of GFP-tagged PUP-1 in a strain generated via bombardment by Zhong et al. (2010).

• Primary Identifier: Expr14773
• Subcellular Localization: In the adult germline, perinuclear PUP-1 foci (P granules) were visible throughout the proliferative and meiotic regions. In maturing oocytes, these foci were distributed in the cytoplasm. Overall, this localization pattern resembles P granules and is similar to expression of GFP-tagged PUP-1 in a strain generated via bombardment by Zhong et al. (2010).

• Primary Identifier: Expr15899
• Subcellular Localization: CDE-1 localized in the cytoplasm and accumulated in the perinuclear region exhibiting distinct foci in the germline of adult animals. We crossed the CDE-1:: GFP strain with the P-granule marker strain mRuby::PGL- 1 and found that CDE-1 largely colocalized with the P-granule marker PGL-1.

11 GO Annotation

7 Homologues

1 Locations

• Feature . Primary Identifier: WBGene00019629
• Start: 5173922
• End: 5180507
• Strand: 1

11 Ontology Annotations

1 Regulates Expr Cluster

Regulated By Treatment	Description	Algorithm	Primary Identifier
	Significantly differentially expressed genes as determined by microarray analysis of wild-type and cde-1 mutant germlines.	RNAs that changed at least 2-fold with a probability of p < 0.05 were considered differentially regulated between wildtype and cde-1.	WBPaper00035269:cde-1_regulated

1 Sequence

• Length: 6586

1 Sequence Ontology Term