WormMine: Gene WBGene00020368

• WormBase Gene ID: WBGene00020368
• Gene Name: ast-1
• Sequence Name: T08H4.3
• Brief Description: ast-1 encodes one of ten C. elegans ETS-box transcription factors; AST-1 is required cell autonomously for proper initiation and maintenance of dopamine (DA) neuron fate; AST-1 acts to specify DA neuron fate by positively regulating expression of a number of DA neuron-specific genes such as dat-1 and cat-2, which encodes a dopamine transporter and tyrosine hydroxylase, respectively; AST-1 is also required for proper navigation of some interneuron axons to their targets, for differentiation of the ventral cord pioneer neuron AVG, and for pharyngeal morphogenesis; AST-1 is transiently expressed in many head neurons late in their differentiation and axon outgrowth, and in a few pharyngeal cells; AST-1 is at first nuclear, but then relocates to spots in cell bodies and even neuronal processes; hypomorphic ast-1 mutants have axons extending laterally, and crossing over from the right axon tract to the left axon bundle; null ast-1(hd92) mutants are inviable, failing to attach a working pharynx to their cuticle during development and then starving as L1 larvae; behaviorally, hypomorphic ast-1 animals are at least superficially normal, indicating that the ventral nerve cord can tolerate at least some miswiring; AST-1 also regulates odr-2 expression, while ast-1 expression is itself regulated by LIN-11.
• Organism: Caenorhabditis elegans
• Automated Description: Predicted to enable DNA-binding transcription factor activity, RNA polymerase II-specific. Involved in several processes, including nematode pharynx morphogenesis; neuron differentiation; and regulation of nematode male tail tip morphogenesis. Located in nucleus. Expressed in intestine; neurons; and rectal gland cell. Human ortholog(s) of this gene implicated in several diseases, including hereditary lymphedema; pulmonary venoocclusive disease; and thrombocytopenia. Is an ortholog of human FLI1 (Fli-1 proto-oncogene, ETS transcription factor).
• Biotype: SO:0001217
• Genetic Position: II :-5.40481 ±0.087312
• Length (nt): 7523

1 Organism

• Name: Caenorhabditis elegans
• Taxon Id: 6239

1 Synonyms

• Value: WBGene00020368

Genomics

1 Transcripts

WormMine ID	Sequence Name	Length (nt)	Chromosome Location
Transcript:T08H4.3.1	T08H4.3.1	1921	II: 4127837-4135359

Other

1 CDSs

WormMine ID	Sequence Name	Length (nt)	Chromosome Location
CDS:T08H4.3	T08H4.3	1134	II: 4128104-4128208

11 RNAi Result

• WBRNAi00114293
• WBRNAi00114058
• WBRNAi00114137
• WBRNAi00114216
• WBRNAi00052909
• WBRNAi00072861
• WBRNAi00035368
• WBRNAi00072860
• WBRNAi00091999
• WBRNAi00107286
• WBRNAi00072862

163 Allele

• gk963801
• gk963053
• rh300
• WBVar01370122
• WBVar01370133
• WBVar01437334
• WBVar01437332
• WBVar01437333
• WBVar01437331
• WBVar01437338
• WBVar01719475
• WBVar01719474
• WBVar02029144
• WBVar02029143
• WBVar02029142
• WBVar02029141
• otn14101
• WBVar01934501
• WBVar01934500
• WBVar01766209
• WBVar01766207
• WBVar01766208
• WBVar01766206
• WBVar01766212
• WBVar01766210
• WBVar01766211
• gk463
• WBVar01393456
• WBVar00234453
• WBVar01504904

1 Chromosome

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

1 Chromosome Location

• Feature . Primary Identifier: WBGene00020368
• Start: 4127837
• End: 4135359
• 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

195 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
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
	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 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 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
	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 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 hpk-1(pk1393) comparing to in N2 at adult day 2.	DESeq 2, fold change > 2, FDR < 0.05.	WBPaper00065581:hpk-1(pk1393)_upregulated
	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
	Genes that showed expression levels higher than the corresponding reference sample (L3/L4 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:dopaminergic-neurons_L3-L4-larva_expressed
	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:glr-1(+)-neurons_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
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 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
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 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
	Genes expressed in N2.	Expressed transcripts were identified on the basis of a Present call in 3 out of 4 N2 experiments as determined by Affymetrix MAS 5.0.	WBPaper00025141:N2_Expressed_Genes
	Transcripts that showed significantly increased expression in animals fed with JM103 bacteria producing Cry5B, comparing to control animals fed with JM103.	ANOVA, p-value < 0.05.	WBPaper00056167:Cry5B_upregulated
heat-shock hlh-1	Genes enriched in HLH-1 heat shock dataset.	A two-class unpaired analysis was performed to identify genes that are elevated 1.7-fold or greater when compared with the reference for each dataset, at a false discovery rate of 1.8% or less for M0 and 1.2% or less for the M24 datasets.	WBPaper00031003:hlh_1_enriched
	Embryonic class (E): genes that significantly increase in abundance at some point during embryogenesis.	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_E

12 Expression Patterns

• Primary Identifier: Expr2009475
• 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: Expr11075
• Pattern: Despite the broad neuronal expression of both ceh-43 and ast-1, they uniquely overlap in dopaminergic neurons plus one additional pair of nondopaminergic neurons in the head and one additional neuron in the midbody region. Coexpression of ast-1, ceh-43, and ceh-20 was detected in SDQL.

• Primary Identifier: Expr13830
• Pattern: ast-1 is expressed in the HSN at L4 coinciding with the onset of differentiation. ast-1 is also expressed in other neurons but not in the ADF serotonergic neuron. AST-1 initiates its expression at postnatal stages (L3 larva). ast-1 expression is maintained in HSN after differentiation.

• Primary Identifier: Expr3990
• Pattern: Expression of this construct started at the end of gastrulation in a few neurons. The number of neurons expressing the AST-1::YFP construct increases until the 3-fold stage. Expression is maintained in the first larval stage, decreases during further development and is only weakly detectable in adults.
• Subcellular Localization: The YFP signal in the embryo is initially confined to the nucleus, but is redistributed later in larval stages to spots outside the nucleus.

• Primary Identifier: Expr7661
• Remark: Clone: pUL#IAH8F12
• Pattern: 2 of 6 independent lines showed expression in a single head nerve cell, weakly from L1 to adult, but strongest in L1. Other nerve cells in head and tail of young larvae showed even weaker expression. Occasionally, expression is seen weakly in posterior intestine L1 to adult, and even more rarely, very generalised expression in L1. Other four lines showed no expression.

• Primary Identifier: Expr3991
• Pattern: Expression started at the end of gastrulation. At the 2-fold stage, about 60 cells in the head express ast-1, most of them neurons, but also a few cells in the pharynx. A single cell in the retrovesicular ganglion expresses AST-1::YFP throughout development from the 1.5-fold stage onward. Using an odr-2::CFP marker and checking for overlap in expression, this cell was identified as the AVG neuron. The ALN neurons in the tail weakly express AST-1::YFP in late embryo and early larval stages. Occasionally, a second pair of cells in the tail was seen based on cell body position most likely the rectV cells. Expression in the tail generally is weak and somewhat variable from animal to animal. In the L1 stage, AST-1::YFP coexpressed with glr-1::CFP in AVA, AVD (weak ast-1), AVE (weak ast-1) RMDD and SMDD as well as AVG. AST-1::YFP expression decreases during larval development and is restricted to few neurons, which continue to express throughout the entire life cycle.
• Subcellular Localization: The YFP signal was initially seen only in the nucleus consistent with AST-1 being a transcription factor. Already beginning in the 3-fold stage, a redistribution of the YFP signal was seen until most of the signal is outside the nucleus mainly in spots in the cell body but also in the neuronal processes.

• Primary Identifier: Expr8565
• Remark: Picture: Fig. 2d.
• Pattern: ast-1 is expressed in several neurons, including all dopaminergic (DA) neurons. ast-1 expression persists in DA neurons throughout postembryonic stages.

• Primary Identifier: Expr3989
• Pattern: Expression of this construct in the embryo was confined to a set of sensory neurons with 6-fold symmetry most likely the inner labial neurons. It was highest between comma and 3-fold stage, fading away afterwards and being absent in larval stages and adults.

• Primary Identifier: Expr1038874
• Pattern: Tiling arrays expression graphs

• Primary Identifier: Expr1156510
• Pattern: Developmental gene expression time-course. Raw data can be downloaded from ftp://caltech.wormbase.org/pub/wormbase/datasets-published/hashimshony2015

• Primary Identifier: Expr2027712
• 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: Expr1011939
• Pattern: Developmental gene expression time-course. Raw data can be downloaded from ftp://caltech.wormbase.org/pub/wormbase/datasets-published/levin2012

23 GO Annotation

28 Homologues

1 Locations

• Feature . Primary Identifier: WBGene00020368
• Start: 4127837
• End: 4135359
• Strand: -1

23 Ontology Annotations

0 Regulates Expr Cluster

1 Sequence

• Length: 7523

1 Sequence Ontology Term

• Name: gene

12 Strains

• WBStrain00026471
• WBStrain00026479
• WBStrain00026477
• WBStrain00026472
• WBStrain00026473
• WBStrain00028724
• WBStrain00029546
• WBStrain00033857
• WBStrain00036873
• WBStrain00037957
• WBStrain00040004
• WBStrain00040024

1 Upstream Intergenic Region

• WormBase ID: intergenic_region_chrII_4135360..4146338
• Length (nt): 10979
• Chromosome Location: II: 4135360-4146338
• Organism: Caenorhabditis elegans