WormMine: Gene WBGene00000903

• WormBase Gene ID: WBGene00000903
• Gene Name: daf-7
• Sequence Name: B0412.2
• Brief Description: daf-7 encodes a member of the transforming growth factor beta superfamily; in C. elegans, DAF-7 functions as part of a signaling pathway that interprets environmental conditions to regulate energy-balance pathways that affect dauer larval formation, adult lifespan, fat metabolism, egg laying, pathogen avoidance behavior, and feeding behavior; daf-7 reporter gene fusions are expressed in the ASI, ADE, and OLQ neurons, and daf-7 expression is induced in both ASI and ASJ chemosensory neurons in response to the pathogenic bacterial strain Pseudomonas aeruginosa PA14.
• Organism: Caenorhabditis elegans
• Automated Description: Predicted to enable cytokine activity and transforming growth factor beta receptor binding activity. Involved in several processes, including cellular response to cGMP; regulation of gene expression; and response to bacterium. Located in extracellular space. Expressed in coelomocyte; head neurons; pharynx; and in male. Human ortholog(s) of this gene implicated in myostatin-related muscle hypertrophy and vertebral hypersegmentation and orofacial anomalies. Is an ortholog of human GDF11 (growth differentiation factor 11).
• Biotype: SO:0001217
• Genetic Position: III :-25.7963 ±0.018589
• Length (nt): 1930

1 Organism

• Name: Caenorhabditis elegans
• Taxon Id: 6239

1 Synonyms

• Value: WBGene00000903

Genomics

1 Transcripts

WormMine ID	Sequence Name	Length (nt)	Chromosome Location
Transcript:B0412.2.1	B0412.2.1	1645	III: 811844-813773

Other

1 CDSs

WormMine ID	Sequence Name	Length (nt)	Chromosome Location
CDS:B0412.2	B0412.2	1053	III: 811938-812066

10 RNAi Result

• WBRNAi00039032
• WBRNAi00009757
• WBRNAi00006581
• WBRNAi00027826
• WBRNAi00060550
• WBRNAi00060549
• WBRNAi00060551
• WBRNAi00060552
• WBRNAi00115226
• WBRNAi00075814

52 Allele

• gk963623
• gk962532
• gk964281
• WBVar01322466
• WBVar00031858
• WBVar00031863
• gk913516
• WBVar02087836
• gk335909
• gk955000
• gk612356
• gk845445
• WBVar01443296
• WBVar01564408
• WBVar01564407
• gk384298
• WBVar01564406
• gk602791
• WBVar01564405
• m434
• WBVar01769202
• e1000
• WBVar00006726
• WBVar00006731
• e1372
• yj11
• n697
• yj12
• n696
• WBVar01255170

1 Chromosome

• WormBase ID: III
• Organism: Caenorhabditis elegans
• Length (nt): 13783801

1 Chromosome Location

• Feature . Primary Identifier: WBGene00000903
• Start: 811844
• End: 813773
• 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_chrIII_813774..816144
• Length (nt): 2371
• Chromosome Location: III: 813774-816144
• Organism: Caenorhabditis elegans

206 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 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
	Transcripts enriched in ASG according to single cell RNAseq.	Genes that pass the Bonferroni threshold for multiple comparisons (q < 0.05) are significantly enriched.	WBPaper00061651:ASG_enriched
	Neuronally enriched transcripts according to a comparison of neuronal nuclei IP samples to total nuclei using isolation of nuclei from tagged specific cell types (INTACT) technology.	DESEQ2, fold change > 2 and FDR < 0.01.	WBPaper00062103:neuron_enriched
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
	Single-cell RNA-Seq cell group 71_0 expressed in neuron.	scVI 0.6.0	WBPaper00065841:71_0
	Transcripts that showed significantly increased expression glp-1(e2141); TU3401 animals comparing to in TU3401 animals.	Fold change > 2, FDR < 0.01.	WBPaper00065993:glp-1(e2141)_upregulated
	Transcripts that showed significantly increased expression in ogt-1(ok1474) neuronal cells isolated by FACs comparing to in FACs isolated neuronal cells from wild type.	DESeq2, fold change > 2, FDR < 0.05.	WBPaper00066485:ogt-1(ok1474)_upregulated_neuron
Bacteria infection: Enterococcus faecalis	Genes with increased expression after 24 hours of infection by E.faecalis Fold changes shown are pathogen vs OP50.	For RNA-seq and tiling arrays, log2 fold changes between gene expression values of infected versus uninfected nematodes were calculated. For log2 fold changes > 0.00001 the values > 81.25th percentile were defined as up-regulated and for log2 fold changes < -0.00001 the values < 18.75th percentile were defined as down-regulated.	WBPaper00038438:E.faecalis_24hr_upregulated_TilingArray
	Upregulated mRNAs and lncRNAs in dot-1.1(knu339); ced-3(n1286) relative to ced-3(n1286).	edgeR, fold change > 2, FDR < 0.05.	WBPaper00065759:dot-1.1(knu339)_upregulated
	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 that showed significantly decreased expression at 5-days-post L4 adult N2 hermaphrodites comparing to 1-day-post L4 adult N2 hermaphrodites.	DESeq2, fold change > 2, FDR < 0.05	WBPaper00065835:Day5_vs_Day1_downregulated
	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
	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 1 adult hermaphrodite comparing to in L4 larva glp-1(e2141) animals.	Fold change > 2, FDR < 0.05	WBPaper00064088:Day-1-adult_vs_L4_upregulated_glp-1(e2141)
	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 increased expression in rrf-3(pk1426) comparing to in N2 at embryo stage.	DESeq2v 1.18.1, fold change > 1.5, adjusted p-value < 0.01.	WBPaper00056169:rrf-3(pk1426)_upregulated_embryo
	Transcripts that showed significantly increased expression in sin-3(tm1276) comparing to in N2.	DESeq2, fold change > 2, p-value < 0.01.	WBPaper00061203:sin-3(tm1276)_upregulated
	Transcripts that showed significantly increased expression in mrg-1(qa6200) comparing to in control animals in primordial germ cells (PGCs) at L1 larva stage.	DESeq2(v1.32.0), FDR < 0.05.	WBPaper00064315:mrg-1(qa6200)_upregulated_PGCs
	Transcripts that showed significantly increased expression in aak-1(tm1944);aak-2(ok524) animals comparing to in N2.	DEseq 1.18.0, adjusted p-value < 0.05.	WBPaper00056471:aak-1(tm1944);aak-2(ok524)_upregulated
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
	Genes that showed significantly increased expression in daf-2(e1370);hel-1(gk148684) comparing to in hel-1(gk148684)	To identify DEGs, Students t test and the log2 median ratio test were performed to compute t values and median ratios for all the annotated genes. The adjusted P values from each test were computed using an empirical distribution of the null hypothesis, which was obtained from random permutations of the samples. Finally, the adjusted P values from the individual tests were combined to compute the overall P values using Stouffers method , and genes with overall P < 0.05 and fold change > 1.5 were selected as DEGs.	WBPaper00047131:daf-2(e1370)_upregulated_hel-1(gk148684)-background
	Genes that showed significantly increased expression in daf-2(e1370) comparing to in N2.	To identify DEGs, Students t test and the log2 median ratio test were performed to compute t values and median ratios for all the annotated genes. The adjusted P values from each test were computed using an empirical distribution of the null hypothesis, which was obtained from random permutations of the samples. Finally, the adjusted P values from the individual tests were combined to compute the overall P values using Stouffers method , and genes with overall P < 0.05 and fold change > 1.5 were selected as DEGs.	WBPaper00047131:daf-2(e1370)_upregulated_N2-background
	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

16 Expression Patterns

• Primary Identifier: Expr1030567
• Pattern: Tiling arrays expression graphs

• Primary Identifier: Expr13309
• Pattern: In the wild-type background, mCherry::DAF-7 fluorescence was detected in neurons as well as in the pharyngeal muscles. In neurons, punctate fluorescence was observed in the cell bodies and in the area posterior to the ASI cell body. In contrast to DAF-28::mCherry, which was present in axons but excluded from dendrites, mCherry::DAF-7 protein was mainly detected along the dendrites of the ASI neurons. Only rare small puncta were noted in the proximal axons. Consistent with dendritic trafficking, a large accumulation of the fluorescent signal was observed surrounding the base of the ASI sensory cilia located at the distal end of the dendrite.

• Primary Identifier: Expr13310
• Pattern: Expression of the established daf-7 promoter-GFP transcriptional reporter ksIs2 was detected in multiple developing neurons in comma-stage embryos, as well as in several neurons in 3-fold embryos. Importantly, accumulation of secreted mCherry::DAF-7 protein was detected in the extraembryonic fluid at the same embryonic stages as the SMAD::GFP fluorescence, suggesting that DAF-7 activity may have a physiological role in the early embryos. We also detected pharyngeal expression and localization to coelomocytes in 3-fold embryos.

• Primary Identifier: Expr13234
• Pattern: daf-7 expression is maintained throughout the life of adult animals in the ASI neurons. daf-7 expression was also observed in the ASJ neuron pair as animals age, with all animals exhibiting ASJ expression by day 3 of adulthood. daf-7 expression in the ASI neuron pair significantly decreased with age.

• Primary Identifier: Expr13253
• Pattern: Adult males exhibit daf-7 expression in both the ASI and the ASJ neuron pairs in the absence of P. aeruginosa. This expression pattern difference in adult C. elegans, can be observed both through the use of a pdaf-7::gfp transcriptional reporter as well as by fluorescence in situ hybridization (FISH) that directly probes for endogenous daf-7 mRNA. In populations of early larval animals carrying the pdaf-7::gfp transcriptional reporter, males and hermaphrodites were indistinguishable, with fluorescence observed only in the ASI neurons. To determine the onset of daf-7 expression in males, we imaged animals carrying the fluorescent reporter at multiple time points during development beginning in the L4 larval stage and extending into reproductive maturity. We found that daf-7 expression remains off in the ASJ of males through the end of the last (L4) larval stage, but is switched on during young adulthood as the animals reach reproductive maturity. In addition, we examined expression of daf-7 in the ASI neuron pair at several matched timepoints during development and observed a significant drop in the expression of daf-7 in the ASI neurons from L4 to young adulthood (52 hr and 64.5 hr timepoints). At subsequent timepoints during adulthood, however, expression levels in the ASI neurons remained constant as expression in the ASJ neurons increased (64.5 hr and 71.5 hr timepoints).

• Primary Identifier: Marker102
• Pattern: Marker for ASI neurons.

• Primary Identifier: Expr12454
• Pattern: DAF-7::mCherry was hardly detected in ASI neurons and accumulated in the coelomocytes of wild-type animals at the adult stage.

• Primary Identifier: Expr221
• Pattern: Animals with either construct expressed daf-7::GFP in the cell body of one pair of bilaterally symmetric neurons in the lateral ganglia. Based on their positions in the L1, these were identified as the two ASI neurons. GFP was consistently expressed starting in the L1, and expression became stronger in the L2. After the L2, GFP fluorescence became progressively weaker and, by adulthood, was nearly undetectable. Rarely, other cells showed weak daf-7::GFP expression. When seen, there was only one such cell, and its identity varied from animal to animal.

• Primary Identifier: Expr12009
• Pattern: In addition to previously described expression in the ASI neuron pair, daf-7 mRNA was also present in six other sensory neurons, which, using reporter colocalization experiments, were identified as the ADE neuron pair and the OLQ neurons.

• Primary Identifier: Expr623
• Remark: See Expr624 for Expr_pattern for the same locus. This information was extracted from published material (Archana Sharma-Oates, Andrew Mounsey and Ian A. Hope).
• Pattern: In presence of ample food both hermaphrodites and males express GFP in ASI neuron pair. Expression detected in larvae beginning 4-5h after hatching, L1-L4 and in adults. There is no expression in embryos. In starvation-induced dauer larvae, there is no GFP staining detected. Pheromone-induced dauer formation at 25C. GFP expression is suppressed in L1 larvae both in % of animals expressing and in intensity of fluorescence. GFP is undetected as animals enter the dauer stage. GFP expression is restored after recovery from dauer stage (1h after feeding).

• Primary Identifier: Expr1021665
• Pattern: Developmental gene expression time-course. Raw data can be downloaded from ftp://caltech.wormbase.org/pub/wormbase/datasets-published/levin2012

• Primary Identifier: Expr2010782
• 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: Expr624
• Remark: See Expr623 for Expr_pattern for the same locus. This information was extracted from published material (Archana Sharma-Oates, Andrew Mounsey and Ian A. Hope).
• Pattern: A 1.2 kb transcript present in L1, L2 (lower level), L3 (marginally detectable) and in pheromone induced pre dauer (20oC) L2d larvae.

• Primary Identifier: Expr1143194
• Pattern: Developmental gene expression time-course. Raw data can be downloaded from ftp://caltech.wormbase.org/pub/wormbase/datasets-published/hashimshony2015

• Primary Identifier: Expr2029019
• 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: Expr3599
• Subcellular Localization: Diffuse in nerve cords.

47 GO Annotation

59 Homologues

1 Locations

• Feature . Primary Identifier: WBGene00000903
• Start: 811844
• End: 813773
• Strand: 1

47 Ontology Annotations

0 Regulates Expr Cluster

1 Sequence

• Length: 1930

1 Sequence Ontology Term

• Name: gene

26 Strains

• WBStrain00022755
• WBStrain00023548
• WBStrain00026329
• WBStrain00026330
• WBStrain00026331
• WBStrain00030742
• WBStrain00030743
• WBStrain00032980
• WBStrain00035150
• WBStrain00035147
• WBStrain00050825
• WBStrain00050824
• WBStrain00050823
• WBStrain00050822
• WBStrain00050852
• WBStrain00051573
• WBStrain00000063
• WBStrain00006360
• WBStrain00006202
• WBStrain00004310
• WBStrain00005597
• WBStrain00006387
• WBStrain00006273
• WBStrain00007510
• WBStrain00006388
• WBStrain00006172

1 Upstream Intergenic Region

• WormBase ID: intergenic_region_chrIII_809438..811843
• Length (nt): 2406
• Chromosome Location: III: 809438-811843
• Organism: Caenorhabditis elegans