WormMine: Gene WBGene00001401

• WormBase Gene ID: WBGene00001401
• Gene Name: fbf-1
• Sequence Name: H12I13.4
• Brief Description: fbf-1 encodes an RNA-binding protein that is one of 12 C. elegans members of the PUF family (Pumilio and FBF) of translational regulators; FBF-1 is nearly identical to FBF-2 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; FBF-1 also plays a role in regulating adaptation in the AWC chemosensory neuron by binding and enhancing translation of the egl-4 mRNA; 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 several processes, including germline cell cycle switching, mitotic to meiotic cell cycle; olfactory learning; and regulation of gene expression. Located in germ cell nucleus and perinuclear region of cytoplasm. Expressed in germ line.
• Biotype: SO:0001217
• Genetic Position: II :-0.571982 ±0.010563
• Length (nt): 2581

1 Organism

• Name: Caenorhabditis elegans
• Taxon Id: 6239

1 Synonyms

• Value: WBGene00001401

Genomics

1 Transcripts

WormMine ID	Sequence Name	Length (nt)	Chromosome Location
Transcript:H12I13.4.1	H12I13.4.1	2255	II: 6078263-6080843

Other

1 CDSs

WormMine ID	Sequence Name	Length (nt)	Chromosome Location
CDS:H12I13.4	H12I13.4	1845	II: 6078550-6078748

58 RNAi Result

• WBRNAi00092445
• WBRNAi00092444
• WBRNAi00049385
• WBRNAi00025169
• WBRNAi00082442
• WBRNAi00092448
• WBRNAi00061200
• WBRNAi00092447
• WBRNAi00092450
• WBRNAi00092449
• WBRNAi00061203
• WBRNAi00061204
• WBRNAi00061205
• WBRNAi00061206
• WBRNAi00061207
• WBRNAi00061208
• WBRNAi00061201
• WBRNAi00061202
• WBRNAi00064571
• WBRNAi00064611
• WBRNAi00013710
• WBRNAi00016250
• WBRNAi00075630
• WBRNAi00094039
• WBRNAi00078206
• WBRNAi00078207
• WBRNAi00077433
• WBRNAi00061209
• WBRNAi00071150
• WBRNAi00117256

53 Allele

• gk963801
• gk963053
• q678
• q662
• h10860
• h3551
• WBVar02122541
• ok224
• WBVar01989138
• gk144224
• gk144223
• gk144226
• WBVar01626579
• gk144225
• WBVar01626580
• WBVar01626581
• gk144220
• WBVar01626582
• gk144222
• gk144221
• WBVar02124678
• WBVar01306735
• gk144228
• gk144227
• gk144229
• gk825705
• gk572601
• gk718929
• gk798017
• gk545085

1 Chromosome

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

1 Chromosome Location

• Feature . Primary Identifier: WBGene00001401
• Start: 6078263
• End: 6080843
• 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

135 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 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
	Proteins interacting with NHR-49-GFP according to co-IP and LC-MS.	N.A.	WBPaper00064071:NHR-49_interacting
	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 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
	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 changed expression in 6-day post-L4 adult hermaphrodite comparing to in 1-day post L4 adult hermaphrodite animals.	Sleuth	WBPaper00051558:aging_regulated
	Transcripts that showed significantly increased expression in sftb-1(cer6) deletion homozygous comparing to to in N2 animals at L4 larva stage.	DESeq2, fold change > 2	WBPaper00058725:sftb-1(cer6)_downregulated
	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
	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 increased expression in hda-1(RNAi) embryos comparing to control animals.	DESeq2, fold change > 2, FDR < 0.05.	WBPaper00067044:hda-1(RNAi)_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
	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
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
	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
	Genes that showed expression levels higher than the corresponding reference sample (embryonic 24hr 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:hypodermis_L1-larva_expressed
	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
	Transcripts that showed significantly increased expression in cfp-1(tm6369) comparing to in N2 at early embryo stage.	DESeq2, FDR < 0.05	WBPaper00058691:cfp-1(tm6369)_upregulated

14 Expression Patterns

• Primary Identifier: Expr1030839
• Pattern: Tiling arrays expression graphs

• Primary Identifier: Expr3517
• Pattern: FBF-1-specific antibodies stain weakly in the most distal mitotic nuclei of wild-type germlines and more strongly in the proximal three-fourths of the mitotic region. Strong FBF-1 staining begins ~6 germ cell diameters from the distal tip and extends to ~20 germ cell diameters.

• Primary Identifier: Expr1452
• Remark: From cgc5265: Anti-FBF-1 antibodies are specific for FBF-1: they do not recognize FBF-2 on western blots of protein translated in vitro (not shown) or in stained gonads from fbf-1 deletion mutants.
• Pattern: FBF was detected only in the germ line.
• Subcellular Localization: It is predominantly cytoplasmic. Staining with anti-DNA antibodies reveals nuclei in all tissues of the same animals.

• Primary Identifier: Expr13083
• 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: Expr1892
• Remark: early larva (author) = L1 larva and L2 larva (wjc).
• Pattern: FBF-1 is present uniformly in germline cytoplasm during early larval stages, and becomes enriched in the mitotic region of L4 larval and adult germ lines. There is no detectable staining in an fbf-1 single mutant. Within the mitotic region of wild-type germ lines, the distalmost germ cells possess faint but easily detectable FBF-1 staining, which becomes intense in more proximal mitotic cells. As germ cells leave the mitotic region and enter early meiotic prophase, FBF-1 is reduced to a low level. This pattern is similar in males.
• Subcellular Localization: cytoplasm

• Primary Identifier: Expr14531
• 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: Expr14596
• Pattern: FBF-1 and FBF-2 expression was essentially limited to the germline.

• Primary Identifier: Expr2011443
• 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: Expr1153116
• Pattern: Developmental gene expression time-course. Raw data can be downloaded from ftp://caltech.wormbase.org/pub/wormbase/datasets-published/hashimshony2015

• 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: Expr3796
• Pattern: Expression not detected in the ventral hypodermis of L1, L2, or L3 larvae.

• Primary Identifier: Expr1450
• 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: Expr2029681
• 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: Expr15895
• Subcellular Localization: we found that both endogenous FBF-1 and GFP::FBF-1 foci colocalize with 3xFLAG::CCF-1 foci in SPC (stem and progenitor cells at the distal end of the gonad) cytoplasm.

25 GO Annotation

8 Homologues

1 Locations

• Feature . Primary Identifier: WBGene00001401
• Start: 6078263
• End: 6080843
• Strand: -1

25 Ontology Annotations

5 Regulates Expr Cluster

Regulated By Treatment	Description	Algorithm	Primary Identifier
	FBF-associated probe sets (FDR <2.25%)	SAM assigns a score to each probe set and estimates their false discovery rates (FDRs). SAM deemed 4722 probe sets as significantly enriched at an FDR of 2.25% or lower.	WBPaper00035905:FBF-1_Associated
	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 more abundant in puf-8(q725) fbf-1(ok91);lip-1(zh15) than in puf-8(q725);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:fbf-1_upregulated
	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
	Transcripts less abundant in puf-8(q725) fbf-1(ok91);lip-1(zh15) than in puf-8(q725);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:fbf-1_downregulated

1 Sequence

• Length: 2581

1 Sequence Ontology Term

• Name: gene

9 Strains

• WBStrain00022640
• WBStrain00022602
• WBStrain00022603
• WBStrain00022612
• WBStrain00022628
• WBStrain00022400
• WBStrain00022344
• WBStrain00022346
• WBStrain00022396

0 Upstream Intergenic Region