WormMine: Gene WBGene00012484

• WormBase Gene ID: WBGene00012484
• Gene Name: car-1
• Sequence Name: Y18D10A.17
• Brief Description: car-1 encodes a putative RNA-binding protein orthologous to buddingyeast Scd6p, fission yeast Sum2p, Drosophila TRAL, and human LSM14A andLSM14B; CAR-1 inhibits physiological apoptosis in oocytes, keeping itdown to a normal level of ~50% in hermaphrodite gonads; independently ofapoptosis, CAR-1 is also required for normal oogenesis, early embryoniccytokinesis, and normally organized endoplasmic reticulum (ER); CAR-1has an N-terminal Sm-related domain that is dispensable for subcellularlocalization, but directly binds RNA and is critical for CAR-1'sfunction; CAR-1 expressed in the germline; CAR-1 associates with CGH-1,DCAP-1, and CEY-2/3/4, in P granules and other cytoplasmic particles ofthe early embryo; CAR-1 also localizes to the mitotic spindle ofdividing 1-cell embryos, and to ER; CAR-1 requires CGH-1 for normallocalization in meiotic germ cells, and binds CGH-1 in an RNA-dependentmanner; car-1(tm1753) or car-1(RNAi) embryos display abnormalcytokinesis, with aberrant cleavage furrow ingression and anaphasespindle structure, and mislocalized AIR-2, SPD-1, and ZEN-4; car-1(RNAi)also results in elevated (though not 100%) physiological germ cellapoptosis, reduced fertility, and failed oocyte diakinesis; maternalCAR-1 is sufficient to rescue car-1(tm1753) homozygotes throughdevelopment to adulthood; in car-1(RNAi) animals, excess physiologicalapoptosis actually promotes fertility, since car-1(RNAi) hermaphroditeshave larger brood sizes than those with apoptosis suppressed byced-3(n717).
• Organism: Caenorhabditis elegans
• Automated Description: Enables RNA polymerase II core promoter sequence-specific DNA binding activity. Involved in positive regulation of gene expression. Located in endoplasmic reticulum and intracellular non-membrane-bounded organelle. Part of ribonucleoprotein complex. Expressed in germ line; gonad; neurons; somatic cell; and touch receptor neurons. Is an ortholog of human LSM14B (LSM family member 14B).
• Biotype: SO:0001217
• Genetic Position: I :14.1828 ±0.004108
• Length (nt): 1571

1 Organism

• Name: Caenorhabditis elegans
• Taxon Id: 6239

1 Synonyms

• Value: WBGene00012484

Genomics

1 Transcripts

WormMine ID	Sequence Name	Length (nt)	Chromosome Location
Transcript:Y18D10A.17.1	Y18D10A.17.1	1422	I: 12904470-12906040

Other

1 CDSs

WormMine ID	Sequence Name	Length (nt)	Chromosome Location
CDS:Y18D10A.17	Y18D10A.17	1023	I: 12904476-12904721

29 RNAi Result

• WBRNAi00095771
• WBRNAi00083333
• WBRNAi00026616
• WBRNAi00086668
• WBRNAi00086677
• WBRNAi00062674
• WBRNAi00086693
• WBRNAi00083336
• WBRNAi00097878
• WBRNAi00062673
• WBRNAi00022675
• WBRNAi00062676
• WBRNAi00062677
• WBRNAi00000120
• WBRNAi00036693
• WBRNAi00055610
• WBRNAi00026615
• WBRNAi00116628
• WBRNAi00083331
• WBRNAi00083334
• WBRNAi00093906
• WBRNAi00093963
• WBRNAi00093929
• WBRNAi00097881
• WBRNAi00086659
• WBRNAi00091397
• WBRNAi00083332
• WBRNAi00081332
• WBRNAi00062675

34 Allele

• gk963849
• gk964175
• WBVar01932796
• gk383870
• gk839877
• gk610179
• gk583495
• gk842190
• gk897168
• gk795209
• gk928147
• gk317391
• gk814586
• gk610180
• gk460793
• gk354776
• gk558713
• gk429589
• gk805607
• tm1753
• gk940657
• gk940658
• WBVar01993690
• gk1706
• WBVar00160019
• WBVar02124866
• WBVar01641422
• WBVar00541563
• WBVar00541562
• gk125944

1 Chromosome

• WormBase ID: I
• Organism: Caenorhabditis elegans
• Length (nt): 15072434

1 Chromosome Location

• Feature . Primary Identifier: WBGene00012484
• Start: 12904470
• End: 12906040
• 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_chrI_12906041..12906461
• Length (nt): 421
• Chromosome Location: I: 12906041-12906461
• Organism: Caenorhabditis elegans

211 Expression Clusters

Regulated By Treatment	Description	Algorithm	Primary Identifier
	oocyte proteins identified by two or more unique peptides during proteomics study.	In the pooled data set, 1453 C. elegans proteins were identified with a probability >= 0.9 according to ProteinProphet, of which 1165 proteins were identified by more than one unique peptide.	WBPaper00038289:oocyte_protein
	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
	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
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
	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
	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
	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 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
	Genes with expression level regulated by genotype (N2 vs CB4856) and age at old adults stage (214 hours at 24 centigrade).	For model 2, authors used 100 permutations to estimate the FDR threshold. Per permutation, genotypes and ages were independently randomly distributed, keeping the among-gene structure intact. Then for each spot (23,232) on the array, model 2 was tested. The obtained P-values were used to estimate a threshold for each of the explanatory factors. Authors also used a genome-wide threshold of -log10 P-value = 2, which resembles an FDR of 0.072 and 0.060 for marker and the interaction age-marker for the developing worms and FDR of 0.050 and 0.065 for marker and age-marker for the aging worms. For the physiological age effect, authors used a log10 P-value = 8 in developing worms (0.012 FDR) and -log10 P-value = 6 (0.032 FDR).	WBPaper00040858:eQTL_age_regulated_aging
	Transcripts expressed in seam cells, according to PAT-Seq analysis using Pgrd-10-GFP-3XFLAG mRNA tagging.	Cufflinks FPKM value >=1.	WBPaper00050990:seam_expressed
	Genes with expression level regulated by genotype (N2 vs CB4856) at old adults stage (214 hours at 24 centigrade).	For model 2, authors used 100 permutations to estimate the FDR threshold. Per permutation, genotypes and ages were independently randomly distributed, keeping the among-gene structure intact. Then for each spot (23,232) on the array, model 2 was tested. The obtained P-values were used to estimate a threshold for each of the explanatory factors. Authors also used a genome-wide threshold of -log10 P-value = 2, which resembles an FDR of 0.072 and 0.060 for marker and the interaction age-marker for the developing worms and FDR of 0.050 and 0.065 for marker and age-marker for the aging worms. For the physiological age effect, authors used a log10 P-value = 8 in developing worms (0.012 FDR) and -log10 P-value = 6 (0.032 FDR).	WBPaper00040858:eQTL_regulated_aging
	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
	Transcripts that showed significantly changed expression in 6-day post-L4 adult hermaphrodite comparing to in 1-day post L4 adult hermaphrodite animals.	Sleuth	WBPaper00051558:aging_regulated
	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
25C vs. 20C	Transcripts that showed significantly increased expression in 1-day post L4 adult hermaphrodite N2 grown at 25C, comparing to in N2 animals grown at 20C.	CuffDiff, fold change > 2.	WBPaper00065096:25C_vs_20C_upregulated
	Transcripts that showed significantly increased expression in 10-days post L4 adult hermaphrodite N2 grown at 20C, comparing to in 1-day post L4 adult hermaphrodite N2 animals grown at 20C.	CuffDiff, fold change > 2.	WBPaper00065096:Day10_vs_Day1_upregulated
	Transcripts detected in body muscle nuclei according to a nuclear FACS-based strategy.	Cufflinks	WBPaper00065120:body-muscle-transcriptome
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

13 Expression Patterns

• Primary Identifier: Expr4816
• Remark: Picture: Fig. 3 B, D, and E and Video 4.
• Subcellular Localization: The formation of the small GFPLAP:CAR-1 containing particles in both daughter cells after completion of the first cytokinesis was particularly prominent in these sequences. The number of small particles increased as embryos proceeded into the four- and eight-cell stages, but the particles were not detected in older embryos. In summary, consistent with the RNA-binding motifs in its primary sequence, CAR-1 localizes to P-granules that are partitioned to the germline precursors and to smaller particles that are present in all cells of early embryos.

• Primary Identifier: Expr4815
• Remark: Depletion of CAR-1 did not affect P-granule formation or distribution, which indicated that CAR-1 is not necessary for either of these events. Particles were not detected in car-1(RNAi) embryos, which confirmed the specificity of the localization. Picture: Figure 2.
• Subcellular Localization: CAR-1 localized to cytoplasmic particles whose size and distribution varied during the early embryonic divisions. From the latter half of the first division onward, CAR-1 localized prominently to large particles that were similar in size and distribution to P-granules. By performing immunofluorescence in a strain expressing GFP:PGL-1, authors confirmed that a subset of CAR-1 colocalizes with PGL-1 to P-granules. A more detailed comparison revealed a dynamic nature to the particulate localization of CAR-1 and PGL-1. In embryos in which the female pronucleus was completing meiosis, both proteins localized to numerous small particles that were distributed throughout the embryo. However, although particles that contained the two markers were juxtaposed, they were not coincident. By metaphase of the first mitotic division, most particulate CAR-1 colocalized with PGL-1 in large P-granules in the embryo posterior. However, a few smaller particles containing CAR-1, but not PGL-1, remained scattered throughout the embryo. In two- and four-cell embryos, CAR-1 continued to colocalize with P-granules in the germline precursors, but numerous additional smaller CAR-1 containing particles also were evident throughout the cytoplasm of all cells. These smaller CAR-1 containing particles were not detected after the 50 to 100-cell stage.

• Primary Identifier: Expr2009720
• 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: Expr14944
• Pattern: We performed smFISH for endogenous car-1 mRNAs and observed widespread expression in somatic cells including touch receptor neurons (TRNs) and other neurons besides the germline.

• Primary Identifier: Expr9704
• 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 car-1 3' UTR expressed GFP::H2B ubiquitously in the germline.

• Primary Identifier: Expr3742
• Pattern: In adult hermaphrodites, the CAR-1 protein was detectable by western blotting exclusively in the germline.

• Primary Identifier: Expr4032
• Remark: Curated by authors based on online in-situ hybridization database (Y. Kohara, personal communication; http://nematode.lab.nig.ac.jp).
• Pattern: Broadly expressed in gonad.

• Primary Identifier: Expr1035532
• Pattern: Tiling arrays expression graphs

• Primary Identifier: Expr1159117
• Pattern: Developmental gene expression time-course. Raw data can be downloaded from ftp://caltech.wormbase.org/pub/wormbase/datasets-published/hashimshony2015

• Primary Identifier: Expr3744
• Subcellular Localization: CAR-1 levels were modest in the proliferating stem cells at the distal end of the gonad, then increased upon entry into meiosis. Throughout the gonad some CAR-1 staining was localized to perinuclear particles, where it overlapped substantially with staining for CGH-1 and PGL-1. After germ cells entered meiosis, CAR-1 appeared in cytoplasmic granules within the syncytial gonad core, in parallel with CGH-1. Within the core, most CAR-1 particles colocalized with CGH-1, although some distinct CAR-1 and CGH-1 foci were also present.

• Primary Identifier: Expr1012111
• Pattern: Developmental gene expression time-course. Raw data can be downloaded from ftp://caltech.wormbase.org/pub/wormbase/datasets-published/levin2012

• Primary Identifier: Expr3784
• Subcellular Localization: CAR-1 localized diffusely throughout the cytoplasm, weakly to the mitotic spindle in the GFP::CAR-1 strain and strongly to large and small puncta (mean large = 1.0 +/- 0.3 N5m; mean small = 0.5 +/- 0.1 N5m; N = 8 embryos and 40 puncta of each category). Only a few small CAR-1 containing puncta were seen in the one cell embryo and the interphase 2-cell embryo. However, there was a dramatic increase in the number of small puncta during and after the division of the anterior (AB) cell, whereas the diffuse cytoplasmic signal decreased with subsequent cell divisions. The population of these smaller puncta did not noticeably change in a cyclical manner, suggesting that they are not under cell cycle regulation. In addition to the strongly labeled puncta, labeled CAR-1 could be found in the spindle region during mitosis in live C. elegans embryos. The intensity of this signal increased as mitosis progressed and, as the chromosomes separated, the signal extended along the elongating spindle to include the pericentriolar region, resembling the organization of the ER.

• Primary Identifier: Expr2027959
• 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).

23 GO Annotation

8 Homologues

1 Locations

• Feature . Primary Identifier: WBGene00012484
• Start: 12904470
• End: 12906040
• Strand: 1

23 Ontology Annotations

1 Regulates Expr Cluster

Regulated By Treatment	Description	Algorithm	Primary Identifier
	Transcripts the interact with GFP-CAR-1 according to single-end enhanced crosslinking and immunoprecipitation (seCLIP).	Cuffdiff (p value < 0.05)	WBPaper00059203:CAR-1_interacting

1 Sequence

• Length: 1571

1 Sequence Ontology Term