WormMine: Gene WBGene00006379

• WormBase Gene ID: WBGene00006379
• Gene Name: sys-1
• Sequence Name: T23D8.9
• Brief Description: sys-1 encodes a novel protein that contains three divergent armadillo repeats; during gonadogenesis, SYS-1 functions in a Wnt/MAPK signaling pathway as a dosage-dependent beta-catenin-like transcriptional coactivator required for specification of distal cell fates; consistent with its role as a beta-catenin, SYS-1 interacts, in yeast two-hybrid and coimmunoprecipitation assays, with the POP-1/TCF transcription factor with which it can stimulate transcription via TCF binding sites; in two hybrid-assays, the POP-1/SYS-1 interaction requires the N-terminal beta-catenin binding domain of POP-1, and most of the SYS-1 protein; a VNS::SYS-1 reporter fusion protein is expressed in several tissues during embryonic and larval development and localizes to both the nucleus and cytoplasm as well as to what appears to be the centrosomes; in many tissues, SYS-1 is distributed asymmetrically, in a manner reciprocal to the asymmetric distribution of POP-1.
• Organism: Caenorhabditis elegans
• Automated Description: Enables RNA polymerase II-specific DNA-binding transcription factor binding activity; scaffold protein binding activity; and transcription coactivator activity. Involved in several processes, including cell fate commitment involved in formation of primary germ layer; gonad development; and regulation of gene expression. Located in several cellular components, including cell cortex; kinetochore; and pericentriolar material. Expressed in several structures, including ABplpapaap; ABprpapaap; Z1.aa; posterior distal tip cell; and tail hypodermis.
• Biotype: SO:0001217
• Genetic Position: I :4.13437 ±0.001519
• Length (nt): 4732

1 Organism

• Name: Caenorhabditis elegans
• Taxon Id: 6239

1 Synonyms

• Value: WBGene00006379

Genomics

3 Transcripts

WormMine ID	Sequence Name	Length (nt)	Chromosome Location
Transcript:T23D8.9b.1	T23D8.9b.1	2878	I: 9980063-9984786
Transcript:T23D8.9a.1	T23D8.9a.1	2875	I: 9980063-9984794
Transcript:T23D8.9c.1	T23D8.9c.1	2037	I: 9980494-9983069

Other

3 CDSs

WormMine ID	Sequence Name	Length (nt)	Chromosome Location
CDS:T23D8.9a	T23D8.9a	2436	I: 9980494-9980576
CDS:T23D8.9b	T23D8.9b	720	I: 9982656-9982683
CDS:T23D8.9c	T23D8.9c	2037	I: 9980494-9980576

86 RNAi Result

• WBRNAi00083470
• WBRNAi00083472
• WBRNAi00083475
• WBRNAi00083476
• WBRNAi00101795
• WBRNAi00101805
• WBRNAi00026377
• WBRNAi00000103
• WBRNAi00000105
• WBRNAi00053926
• WBRNAi00026371
• WBRNAi00087871
• WBRNAi00099947
• WBRNAi00100475
• WBRNAi00094022
• WBRNAi00101461
• WBRNAi00081384
• WBRNAi00081385
• WBRNAi00087713
• WBRNAi00098962
• WBRNAi00100849
• WBRNAi00101135
• WBRNAi00099147
• WBRNAi00101240
• WBRNAi00101259
• WBRNAi00101278
• WBRNAi00101309
• WBRNAi00101311
• WBRNAi00101310
• WBRNAi00101313

61 Allele

• gk962858
• gk962706
• gk963902
• gk963849
• h12040
• h3245
• gk962844
• q544
• q736
• q7
• gk963993
• WBVar01432660
• WBVar01432661
• WBVar01432662
• WBVar01432663
• WBVar01283704
• WBVar01283702
• WBVar00064934
• WBVar00064939
• os63
• gk394820
• gk350124
• gk585620
• gk429326
• gk497468
• gk640193
• gk573682
• gk848214
• gk379876
• gk853389

1 Chromosome

• WormBase ID: I
• Organism: Caenorhabditis elegans
• Length (nt): 15072434

1 Chromosome Location

• Feature . Primary Identifier: WBGene00006379
• Start: 9980063
• End: 9984794
• Strand: -1

3 Data Sets

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

1 Downstream Intergenic Region

• WormBase ID: intergenic_region_chrI_9979663..9980062
• Length (nt): 400
• Chromosome Location: I: 9979663-9980062
• Organism: Caenorhabditis elegans

170 Expression Clusters

Regulated By Treatment	Description	Algorithm	Primary Identifier
	Genes with expression altered >= 3-fold in dpy-10(e128) mutants.	Data across the wild type series was analyzed using the Significance analysis of Microarrays (SAM) algorithm (to calculate the False Discovery Rate (FDR)).	WBPaper00035873:dpy-10_regulated
	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
	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:bodywall-muscle_L1-larva_expressed
	Transcripts that showed significantly higher expression in somatic gonad precursor cells (SGP) vs. head mesodermal cells (hmc).	DESeq2, fold change >= 2, FDR <= 0.01.	WBPaper00056826:SGP_biased
	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
	Genes with expression level regulated by genotype (N2 vs CB4856) 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_regulated_aging
	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)
Bacteria infection: Bacillus thuringiensis	mRNAs that showed significantly decreased expression after pathogenic bacteria Bacillus thuringiensis infections comparing to non pathogenic BT (BT247(1 to 10 mix) vs BT407 12h), according to RNAseq.	Cuffdiff, ajusted p-value < 0.01.	WBPaper00046497:B.thuringiensis_0.1mix_downregulated_12h
	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
Bacteria infection: Bacillus thuringiensis	mRNAs that showed significantly decreased expression after pathogenic bacteria Bacillus thuringiensis infections comparing to non pathogenic BT (BT247(1 to 2 mix) vs BT407 12h), according to RNAseq.	Cuffdiff, ajusted p-value < 0.01.	WBPaper00046497:B.thuringiensis_0.5mix_downregulated_12h
	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
	Significantly differentially expressed genes as determined by microarray analysis of wild-type and cde-1 mutant germlines.	RNAs that changed at least 2-fold with a probability of p < 0.05 were considered differentially regulated between wildtype and cde-1.	WBPaper00035269:cde-1_regulated
	Genes down regulated by mir-243(n4759).	RNAs that changed at least 2-fold with a probability of p > 0.05 in three biological replicates were considered differentially regulated between wild-type and mir-243.	WBPaper00036130:mir-243_down_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
25C vs. 20C	Transcripts that showed significantly increased expression in 1-day post L4 adult hermaphrodite N2 grown at 25C, comparing to in N2 animals grown at 20C.	CuffDiff, fold change > 2.	WBPaper00065096:25C_vs_20C_upregulated
	Transcripts that showed significantly increased expression in 10-days post L4 adult hermaphrodite N2 grown at 20C, comparing to in 1-day post L4 adult hermaphrodite N2 animals grown at 20C.	CuffDiff, fold change > 2.	WBPaper00065096:Day10_vs_Day1_upregulated
	Transcripts that showed significantly decreased expression in tetraploid N2 comparing to diploid N2 animals at L4 larva stage.	DESeq2 R package (1.20.0), fold change > 2, and FDR < 0.05.	WBPaper00066110:tetraploid_vs_diploid_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:coelomocytes_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 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 significantly decreased expression in the neurons of bcat-1(RNAi) animals at 5-days post L4 adult hermaphrodite stage, comparing to animals injected with empty vector.	DESeq2. FDR < 0.05.	WBPaper00060459:bcat-1(RNAi)_downregulated
	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
	Transcripts that showed decreased expression in hlh-11(ko1) knockout strain comparing to in wild type background.	DESeq2, FDR < 0.05	WBPaper00060683:hlh-11(ko1)_downregulated
Bacteria infection: Enterococcus faecalis OG1RF. Exposure for 16 hours.	Transcripts that showed significantly decreased expression in hpx-2(dg047) after animals were exposed to E. faecalis OG1RF for 16 hours comparing to exposure to E. Coli OP50.	Cuffcompare and Cuffdiff	WBPaper00056090:E.faecalis_downregulated_hpx-2(dg047)
	Genes found to be regulated by low-copy overexpression of sir-2.1 with p < 0.014.	N.A.	WBPaper00026929:sir-2.1_overexpression_regulated
Heat shock: 34C 30min.	Transcripts that showed significantly increased expression in L2 larva stage C. elegans animals after incubated in a 34C water bath for 30min.	DESeq2 v 1.18.1, fold change > 2, FDR < 0.01.	WBPaper00058955:heatshock_upregulated_CE
	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

12 Expression Patterns

• Primary Identifier: Expr4710
• Pattern: VNS::SYS-1 was not found in SGPs of newly hatched L1 larvae (n = 23) but was detectable ~1 h before their division (n = 48). VNS::SYS-1 was present in both nucleus and cytoplasm but was enriched in granules often localized to the proximal edge of the SGP. During the SGP division, VNS::SYS-1 localized to large puncta in each of the two daughters, at a position suggesting localization to the centrosome; no SYS-1 asymmetry was seen at this point. After the division, VNS::SYS-1 was easily seen in distal daughters but either was not seen or was barely detectable in proximal daughters. In the next division, VNS::SYS-1 was in the distal-most SGP granddaughters (Z1aa, Z4pp) but not their proximal sisters (Z1ap, Z4pa); by contrast, VNS::SYS-1 was not in SGP proximal granddaughters (Z1pa, Z1pp, Z4aa, Z4ap). VNS::SYS-1 was expressed in many cells during embryogenesis and larval development. Furthermore, SYS-1 was asymmetrically distributed in daughters of many asymmetric divisions, and SYS-1 asymmetry was the reciprocal of POP-1 asymmetry in all cases. For example, the E blastomere has lower POP-1 than the MS blastomere, but E has higher SYS-1 than MS. In addition, posterior daughters in the embryonic hypodermis and larval T cell have lower POP-1 than anterior daughters, but those posterior daughters have higher SYS-1 than anterior daughters. A similar situation holds true for distal daughters and granddaughters in the vulval lineage.
• Subcellular Localization: As seen in the SGPs, SYS-1 localized to large puncta in each daughter at a predicted centrosomal position, and in all cases, SYS-1 levels were similar at the two putative centrosomes.

• Primary Identifier: Expr2035324
• 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: Expr1032576
• Pattern: Tiling arrays expression graphs

• Primary Identifier: Expr8390
• Remark: Picture: Figure 3A.
• Pattern: A rescuing fluorescent SYS-1 fusion protein (VNS::SYS-1) is also asymmetrically localized in a high (P7.pa)/low (P7.pp) pattern reciprocal to POP-1.

• Primary Identifier: Expr11051
• Pattern: A transgenic strain expressing a SYS-1::GFP fusion protein shows faint cytoplasmic expression in hyp8 and hyp11 but not in hyp9 or hyp10.

• Primary Identifier: Expr1020461
• Pattern: Developmental gene expression time-course. Raw data can be downloaded from ftp://caltech.wormbase.org/pub/wormbase/datasets-published/levin2012

• Primary Identifier: Expr12415
• Pattern: Following asymmetric division of their mother cell, the anterior NBSMDD/AIY neuroblast (ABplpapaaa, ABprpapaaa) displays a high nuclear concentration of POP-1 and low concentration of SYS-1 while the posterior NBSIAD/SIBV neuroblast (ABplpapaap, ABprpapaap) has a low nuclear concentration of POP-1 and high concentration of SYS-1.

• Primary Identifier: Expr1157471
• Pattern: Developmental gene expression time-course. Raw data can be downloaded from ftp://caltech.wormbase.org/pub/wormbase/datasets-published/hashimshony2015

• Primary Identifier: Expr12450
• Remark: Asymmetric localization.
• Subcellular Localization: SYS-1 is normally nuclear localized with an asymmetry that favors stronger localization in the posterior nucleus.

• Primary Identifier: Expr12537
• Subcellular Localization: SYS-1 colocalized with gamma-tubulin at mitotic centrosomes in vivo. Interestingly, SYS-1 puncta consistently appeared larger than those of gamma-tubulin, consistent with the idea that SYS-1 localizes to the centrosome pericentriolar material (PCM). YFP::SYS-1 simultaneously localized to both the nucleus and centrosomes in cells at prometaphase. SYS-1 colocalized with gamma-tubulin at mitotic centrosomes in vivo. Interestingly, SYS-1 puncta consistently appeared larger than those of gamma-tubulin, consistent with the idea that SYS-1 localizes to the centrosome pericentriolar material (PCM).

• Primary Identifier: Expr2017188
• 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: Expr11812
• Subcellular Localization: Between divisions, SYS-1 localizes weakly to the cortex and cytoplasm. Prior to metaphase, SYS-1 localizes to the nucleus and cytoplasm. During metaphase and anaphase, SYS-1 localizes to bright puncta that behave similarly to centrosomes. Centrosomal localization was confirmed by colocalizing mCherry::SYS-1 with GFP-tagged beta-tubulin, consistent with SYS-1 centrosomal localization observed in other tissues (Phillips et al., 2007; Huang et al., 2007). Asymmetric localization of SYS-1 is established during early telophase when SYS-1 levels are rapidly lowered in the anterior daughter while SYS-1 levels increase in the nuclear region of the posterior daughter. SYS-1 asymmetry is maintained after cytokinesis into late telophase when it localizes primarily to the nucleus of the posterior daughter. Within an hour after division, nuclear SYS-1 decreases and localization increases at the cortex and cytoplasm, but SYS-1 eventually becomes undetectable two hours after division.

45 GO Annotation

0 Homologues

1 Locations

• Feature . Primary Identifier: WBGene00006379
• Start: 9980063
• End: 9984794
• Strand: -1

45 Ontology Annotations

0 Regulates Expr Cluster

1 Sequence

• Length: 4732

1 Sequence Ontology Term

• Name: gene

5 Strains

• WBStrain00022636
• WBStrain00022617
• WBStrain00022575
• WBStrain00022587
• WBStrain00022589

1 Upstream Intergenic Region

• WormBase ID: intergenic_region_chrI_9984795..9986342
• Length (nt): 1548
• Chromosome Location: I: 9984795-9986342
• Organism: Caenorhabditis elegans