WormMine: Gene WBGene00004244

• WormBase Gene ID: WBGene00004244
• Gene Name: puf-8
• Sequence Name: C30G12.7
• Brief Description: puf-8 encodes a member of the PUF family of RNA binding proteins.
• Organism: Caenorhabditis elegans
• Automated Description: Enables mRNA 3'-UTR binding activity. Involved in male meiotic nuclear division; negative regulation of MAPK cascade; and spermatogenesis. Located in P granule and nuclear periphery. Expressed in several structures, including P3.p hermaphrodite; P4.p hermaphrodite; P8.p hermaphrodite; germ line; and vulva. Used to study obesity. Human ortholog(s) of this gene implicated in cerebellar ataxia type 47. Is an ortholog of human PUM1 (pumilio RNA binding family member 1) and PUM2 (pumilio RNA binding family member 2).
• Biotype: SO:0001217
• Genetic Position: II :0.500136 ±0.000128
• Length (nt): 2138

1 Organism

• Name: Caenorhabditis elegans
• Taxon Id: 6239

1 Synonyms

• Value: WBGene00004244

Genomics

1 Transcripts

WormMine ID	Sequence Name	Length (nt)	Chromosome Location
Transcript:C30G12.7.1	C30G12.7.1	1820	II: 7296110-7298247

Other

1 CDSs

WormMine ID	Sequence Name	Length (nt)	Chromosome Location
CDS:C30G12.7	C30G12.7	1608	II: 7296304-7296377

24 RNAi Result

• WBRNAi00041565
• WBRNAi00061016
• WBRNAi00061017
• WBRNAi00022862
• WBRNAi00103802
• WBRNAi00103801
• WBRNAi00011396
• WBRNAi00113531
• WBRNAi00078205
• WBRNAi00022863
• WBRNAi00022864
• WBRNAi00022866
• WBRNAi00022867
• WBRNAi00029365
• WBRNAi00082511
• WBRNAi00082581
• WBRNAi00086642
• WBRNAi00061743
• WBRNAi00103800
• WBRNAi00091433
• WBRNAi00022865
• WBRNAi00059891
• WBRNAi00059892
• WBRNAi00117255

42 Allele

• gk963801
• gk963053
• gk962682
• q725
• gk963353
• gk963352
• h15849
• gk594295
• gk857913
• gk433216
• gk791285
• gk705890
• gk546485
• gk897676
• gk319075
• gk339204
• gk815314
• gk911113
• gk351870
• gk651654
• gk318638
• gk838623
• WBVar00268802
• zh17
• ust221
• ust222
• ust223
• ust245
• ust246
• ok302

1 Chromosome

• WormBase ID: II
• Organism: Caenorhabditis elegans
• Length (nt): 15279421

1 Chromosome Location

• Feature . Primary Identifier: WBGene00004244
• Start: 7296110
• End: 7298247
• 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_chrII_7296018..7296109
• Length (nt): 92
• Chromosome Location: II: 7296018-7296109
• Organism: Caenorhabditis elegans

133 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
	Transcripts that showed significantly increased expression in day 1 adult hermaphrodite comparing to in L4 larva daf-16(mu86);glp-1(e2141) animals.	Fold change > 2, FDR < 0.05	WBPaper00064088:Day-1-adult_vs_L4_upregulated_daf-16(mu86);glp-1(e2141)
	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 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 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
Bacteria infection: Staphylococcus aureus MW2. 4 hours of exposure.	Transcripts that showed significantly increased expression after N2 animals had 4 hours of infection by Staphylococcus aureus (MW2).	DEseq 1.18.0, adjusted p-value < 0.05.	WBPaper00056471:S.aureus-4h_upregulated_N2
	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
	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
	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
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 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 mbl-1(syb4318), referred to as mbl-1short(ex7-), comparing to in N2 at L4 larva stage.	DESeq2, Fold change > 2 and FDR < 0.05	WBPaper00066410:mbl-1(syb4318)_upregulated
	Transcripts that showed significantly decreased expression in rbr-2(tm3141) comparing to in N2 animals.	Mapped reads were analyzed for transcript assembly and differential expression using Cufflinks 2.1.1 with a filter of twofold difference and FDR correction (P < 0.05).	WBPaper00050080:rbr-2(tm3141)_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
	Transcripts that showed significantly decreased expression in FACS sorted neuron cells (labelled by pan-neuronal GFP) from edIs6[unc-119::GFP + rol-6(su1006)]; thoc-5(wy822) comparing to in edIs6.	DESeq2, log2 fold change > 2, adjusted p-value < 0.005.	WBPaper00055103:thoc-5(wy822)_downregulated
	Transcripts detected in germline isolated from day-1 adult hermaphrodite animals.	All three experiments have CPM >= 1.	WBPaper00067147:germline_expressed
	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 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
	Up-regulated genes (fold change > 1.5) in two CoQ-deficient clk-1 mutant strains (e2519, qm30) compared to wild types N2.	Fold-changes of intensities were calculated from the arithmetic mean of gene expression values between experimental and corresponding control group. Fold change >= 1.5 was used as cut-off.	WBPaper00045774:clk-1_upregulated
	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)
	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

11 Expression Patterns

• Primary Identifier: Expr8707
• Remark: Picture: Fig. 1.
• Pattern: GFP was first observed in the descendants of the primordial germ cells in the early L1 larva. While GFP fluorescence was observed in the cytoplasm, stronger, punctuate fluorescence around the nucleus was unmistakable. This expression pattern continued through L2 and L3 stages. At L4 and adult stages, GFP expression was strongest in the mitotic germ cells and gradually decreased as the germ cells progressed through meiosis.
• Subcellular Localization: Many of the P granule-positive foci also contain PUF-8::GFP, indicating that PUF-8 is indeed localized on P granules.

• Primary Identifier: Expr1032094
• Pattern: Tiling arrays expression graphs

• Primary Identifier: Expr2310
• Pattern: Northern analysis revealed that puf-8 is expressed primarily in the germline.

• Primary Identifier: Expr3963
• Pattern: PUF-8::GFP was expressed in various tissues including the pharyngeal muscles, the hypodermis, the ventral cord motor neurons and the vulval cells. Before vulval induction in L2 larvae, PUF-8::GFP was expressed in all six vulval precursor cells at equal levels. After vulval induction in early L3 larvae, PUF-8::GFP was upregulated in the descendants of the tertiary distal VPCs (P3.p, P4.p and P8.p), while expression faded in the primary and secondary descendants of the proximal VPCs (P5.p, P6.p and P7.p). In addition, PUF-8::GFP expression was detected in the VulC sublineage of the secondary cells at the Pn.pxxx stage.

• Primary Identifier: Expr10651
• Pattern: PUF- 8::GFP is expressed throughout the distal end of the gonad, with slightly lower levels within the first third to half of the proliferative zone. Protein levels gradually decrease proximally until eventually plateauing at ~40 cell diameters, well beyond where all cellsnormally have entered into meiotic prophase. PUF-8 is at its maximum expression level in the approximate region of the proliferative zone where cells are likely entering pre-meiotic S-phase.

• Primary Identifier: Expr1020627
• Pattern: Developmental gene expression time-course. Raw data can be downloaded from ftp://caltech.wormbase.org/pub/wormbase/datasets-published/levin2012

• Primary Identifier: Expr2309
• Remark: Reporter gene fusion type not specified.
• Pattern: Expressed strongly in sperm.

• Primary Identifier: Expr10746
• Subcellular Localization: As reported previously (Ariz et al., 2009), we observed a perinuclear distribution of PUF-8::GFP that is reminiscent of germ cell-specific P granules. Significantly, we noticed PUF-8::GFP in the nucleus as well, where it was distributed in a diffuse pattern at the inner periphery of thenucleus. In several nuclei, the PUF-8::GFP distribution was asymmetrical, with a crescent-shaped pattern that was strikingly similar to that of TCER-1.

• Primary Identifier: Expr2015191
• 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: Expr2033425
• 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: Expr1145584
• Pattern: Developmental gene expression time-course. Raw data can be downloaded from ftp://caltech.wormbase.org/pub/wormbase/datasets-published/hashimshony2015

13 GO Annotation

8 Homologues

1 Locations

• Feature . Primary Identifier: WBGene00004244
• Start: 7296110
• End: 7298247
• Strand: -1

13 Ontology Annotations

2 Regulates Expr Cluster

Regulated By Treatment	Description	Algorithm	Primary Identifier
	Transcripts less abundant in puf-8(q725) fbf-1(ok91);lip-1(zh15) than in fbf-1(ok91);lip-1(zh15).	DEXSeq (version 1.2.0) was used for differential expression analysis, with FDR cutoff of <0.01 and a minimum fold change requirement of 2-fold and excluded transcripts with <10 read counts.	WBPaper00045618:puf-8_downregulated
	Transcripts more abundant in puf-8(q725) fbf-1(ok91);lip-1(zh15) than in fbf-1(ok91);lip-1(zh15).	DEXSeq (version 1.2.0) was used for differential expression analysis, with FDR cutoff of <0.01 and a minimum fold change requirement of 2-fold and excluded transcripts with <10 read counts.	WBPaper00045618:puf-8_upregulated

1 Sequence

• Length: 2138

1 Sequence Ontology Term

• Name: gene

4 Strains

• WBStrain00022639
• WBStrain00022619
• WBStrain00022254
• WBStrain00022166

1 Upstream Intergenic Region

• WormBase ID: intergenic_region_chrII_7298248..7299341
• Length (nt): 1094
• Chromosome Location: II: 7298248-7299341
• Organism: Caenorhabditis elegans