WormMine: Gene WBGene00016625

• WormBase Gene ID: WBGene00016625
• Gene Name: aff-1
• Sequence Name: C44B7.3
• Brief Description: aff-1 encodes a cell-surface protein required in late L4 larvae forvarious cell fusions, of which at least one (AC-utse) does not requireEFF-1; in vulval development, AFF-1 is required for fusion of the anchorcell (AC) with the utse syncytium, of A cells to one another, and of Dcells to one another; AFF-1 is also required for lateral seam cellfusions; since aff-1 mutants fail to mix AC with utse cytoplasm, AFF-1is probably required to begin cell fusion by forming intercellularpores; AFF-1 has no obvious non-nematode orthologs, but is paralogous toEFF-1 and C26D10.7; AFF-1 is predicted to be largely extracellular, witheight conserved predicted disulfide bonds in its ectodomain and a singleC-terminal transmembrane domain; AFF-1 is expressed in the AC, beginningaround the AC's invasion of basement membrane in mid-L3 larvae, andcontinuing until the AC's fusion to utse; AFF-1 is also expressed inutse, beginning in L4 larvae, after which AC-utse fusion immediatelyensues; in both AC and utse, AFF-1 expression requires FOS-1, and theaff-1 promoter has predicted FOS-1 binding sites; other sites of AFF-1expression include embryonic hyp5 cells, pharyngeal muscles (Pm3 andPm5), head and tail neurons, sheath cells of chemosensory neurons, andmale tail neurons; subcellularly, AFF-1::GFP localizes to plasmamembrane and (undefined) intracellular organelles; generally, AFF-1 isexpressed in cells whose fusion does not require EFF-1, which mayexplain why AFF-1 and EFF-1 are redundantly required for viability; heatshock-driven overexpression of AFF-1, even in an eff-1 null mutantbackground, can induce ectopic cell fusion, and heterologous AFF-1 caninduce insect Sf9 cells to fuse in vitro.
• Organism: Caenorhabditis elegans
• Automated Description: Involved in regulation of egg-laying behavior and syncytium formation by plasma membrane fusion. Located in plasma membrane. Expressed in anchor cell; egg-laying apparatus; epithelial cell; neurons; and pharyngeal muscle cell.
• Biotype: SO:0001217
• Genetic Position: II :0.125694 ±0.001371
• Length (nt): 3171

1 Organism

• Name: Caenorhabditis elegans
• Taxon Id: 6239

1 Synonyms

• Value: WBGene00016625

Genomics

1 Transcripts

WormMine ID	Sequence Name	Length (nt)	Chromosome Location
Transcript:C44B7.3.1	C44B7.3.1	1977	II: 6860582-6863752

Other

1 CDSs

WormMine ID	Sequence Name	Length (nt)	Chromosome Location
CDS:C44B7.3	C44B7.3	1770	II: 6860789-6860950

11 RNAi Result

• WBRNAi00107675
• WBRNAi00042428
• WBRNAi00024814
• WBRNAi00065919
• WBRNAi00027223
• WBRNAi00011912
• WBRNAi00071778
• WBRNAi00071157
• WBRNAi00065903
• WBRNAi00107654
• WBRNAi00107655

26 Allele

• gk963801
• gk963053
• WBVar01695563
• gk556537
• gk746243
• gk430442
• gk895994
• gk419713
• gk484942
• gk532688
• gk507837
• gk364751
• gk867868
• gk617148
• gk692880
• tm2214
• gk145806
• gk145804
• gk145805
• gk145802
• gk145803
• WBVar00268771
• ty4
• WBVar01240808
• WBVar01240805
• ok1873

1 Chromosome

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

1 Chromosome Location

• Feature . Primary Identifier: WBGene00016625
• Start: 6860582
• End: 6863752
• Strand: -1

3 Data Sets

• WormBaseAcedbConverter
• GO Annotation data set
• C. elegans genomic annotations (GFF3 Gene)

1 Downstream Intergenic Region

• WormBase ID: intergenic_region_chrII_6858302..6860581
• Length (nt): 2280
• Chromosome Location: II: 6858302-6860581
• Organism: Caenorhabditis elegans

146 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
	Genes significantly enriched (> 2x, FDR < 5%) in a particular cell-type versus a reference sample of all cells at the same stage.	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:A-class-motor-neurons_larva_enriched
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 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
	Transcripts that showed significantly increased 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_upregulated
	Transcripts that showed significantly decreased expression in atfs-1(cmh15) (null allele) animals comparing to in N2 animals at L4 larva stage.	edgeR, fold change > 2, FDR < 0.05	WBPaper00060909:atfs-1(cmh15)_downregulated
	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)
	Transcripts that showed significantly decreased expression in day 3 adult hermaphrodite comparing to in L4 larva glp-1(e2141) animals.	Fold change > 2, FDR < 0.05	WBPaper00064088:Day-3-adult_vs_L4_downregulated_glp-1(e2141)
	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 after four-day-old young adult worms were placed on NGM plates seeded with OP50 in the presence 5% Agaro-oligosaccharides(AGO) for 24 h, comparing to animals grown in the absence of AGO.	Fold change > 2.	WBPaper00064306:Agaro-oligosaccharides_upregulated
	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 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
	Top 300 transcripts enriched in excretory duct, excretory pore according to single cell RNAseq.	Top 300 enriched transcripts were determined by log2.ratio of the tpm in the cell type vs the tpm in the other cells * the log2 of the cell.type tpm.	WBPaper00061340:Excretory_duct_and_pore
	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 decreased expression in sin-3(tm1276) comparing to in N2 at early embryo when there were only 3 -5 eggs in the adult.	DESeq2, fold change > 2, adjusted p-value < 0.01	WBPaper00058598:sin-3(tm1276)_downregulated
	Transcripts that showed significantly increased expression in xrep-4(lax137).	DESeq2. Genes were selected if their p value < 0.01.	WBPaper00066062:xrep-4(lax137)_upregulated
	Genes that showed oscillating mRNA expression level throughout the 16 hour time courses from L3 larva to young adult.	The following three lines of R code were used to perform the classification: increasing <-2*amplitude-PC1 < -1.7; oscillating <-!increasing & (amplitude > 0.55); flat <-!increasing & !oscillating; Note that the amplitude of a sinusoidal wave corresponds to only half the fold change between trough and peak.	WBPaper00044736:oscillating_dev_expression
	Transcripts that showed significantly increased expression in hda-1(ne4752[3xFLAG-Degron-HDA-1]) in gonads dissected from 1-day old adult animals.	Salmon was used to map the mRNA-seq reads with the worm database WS268, and its output files were imported to DESeq2 in R. The differentially expressed genes were filtered by fold change more than 2 and adjusted p-value < 0.05. The scatter plots were generated by the plot function in R.	WBPaper00061479:hda-1(ne4752)_upregulated
	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 increased expression in npr-15(tm12539) comparing to in N2 at L4 larva stage.	Fold change > 2, FDR < 0.05.	WBPaper00066608:npr-15(tm12539)_upregulated
Bacteria infection: Pseudomonas aeruginosa PA14. 4 hours at 25C.	Transcripts that showed significantly decreased expression after N2 L4 animals were infected by P. aeruginosa (PA14) bacteria for 24 hours at 25C.	DESeq R package (1.18.0), FDR < 0.05 and fold change > 2.	WBPaper00062184:PA14_downregulated
	Transcripts that showed significantly increased expression in srbc-48(ac23);kyIs262;fer-1(b232ts) comparing to in kyIs262;fer-1(b232ts), 24h after infection with P.aeruginosa.	DESeq2, FDR <0.05, fold change > 2.	WBPaper00059664:srbc-48(ac23)_upregulated
	Transcripts that showed significantly altered expression in rnp-6(dh1127) animals comparing to in N2 when fed with live S. aureus.	Differentially expressed genes (DEGs) (q-value <0.05) between different samples were identified using the stringtie version 1.3.0, followed by Cufflinks version 2.2.	WBPaper00059824:rnp-6(dh1127)_regulated_S.aureus
	Transcripts that showed significantly increased expression in daf-2(e1370) comparing to in N2.	Student's t-test, fold change > 2, p-value < 0.05.	WBPaper00055386:daf-2(e1370)_upregulated
	Transcripts that showed significantly decreased expression in set-2(tm1630) animals at embryo stage, comparing to in N2 animals.	DESeq2 (v2.1.8.3) was used to determine DE genes and to generate principal component and scatter plots. DE genes with FDR < 0.05 were analysed using g:Profiler with Bonferroni correction.	WBPaper00060014:set-2(tm1630)_downregulated
	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
	Transcripts that showed significantly increased expression in animals lacking P granules by RNAi experiments targeting pgl-1, pgl-3, glh-1 and glh-4, and unc-119-GFP(+), comparing to in control animals, at 2-day post L4 adult hermaphrodite stage.	DESeq2, Benjamini-Hochberg multiple hypothesis corrected p-value < 0.05 and fold change > 2.	WBPaper00050859:upregulated_P-granule(-)GFP(+)_vs_control_day2-adult

13 Expression Patterns

• Primary Identifier: Expr4654
• Remark: Since utse aff-1 expression and AC-utse fusion occur almost simultaneously, it is possible that aff-1 expression detected in the utse is actually a contribution from the AC cytoplasm after the fusion event. To test this, authors examined utse aff-1 expression in lin-29(n482) mutant worms where AC-utse fusion does not occur. aff-1 expression in the utse in these mutants indicated that aff-1 is specifically expressed in the utse cells and is not a consequence of AC to utse cytoplasmic GFP diffusion after fusion.
• Pattern: Specific and continuous expression was detected in the AC from the invasion of the vulval primordium at mid-L3 until its fusion with the utse cells. As the vulva completes its invagination in the L4, the utse syncytium starts to express aff-1, resulting in coexpression of aff-1 in both cells prior to their fusion. Thus, AFF-1 is dynamically expressed in a specific group of cells that undergo cell fusion during normal development. aff-1 expression is first detected in the embryonic hyp5 cell and later during larval development in various cell types, including pharyngeal muscles (Pm3 and Pm5), uterine rings (Ut2 and Ut4), head and tail neurons, sheath cells of chemosensory neurons, and male tail neurons). aff-1 is also expressed in vulval vulD and the seam cells shortly before these cells fuse. In general, the myoepithelial cells of the pharynx and the epithelial cells in the uterus, vulva, and hypodermis that express aff-1 undergo fusion. Thus, AFF-1 is dynamically expressed in a specific group of cells that undergo cell fusion during normal development.

• Primary Identifier: Expr4655
• Pattern: AFF-1::GFP was weakly expressed on the plasma membrane and in intracellular organelles in hyp5, seam cells, vulD vulval precursors, and AC before, during, and after cell-cell fusion.
• Subcellular Localization: Expressed on the plasma membrane and in intracellular organelles.

• Primary Identifier: Expr4656
• Subcellular Localization: The reporter was found to be strongly expressed in intracellular organelles, and on the surface of the AC from the time of invasion of the vulval primordium to the fusion to the utse.

• Primary Identifier: Expr2009256
• 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: Expr7301
• Pattern: Click the movie links below for interactive 4D movies of a fluorescence reporter. http://glowormnotes.blogspot.com/2009/11/aff-1gfp-transcriptional-fusion.html

• Primary Identifier: Expr8130
• Remark: Picture:Figure 6C.
• Pattern: aff-1::GFP was expressed in the wild-type pm8 beginning at about 7.2 hr, but was never expressed in vpi1.

• Primary Identifier: Expr14390
• Pattern: A transcriptional reporter that fuses 5.4kb of the aff-1 upstream genomic sequence (aff-1pro) to nuclear-localized green fluorescent protein (NLS-GFP) was expressed in the duct beginning at the 1.5-fold stage of embryogenesis, around the time when auto-fusion occurs, but was never observed in the pore.

• Primary Identifier: Expr13325
• Pattern: AFF-1 could not be detected in the PVD at any stage during development. Instead, AFF-1 is strongly expressed on the plasma membrane, filopodia, and internal puncta in the epidermal lateral seam cells. Using live SDC microscopy, we found that the vesicles containing AFF-1::GFP were observed outside the seam cells in control animals. AFF-1::GFP is expressed in vesicles inside and outside of the seam cells, in the anchor cell (AC) and in VulA ring.

• Primary Identifier: Expr2027493
• 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: Expr1037146
• Pattern: Tiling arrays expression graphs

• Primary Identifier: Expr1026865
• Pattern: Developmental gene expression time-course. Raw data can be downloaded from ftp://caltech.wormbase.org/pub/wormbase/datasets-published/levin2012

• Primary Identifier: Expr1146417
• Pattern: Developmental gene expression time-course. Raw data can be downloaded from ftp://caltech.wormbase.org/pub/wormbase/datasets-published/hashimshony2015

• Primary Identifier: Expr14391
• Subcellular Localization: In 1.5-2-fold embryos, around the time of auto-fusion, AFF-1::mCherry localized specifically to duct apical membranes. In later embryos and larvae, AFF-1::mCherry relocated and accumulated in puncta throughout the duct cell, most of which were located at or near the basal plasma membrane by L1 stage.

9 GO Annotation

0 Homologues

1 Locations

• Feature . Primary Identifier: WBGene00016625
• Start: 6860582
• End: 6863752
• Strand: -1

9 Ontology Annotations

0 Regulates Expr Cluster

1 Sequence

• Length: 3171

1 Sequence Ontology Term

• Name: gene

6 Strains

• WBStrain00047003
• WBStrain00003886
• WBStrain00003885
• WBStrain00000197
• WBStrain00003881
• WBStrain00003884

1 Upstream Intergenic Region

• WormBase ID: intergenic_region_chrII_6863753..6865563
• Length (nt): 1811
• Chromosome Location: II: 6863753-6865563
• Organism: Caenorhabditis elegans