WormMine: Gene WBGene00001402

• WormBase Gene ID: WBGene00001402
• Gene Name: fbf-2
• Sequence Name: F21H12.5
• Brief Description: fbf-2 encodes an RNA-binding protein that is one of 11 C. elegans members of the PUF family (Pumilio and FBF) of translational regulators; FBF-2 is nearly identical to FBF-1 with which it is largely redundant in regulating two aspects of germline development: 1)maintenance of stem cell proliferation, and 2)the hermaphroditic switch between spermatogenesis and oogenesis; in maintaining germline stem cells, the FBF proteins, acting through NOS-3, negatively regulate the activity of gld-1 mRNA, which encodes a translational repressor required for meiotic entry; in regulating the sperm-to-oocyte switch, the FBFs act downstream of GLD-3 to negatively regulate the activity of fem-3 mRNA, which encodes a novel protein required for germline sex determination; consistent with their role in germline development, FBF-1 and FBF-2 are expressed in the germline cytoplasm, becoming enriched in the mitotic region during the L4 larval and adult stages.
• Organism: Caenorhabditis elegans
• Automated Description: Enables mRNA 3'-UTR binding activity. Involved in negative regulation of translation. Located in P granule. Used to study obesity.
• Biotype: SO:0001217
• Genetic Position: II :-0.523905 ±0.013695
• Length (nt): 2618

1 Organism

• Name: Caenorhabditis elegans
• Taxon Id: 6239

1 Synonyms

• Value: WBGene00001402

Genomics

1 Transcripts

WormMine ID	Sequence Name	Length (nt)	Chromosome Location
Transcript:F21H12.5.1	F21H12.5.1	2286	II: 6088863-6091480

Other

1 CDSs

WormMine ID	Sequence Name	Length (nt)	Chromosome Location
CDS:F21H12.5	F21H12.5	1899	II: 6089142-6089388

70 RNAi Result

• WBRNAi00092445
• WBRNAi00092444
• WBRNAi00045249
• WBRNAi00025169
• WBRNAi00082442
• WBRNAi00074171
• WBRNAi00072429
• WBRNAi00092448
• WBRNAi00061200
• WBRNAi00092447
• WBRNAi00092450
• WBRNAi00092449
• WBRNAi00061203
• WBRNAi00061204
• WBRNAi00061205
• WBRNAi00061206
• WBRNAi00061207
• WBRNAi00061208
• WBRNAi00061201
• WBRNAi00061202
• WBRNAi00064571
• WBRNAi00064611
• WBRNAi00074169
• WBRNAi00074170
• WBRNAi00074173
• WBRNAi00074172
• WBRNAi00074175
• WBRNAi00074174
• WBRNAi00074176
• WBRNAi00013710

52 Allele

• gk963801
• gk963053
• q655
• q704
• q735
• q738
• WBVar01603998
• WBVar01823149
• WBVar01823148
• h3280
• gk358588
• gk520908
• gk618201
• gk936010
• gk537305
• gk639133
• gk536150
• gk675144
• gk932493
• gk920737
• gk908459
• WBVar01626588
• WBVar01626589
• q932
• WBVar01626590
• gk743394
• gk646048
• gk597248
• gk640918
• gk694657

1 Chromosome

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

1 Chromosome Location

• Feature . Primary Identifier: WBGene00001402
• Start: 6088863
• End: 6091480
• 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

119 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
Osmotic stress	Transcripts that showed significantly altered expression with 500 mM salt (NaCl) vs 100 mM salt when no food was present	DESeq(version 1.10.1), FDR < 0.05.	WBPaper00050726:OsmoticStress_regulated_NoFood
Heat shock: 35C for 1 hour.	Transcripts that showed significantly increased expression immediately after 1-day post L4 adult hermaphrodite N2 animals were exposed to 35C for 1 hour.	The DESeq2 (GalaxyVersion 2.11.40.6 + galaxy1) was used to determine differentiallyexpressed features from count tables of differential transcript abundances. log2FC > 1, FDR < 0.01.	WBPaper00065749:Heat-Shock_upregulated_N2
	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 decreased expression in day 3 adult hermaphrodite comparing to in L4 larva daf-16(mu86);glp-1(e2141) animals.	Fold change > 2, FDR < 0.05	WBPaper00064088:Day-3-adult_vs_L4_downregulated_daf-16(mu86);glp-1(e2141)
	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)
	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
	Transcripts that showed significantly altered expression after 24 hour exposure to stavudine (d4T) starting at L1 lava stage.	DESeq	WBPaper00053302:stavudine_24h_regulated
	Transcripts that showed significantly increased expression in oocyte germline cells comparing to in mitosis germline cells.	Log2 Fold change > 2 or <-1, p-value < 0.05.	WBPaper00053599:oocyte_vs_mitosis_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
Temprature shift to 28C for 48 hours.	Transcripts that showed significantly decreased expression after animals were exposed to 28C temperature for 48 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_48h_downregulated
	Proteins that showed significantly decreased expression after 1-day-old wild type adults were exposed to cisplatin (300ug per mL) for 6 hours.	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:Cisplatin_downregulated_WT
	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
	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
	Genes that showed expression levels higher than the corresponding reference sample (L2 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:intestine_L2-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 increased expression in hda-2(ok1479) comparing to in N2 animals.	DESeq2 (version 1.28.1), FDR < 0.01, fold change > 2.	WBPaper00062159:hda-2(ok1479)_upregulated
	Transcripts that showed significantly decreased expression after animals were treated with 100uM Rapamycin and 50uM Rifampicin from day 1 to day 3 adult hermaphradite.	DESeq2(v1.14.1), fold change > 2, p-value < 0.05	WBPaper00055354:Rapamycin-Rifampicin_downregulated
	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
	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
Starvation	Transcripts that showed significantly altered expression by starvation with 100 mM salt (NaCl)	DESeq(version 1.10.1), FDR < 0.05.	WBPaper00050726:starvation_regulated_LowSalt
	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 that showed significantly increased expression in sin-3(tm1276) comparing to in N2 at early embryo stage.	DESeq2, FDR < 0.05	WBPaper00058691:sin-3(tm1276)_upregulated

12 Expression Patterns

• Primary Identifier: Expr3518
• Remark: The FBF-2 antibody did not detect protein in fbf-2(q738), fbf-2(q655), or fbf-2(q735) germlines and, therefore, it is specific.
• Pattern: By immunocytochemistry, FBF-2 staining was faint, but reproducible, in germ cells directly adjacent to the distal tip cell, extending proximally ~17 germ cell diameters.

• Primary Identifier: Expr13420
• Subcellular Localization: As previously reported, wild-type GFP::FBF-2 localized to P granules in the distal cells.

• Primary Identifier: Expr14532
• Pattern: Each of the FBF-1 and FBF-2 transgenes rescued fbf-1 fbf-2 double mutants to fertility (100%; n = 20 animals for each transgene). Rescued animals were phenotypically wild-type and FLAG-tagged FBF proteins were enriched in the distal germline, which includes the germline stem cells, consistent with their endogenous expression patterns (Lamont et al. 2004; Voronina et al. 2012). Also, their expression was essentially limited to the germline.

• Primary Identifier: Expr14597
• Pattern: FBF-1 and FBF-2 expression was essentially limited to the germline.

• Primary Identifier: Expr10596
• Subcellular Localization: FBF-1 and FBF-2 were detected in the distal arm of the germline. FBF-1 levels were uniformly high throughout the mitotic zone; by contrast, FBF-2 levels were low in the first four to six rows and increased by 5-fold in subsequent rows. FBF-1 and FBF-2 also differed in their subcellular distributions: FBF-1 localized to numerous cytoplasmic and perinuclear foci, whereas FBF-2 localized primarily to perinuclear foci and was more diffusely distributed in the cytoplasm. Co-localization studies showed that FBF-1 localization do not coincide with P granules. By contrast, FBF-2 localizes primarily to perinuclear foci that overlap with P granules and on occasion overlap with FBF-1 foci.

• Primary Identifier: Expr2011444
• 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: Expr1149178
• Pattern: Developmental gene expression time-course. Raw data can be downloaded from ftp://caltech.wormbase.org/pub/wormbase/datasets-published/hashimshony2015

• Primary Identifier: Expr1017538
• Pattern: Developmental gene expression time-course. Raw data can be downloaded from ftp://caltech.wormbase.org/pub/wormbase/datasets-published/levin2012

• Primary Identifier: Expr3798
• Pattern: Expression not detected in the ventral hypodermis of L1, L2, or L3 larvae.

• Primary Identifier: Expr1451
• Remark: Embryo expression data was not described. fbf mRNA is not detected in glp-1 mutants, which lack a germ line.
• Pattern: fbf mRNA increases in abundance during post-embryonic development and peaks during the fourth larval stage, when the sperm/oocyte switch occurs.

• Primary Identifier: Expr3519
• Pattern: In wild-type germlines, the antisense, but not the sense, probe detected RNAs broadly distributed in the distal germline. To examine fbf-1 mRNA specifically, dissected fbf-2(q738) germlines were hybridized and found staining with the antisense probe throughout the distal arm. To examine fbf-2 mRNA specifically, dissected fbf-1(ok91) germlines were hybridized and found staining with the antisense probe that was most abundant in the distal end.

• Primary Identifier: Expr2029682
• 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).

15 GO Annotation

8 Homologues

1 Locations

• Feature . Primary Identifier: WBGene00001402
• Start: 6088863
• End: 6091480
• Strand: -1

15 Ontology Annotations

2 Regulates Expr Cluster

Regulated By Treatment	Description	Algorithm	Primary Identifier
	Transcripts that bind FLAG-FBF-1 and FLAG-FBF-2 as detected by iCLIP analysis, with significantly lower expression in spermatogenic animals fem-3(q22) (JK5140 and JK5545) comparing to oogenic animals (JK5181 and JK5182).	DESeq2 v1.18.1, p < 0.01	WBPaper00055804:FBF-1-FBF-2-associated_oogenic-enriched
	Transcripts that bind FLAG-FBF-1 and FLAG-FBF-2 as detected by iCLIP analysis, with significantly higher expression in spermatogenic animals fem-3(q22) (JK5140 and JK5545) comparing to oogenic animals (JK5181 and JK5182).	DESeq2 v1.18.1, p < 0.01	WBPaper00055804:FBF-1-FBF-2-associated_spermatogenic-enriched

1 Sequence

• Length: 2618

1 Sequence Ontology Term