WormMine: Gene WBGene00014115

• WormBase Gene ID: WBGene00014115
• Gene Name: gld-4
• Sequence Name: ZK858.1
• Brief Description: gld-4 encodes a noncanonical poly(A) polymerase orthologous to Saccharomyces cerevisiae Trf4/5p; GLD-4 activity is required for early meiotic progression of male and female gametes in the absence of GLD-2 and for regulation of gld-1 mRNA levels; GLD-4 physically interacts with GLS-1 which stimulates GLD-4 poly(A) polymerase activity in vivo; GLD-4 is expressed predominantly in germ cells and localizes to the cytoplasm and to P granules.
• Organism: Caenorhabditis elegans
• Automated Description: Enables poly(A) RNA polymerase activity. Involved in cytosolic mRNA polyadenylation and positive regulation of meiotic cell cycle. Located in P granule. Expressed in Z2; Z3; and germ line. Is an ortholog of human TENT4A (terminal nucleotidyltransferase 4A) and TENT4B (terminal nucleotidyltransferase 4B).
• Biotype: SO:0001217
• Genetic Position: I :3.59898 ±0.008849
• Length (nt): 5067

1 Organism

• Name: Caenorhabditis elegans
• Taxon Id: 6239

1 Synonyms

• Value: WBGene00014115

Genomics

1 Transcripts

WormMine ID	Sequence Name	Length (nt)	Chromosome Location
Transcript:ZK858.1.1	ZK858.1.1	3958	I: 9118115-9123181

Other

1 CDSs

WormMine ID	Sequence Name	Length (nt)	Chromosome Location
CDS:ZK858.1	ZK858.1	2538	I: 9118115-9118267

11 RNAi Result

• WBRNAi00059781
• WBRNAi00059782
• WBRNAi00027112
• WBRNAi00081931
• WBRNAi00004948
• WBRNAi00004949
• WBRNAi00081933
• WBRNAi00081932
• WBRNAi00027113
• WBRNAi00087785
• WBRNAi00087854

61 Allele

• gk962858
• gk962706
• gk963902
• gk963849
• gk964316
• WBVar01432449
• WBVar01432452
• ef9
• ef15
• gk495149
• gk455231
• WBVar01902429
• pk2351
• gk118127
• gk118128
• gk118129
• gk118130
• WBVar00155565
• WBVar00155566
• WBVar00155563
• gk118125
• WBVar00155564
• gk118126
• gk118135
• gk118136
• WBVar00155567
• gk344936
• gk118131
• gk608370
• gk118132

1 Chromosome

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

1 Chromosome Location

• Feature . Primary Identifier: WBGene00014115
• Start: 9118115
• End: 9123181
• 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

141 Expression Clusters

Regulated By Treatment	Description	Algorithm	Primary Identifier
	Transcripts that showed significantly increased expression in L1 neural cells comparing to in adult neural cells.	DESeq2 (v1.18.1) fold change > 2, P-adj<0.05, using BenjaminiHochberg correction.	WBPaper00060811:L1_vs_adult_upregulated_neural
	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
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 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
	Genes with expression level regulated by genotype (N2 vs CB4856) and age at L3 larva and Late reproduction stage (96 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_developing
	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)
	Genes with expression level regulated by genotype (N2 vs CB4856) at L3 larva and Late reproduction stage (96 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_developing
	Genes with expression level regulated by genotype (N2 vs CB4856) at Late reproduction stage (96 hours at 24 centigrade).	Authors permuted transcript values and used a genome-wide threshold of log10 P-value = 2, which resembles a false discovery rate (FDR) of 0.0118.	WBPaper00040858:eQTL_regulated_reproductive
	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: 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 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 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 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
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
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
	Proteins that showed significantly decreased expression in 1-day-old sek-1(km4) adults comparing to in wild type animals, both with 6 hours of cisplatin treatment.	The differential expression analysis was performed in R. Differentially expressed proteins were identified by using a two-sided t-test on log-transformed data.	WBPaper00065373:sek-1(km4)_downregulated_cisplatin
	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

7 Expression Patterns

• Primary Identifier: Expr1163210
• Pattern: Developmental gene expression time-course. Raw data can be downloaded from ftp://caltech.wormbase.org/pub/wormbase/datasets-published/hashimshony2015

• Primary Identifier: Expr8623
• Remark: Picture: Fig 2.
• Pattern: Adult hermaphrodites and males expressed more GLD-4 than animals containing no germline. By immunocytochemistry, GLD-4 was found to be cytoplasmic in the hermaphrodite germline and primordial germ cells throughout embryogenesis. In the late embryo, GLD-4 expression became limited to the germ cell lineage and its localization correlated perfectly with embryonic P granules. GLD-4 was detected throughout embryonic development in the entire P-cell lineage, which gives rise to the two primordial germ cells Z2 and Z3.
• Subcellular Localization: Subcellularly, GLD-4 localizes also to cytoplasmic structures that are nuclear envelope-associated and the staining pattern is reminiscent of P granules. Indeed, GLD-4 overlaps in colocalization experiments with PGL-1, a molecular marker for P granules. The staining pattern was observed with both C-terminal anti-GLD-4 antibodies and is reduced to background signals in the gld-4(ef15) allele. The P granule association of GLD-4 was less apparent during pachytene, became obvious again in maturing oocytes, and was most prominently visible in developing embryos.

• Primary Identifier: Expr11998
• Pattern: GLD-4 is expressed equally strong within the entire proliferative zone and in meiosis.

• Primary Identifier: Expr1036324
• Pattern: Tiling arrays expression graphs

• Primary Identifier: Expr2030325
• 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: Expr2012089
• 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: Expr1022314
• Pattern: Developmental gene expression time-course. Raw data can be downloaded from ftp://caltech.wormbase.org/pub/wormbase/datasets-published/levin2012

21 GO Annotation

9 Homologues

1 Locations

• Feature . Primary Identifier: WBGene00014115
• Start: 9118115
• End: 9123181
• Strand: 1

21 Ontology Annotations

2 Regulates Expr Cluster

Regulated By Treatment	Description	Algorithm	Primary Identifier
	Genes that showed significantly decreased expression in gld-4(RNAi) comparing with control RNAi, according to RNAseq.	Using the DESeq package (R 3.0.2, DESeq version 1.14.0), the count data were normalized by the size factor to estimate the effective library size. After calculating the gene dispersion across all samples, the comparison of two different conditions resulted in a list of differentially expressed genes. Genes with a normalized read count smaller than 100 were ignored in the final analysis. A pre-filtering step was used to calculate the number of genes showing a high probability of being differentially regulated. In this step, genes with a probability (unadjusted P-value) above 0.003 were excluded from the differential expression analysis. Genes with a fold-change higher or equal to two, as well as an adjusted P-value of <= 0.05 was then defined as differentially expressed. The P-values are being adjusted to the multiple testing hypotheses to reduce the false discovery rate (FDR).	WBPaper00045729:gld-4(RNAi)_downregulated
	Genes that showed significantly increased expression in gld-4(RNAi) comparing with control RNAi, according to RNAseq.	Using the DESeq package (R 3.0.2, DESeq version 1.14.0), the count data were normalized by the size factor to estimate the effective library size. After calculating the gene dispersion across all samples, the comparison of two different conditions resulted in a list of differentially expressed genes. Genes with a normalized read count smaller than 100 were ignored in the final analysis. A pre-filtering step was used to calculate the number of genes showing a high probability of being differentially regulated. In this step, genes with a probability (unadjusted P-value) above 0.003 were excluded from the differential expression analysis. Genes with a fold-change higher or equal to two, as well as an adjusted P-value of <= 0.05 was then defined as differentially expressed. The P-values are being adjusted to the multiple testing hypotheses to reduce the false discovery rate (FDR).	WBPaper00045729:gld-4(RNAi)_upregulated

1 Sequence

• Length: 5067

1 Sequence Ontology Term

• Name: gene

1 Strains

• WBStrain00007425

1 Upstream Intergenic Region

• WormBase ID: intergenic_region_chrI_9115918..9118114
• Length (nt): 2197
• Chromosome Location: I: 9115918-9118114
• Organism: Caenorhabditis elegans