WormMine: Gene WBGene00012888

• WormBase Gene ID: WBGene00012888
• Gene Name: sas-6
• Sequence Name: Y45F10D.9
• Brief Description: sas-6 is a member of an evolutionarily conserved family of proteins containing a coiled-coil region and a novel PISA (present in SAS-6) motif conserved in similar proteins in at least eight other species that contain basal bodies or centrioles; SAS-6 activity, along with that of ZYG-1, SAS-4, SAS-5, and SPD-2, is essential for centriole duplication; SAS-6 functions in a dose-dependent manner and localizes to centriolar cylinders; SAS-6 co-localizes to centrioles with SAS-4 and SAS-5, and is mutually dependent upon SAS-5, with which it interacts physically, for centriolar localization; SAS-6 localization also requires the activity of the ZYG-1 kinase; in addition to the early embryo, SAS-6 is also detected in sperm; phosphorylation of SAS-6 is critical for centriole formation and thus for faithful cell division; the kinase ZYG-1 phosphorylates SAS-6 at serine 123 and this phosphorylation event is crucial for robust centriole formation and to ensure the maintenance of SAS-6 at the emerging centriole.
• Organism: Caenorhabditis elegans
• Automated Description: Enables identical protein binding activity and protein domain specific binding activity. Involved in centriole replication; protein localization; and regulation of cell cycle. Located in centriole and cytoplasm.
• Biotype: SO:0001217
• Genetic Position: IV :10.8599 ±0.001963
• Length (nt): 1787

1 Organism

• Name: Caenorhabditis elegans
• Taxon Id: 6239

1 Synonyms

• Value: WBGene00012888

Genomics

1 Transcripts

WormMine ID	Sequence Name	Length (nt)	Chromosome Location
Transcript:Y45F10D.9.1	Y45F10D.9.1	1559	IV: 13786945-13788731

Other

1 CDSs

WormMine ID	Sequence Name	Length (nt)	Chromosome Location
CDS:Y45F10D.9	Y45F10D.9	1479	IV: 13787003-13787146

20 RNAi Result

• WBRNAi00009337
• WBRNAi00026710
• WBRNAi00056609
• WBRNAi00099866
• WBRNAi00100872
• WBRNAi00099260
• WBRNAi00099664
• WBRNAi00099462
• WBRNAi00084057
• WBRNAi00000217
• WBRNAi00037101
• WBRNAi00100124
• WBRNAi00100498
• WBRNAi00065068
• WBRNAi00100311
• WBRNAi00088802
• WBRNAi00084056
• WBRNAi00100685
• WBRNAi00101059
• WBRNAi00113852

35 Allele

• gk964078
• gk963546
• gk963547
• gk964500
• gk962765
• gk964111
• gk964110
• gk963691
• gk436015
• gk667198
• gk688135
• gk599904
• gk777169
• gk322365
• gk877649
• gk894736
• gk837614
• gk782536
• gk894150
• gk354397
• gk396489
• gk963692
• WBVar01821419
• tm4896
• tm11231
• h17150
• WBVar00193954
• or1167
• gk217105
• gk217106

1 Chromosome

• WormBase ID: IV
• Organism: Caenorhabditis elegans
• Length (nt): 17493829

1 Chromosome Location

• Feature . Primary Identifier: WBGene00012888
• Start: 13786945
• End: 13788731
• 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

137 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 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
	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:AVE-neuron_L1-larva_expressed
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
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
	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
	Transcripts expressed in hypodermis, according to PAT-Seq analysis using Pdpy-7-GFP-3XFLAG mRNA tagging.	Cufflinks FPKM value >=1.	WBPaper00050990:hypodermis_expressed
	Transcripts expressed in intestine, according to PAT-Seq analysis using Pges-1-GFP-3XFLAG mRNA tagging.	Cufflinks FPKM value >=1.	WBPaper00050990:intestine_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 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)
Bacteria diet: Escherichia coli HB101. Fed for 30 generations.	Transcripts that showed significantly decreased expression after fed by bacteria E. coli HB101 for 30 generations comparing to animals fed by E. coli OP50.	DESeq2 fold change > 2, p-value < 0.01.	WBPaper00061007:HB101_downregulated
Bacteria diet: Sphingomonas aquatilis Yellow. Fed for 30 generations.	Transcripts that showed significantly decreased expression after fed by bacteria Sphingomonas aquatilis (Yellow) for 30 generations comparing to animals fed by E. coli OP50.	DESeq2 fold change > 2, p-value < 0.01.	WBPaper00061007:S.aquatilis_downregulated
	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
	Transcripts that showed significantly altered expression after 24 hour exposure to stavudine (d4T) starting at L1 lava stage.	DESeq	WBPaper00053302:stavudine_24h_regulated
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 (embryonic 0hr 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:germline-precursors_blastula-embryo_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:intestine_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 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 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

13 Expression Patterns

• Primary Identifier: Expr8010
• Remark: Picture: Figure 2A to 2C.. SAS-6 tagged with GFP at the C terminus also exhibited this loss, indicating that it is not caused by a site-specific cleavage event that liberates the GFP and leaves behind a fragment of SAS-6.
• Subcellular Localization: GFP:SAS-6 is first detected at the site of new centriole assembly at S phase onset and its levels steadily increase throughout S phase coincident with the time previously reported for the appearance and expansion of the central tube. As embryos transition into prophase, levels of centriolar GFP:SAS-6 plateau for ~400 s, which is concurrent with compaction of the nuclear chromatin into discrete linear chromosomes. During the second half of mitotic prophase, the amount of centriolar GFP:SAS-6 declines, reaching a low point ~50 s after nuclear envelope breakdown, when the amount of centriolar SAS-6 is ~40% of that observed during the plateau.

• Primary Identifier: Expr1035700
• Pattern: Tiling arrays expression graphs

• Primary Identifier: Expr3188
• Subcellular Localization: Antibodies were raised against C. elegans SAS-6 that recognize a single band of the predicted size in wild-type embryonic extracts, which is severely diminished in sas-6(RNAi) embryonic extracts. These antibodies preferentially label a dot in the centre of the centrosome in early embryos, as well as in the cytoplasm to a lesser extent. The signal is vastly diminished in sas-6(RNAi) embryos, indicating specificity. Furthermore, SAS-6 colocalizes with GFP::SAS-4 and GFP::SAS-5 in sperm cells. The distribution of SAS-6 appears to be more restricted than that of either fusion protein, indicating that SAS-6 may be present in only part of the centrioles, although immunoelectron microscopy will be needed to ascertain this point.

• Primary Identifier: Expr3157
• Subcellular Localization: SAS-6 colocalized with SAS-4 to small focal structures in the center of the centrosome throughout the embryonic cell cycle. SAS-6 also colocalized with SAS-4 in sperm. Immuno-EM on embryos from wild-type hermaphrodites prepared by high-pressure freezing/freeze substitution confirmed the result. In sections containing centrioles, gold particles were observed associated with the centriolar cylinders. The combination of light microscopy and EM analysis indicates that SAS-6, like SAS-4 and SAS-5, is a bona fide centriolar protein.

• Primary Identifier: Expr3189
• Pattern: GFPSAS-6 is essentially not expressed in male germ cells.
• Subcellular Localization: Staining of transgenic embryos with GFP antibodies confirmed the centriolar enrichment, as well as the cytoplasmic distribution. As expected, GFPSAS-6 colocalizes with the centriolar component SAS-4. Quantification of fluorescence intensity in such recordings established that levels of centriolar GFPSAS-6 remain constant throughout the cell cycle.

• Primary Identifier: Expr1160074
• Pattern: Developmental gene expression time-course. Raw data can be downloaded from ftp://caltech.wormbase.org/pub/wormbase/datasets-published/hashimshony2015

• Primary Identifier: Expr1200234
• Pattern: Data from the TransgeneOme project

• Primary Identifier: Expr2033838
• 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: Expr2015603
• 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: Expr14334
• Subcellular Localization: SAS-6::HA displays a stereotypical centrosomal and cytoplasmic localization in 1-cell C. elegans embryos.

• Primary Identifier: Expr3664
• Subcellular Localization: Centriolar.

• Primary Identifier: Expr1016538
• Pattern: Developmental gene expression time-course. Raw data can be downloaded from ftp://caltech.wormbase.org/pub/wormbase/datasets-published/levin2012

• Primary Identifier: Expr16124
• Subcellular Localization: Consistent with previous observations, we found that in control embryos, GFP-SAS-6 was initially detected at centrioles during the first S phase.

20 GO Annotation

5 Homologues

1 Locations

• Feature . Primary Identifier: WBGene00012888
• Start: 13786945
• End: 13788731
• Strand: -1

20 Ontology Annotations

0 Regulates Expr Cluster

1 Sequence

• Length: 1787

1 Sequence Ontology Term

• Name: gene

3 Strains

• WBStrain00034787
• WBStrain00037308
• WBStrain00047273

1 Upstream Intergenic Region

• WormBase ID: intergenic_region_chrIV_13788732..13788906
• Length (nt): 175
• Chromosome Location: IV: 13788732-13788906
• Organism: Caenorhabditis elegans