WormMine: Gene WBGene00006827

• WormBase Gene ID: WBGene00006827
• Gene Name: unc-98
• Sequence Name: F08C6.7
• Brief Description: unc-98 encodes a protein with four C2H2 zinc fingers and several possible nuclear localization and export sequences; UNC-98 is required for normal mobility, M-line, and dense body (Z-disk analog) structures; UNC-98 binds the C-terminal portion of myosin heavy chain, as well as a number of proteins that localize to the base of dense bodies and M lines, including UNC-97/PINCH, suggesting that in vivo UNC-98 functions to link myosin thick filaments to an integrin-associated protein complex at the muscle cell membrane; UNC-98 also interacts with UNC-96, UNC-15/paramyosin, the unconventional myosin HUM-6 and the zinc-finger protein MEP-1; UNC-98 localizes to M-lines, muscle cell nuclei, and perhaps also to dense bodies.
• Organism: Caenorhabditis elegans
• Automated Description: Enables cytoskeletal protein binding activity. Involved in several processes, including locomotory behavior; myofibril assembly; and post-embryonic body morphogenesis. Located in M band and nucleus. Expressed in anal depressor muscle; body wall musculature; head muscle; and vulval muscle.
• Biotype: SO:0001217
• Genetic Position: X :-1.49623 ±0.009635
• Length (nt): 3246

1 Organism

• Name: Caenorhabditis elegans
• Taxon Id: 6239

1 Synonyms

• Value: WBGene00006827

Genomics

1 Transcripts

WormMine ID	Sequence Name	Length (nt)	Chromosome Location
Transcript:F08C6.7.1	F08C6.7.1	1244	X: 7570374-7573619

Other

1 CDSs

WormMine ID	Sequence Name	Length (nt)	Chromosome Location
CDS:F08C6.7	F08C6.7	933	X: 7570640-7570972

15 RNAi Result

• WBRNAi00089768
• WBRNAi00061429
• WBRNAi00001323
• WBRNAi00043984
• WBRNAi00061430
• WBRNAi00012874
• WBRNAi00030641
• WBRNAi00101831
• WBRNAi00089954
• WBRNAi00090114
• WBRNAi00090272
• WBRNAi00090369
• WBRNAi00090416
• WBRNAi00090463
• WBRNAi00090510

65 Allele

• gk964260
• gk963896
• gk963732
• gk963873
• gk963874
• gk964088
• gk964087
• WBVar01690170
• sf19
• su130
• tm601
• h18117
• gk285514
• WBVar01883641
• gk285513
• WBVar01883642
• gk285512
• WBVar01883643
• gk285511
• WBVar01883644
• gk285510
• gk285509
• gk285508
• WBVar01883639
• gk285507
• WBVar01883640
• gk956266
• gk285517
• gk285516
• WBVar01816004

1 Chromosome

• WormBase ID: X
• Organism: Caenorhabditis elegans
• Length (nt): 17718942

1 Chromosome Location

• Feature . Primary Identifier: WBGene00006827
• Start: 7570374
• End: 7573619
• Strand: -1

3 Data Sets

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

1 Downstream Intergenic Region

• WormBase ID: intergenic_region_chrX_7569723..7570373
• Length (nt): 651
• Chromosome Location: X: 7569723-7570373
• Organism: Caenorhabditis elegans

130 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
	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 after animals were treated with 50uM Rifampicin and 250uM Allantoin from day 1 to day 3 adult hermaphradite.	DESeq2(v1.14.1), fold change > 2, p-value < 0.05	WBPaper00055354:Rifampicin-Allantoin_upregulated
	Proteins interacting with NHR-49-GFP according to co-IP and LC-MS.	N.A.	WBPaper00064071:NHR-49_interacting
	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 GABAergic neuron, according to PAT-Seq analysis using Punc-47-GFP-3XFLAG mRNA tagging.	Cufflinks FPKM value >=1.	WBPaper00050990:GABAergic-neuron_expressed
	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 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
	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
	Strictly maternal class (SM): genes that are the subset of maternal genes that are not also classified as embryonic.	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_SM
	Transcripts that showed significantly decreased expression in N2 animals exposed to 0.1mM Paraquat from hatching to reaching adult stage.	DESeq2 version 1.22.2, p < 0.05	WBPaper00064716:paraquat_downregulated
	Significantly upregulated genes from clk-1(qm30) microarrays using SAM algorithm with an FDR < 0.1 from adult-only chips.	SAM algorithm with an FDR < 0.1.	WBPaper00033065:clk-1(qm30)_upregulated
	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
	Expression Pattern Group C, enriched for genes involved in metabolic processes.	The significance (P 0.0001) of the relative age (time) was used to determine if a gene was differentially expressed between the three age (time) groups. The effect of this factor explaining gene expression differences was used to determine if the expression went up or down during the two age/time periods (t1 - t2 and t2 -t3). Authors used a permutation approach to determine the thresholds for the different mapping strategies. For each of the used models for eQTL mapping, authors used 23,000 permutations. For each permutation, authors randomly picked a spot; each spot could only be picked once. The gene expression and relative lifespan values were than randomly distributed over the RILs (and time points) and used for mapping. In this way, authors obtained a threshold for each of the explaining factors. For the single time points, authors used a FDR of 0.01 to adjust for multiple testing. The genome-wide threshold for this FDR is -log10 P = 3.8 for each of the three time points. For the combined models (t1 to t2 and t2 to t3), authors used a genome-wide threshold of -log10 P = 4, which resembles an FDR of 0.006, 0.001, and 0.006 for marker, age, and the interaction between marker and age, respectively. To determine the threshold for the single gene examples, authors used 1000 permutations as in the genome-wide threshold. The difference is that they use the gene under study in all of the permutations. The P-values for the gene specific thresholds were determined at FDR = 0.05.	WBPaper00036286:Pattern_C
	Transcripts depleted in purified oocyte P bodies comparing to in whole oocytes.	DESeq2, FDR < 0.05, fold change > 2.	WBPaper00065975:P-body_vs_oocyte_depleted
	Transcripts depleted in purified oocyte P bodies comparing to in the whole animal.	DESeq2, FDR < 0.05, fold change > 2.	WBPaper00065975:P-body_vs_WholeAnimal_depleted
	Transcripts detected in body muscle nuclei according to a nuclear FACS-based strategy.	Cufflinks	WBPaper00065120:body-muscle-transcriptome
Reduced humidity (98% relative humidity).	Genes that were down-regulated after one day exposure to reduced humidity (98% relative humidity) according to microarray analysis.	Multiple hypothesis testing with the Benjamini-Hochberg correction was applied on calculated p-values. A change in the expression level was considered to be significant if the adjusted p-value was less than 0.001.	WBPaper00044578:reduced-humidity_downregulated_microarray
	Transcripts that showed significantly increased expression in animals with germline-specific inx-14(RNAi) comparing to in aniamls fed with control vector, both exposed to PA14 infection.	DESeq2. Differentially-expressed genes (DEG) were identified based on two criteria: FDR (False discovery rateusing Benjamini-Hochberg adjusted p-values) < 0.01 and absolute value of log2(Fold Change) > 1.	WBPaper00066146:germline-inx-14(RNAi)_upregulated_PA14
	Proteins that showed significantly decreased expression in 1-day-old sek-1(km4) adults comparing to in wild type animals, both with 6 hours of cisplatin treatment.	The differential expression analysis was performed in R. Differentially expressed proteins were identified by using a two-sided t-test on log-transformed data.	WBPaper00065373:sek-1(km4)_downregulated_cisplatin
	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 (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:hypodermis_L3-L4-larva_expressed
	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:PVD-OLL-neurons_L3-L4-larva_expressed
	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

13 Expression Patterns

• Primary Identifier: Expr7497
• Remark: Clone: pUL#JRH/AA9
• Pattern: Many muscles from late embryo to adult - weaker expression in adult. Including: body wall muscles, some vulval, rectal, anterior head muscles.

• Primary Identifier: Chronogram67
• Remark: Original chronogram file: chronogram.1079.xml
• Reporter Gene: [F08C6.7:gfp] transcriptional fusion.

• Primary Identifier: Chronogram56
• Remark: Original chronogram file: chronogram.1048.xml
• Reporter Gene: [F08C6.7:gfp] transcriptional fusion.

• Primary Identifier: Chronogram22
• Remark: Original chronogram file: chronogram.1017.xml
• Reporter Gene: [F08C6.7:gfp] transcriptional fusion.

• Primary Identifier: Expr2036060
• 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: Expr1032891
• Pattern: Tiling arrays expression graphs

• Primary Identifier: Expr2577
• Remark: Five independent lines in a wild-type background showed the same pattern of expression, although the level of expression varied somewhat between transgenic lines. Significantly, the same UNC-98::GFP was used to create two independent lines in an unc-98(su130) background, and both lines are fully rescued with respect to the muscle phenotype. In addition, the UNC-98::GFP showed that same pattern of expression and intracellular localization in both wild-type and unc-98(su130) backgrounds.
• Pattern: Expression was first observed in the developing embryo at the 1.5- to 2-fold stage, also observed in larvae and adults. Expression observed in body wall muscle, anal depressor muscle and vulval muscles.
• Subcellular Localization: Expression was first observed in the developing embryo at the 1.5- to 2-fold stage, in which the UNC-98-GFP protein seemed localized to filamentous tracts, which generally follow myosin heavy chain A antibody staining, and therefore are interpreted to be located in myofibrils. Additionally, expression is seen in undefined puncta located along the filamentous tracts. In larvae and adults, expression was seen in body wall muscle, and in addition, anal depressor muscle and vulval muscles. Within adult body wall muscle, the UNC-98-GFP fusion localizes to dense bodies and M-lines. Within these muscle cells, prominent localization of the UNC-98-GFP in the nucleus was also seen. The UNC-98-GFP colocalizes with the DNA-binding dye DAPI. The signal is excluded from what seems to be the nucleolus and the UNC-98-GFP signal is discontinuous. This nuclear localization is consistent with the presence of the NLS sequences noted above. During development, the nuclear localization of UNC-98::GFP begins at the late L2 to early L3 larval stages.

• Primary Identifier: Expr1200172
• Pattern: Data from the TransgeneOme project

• Primary Identifier: Chronogram287
• Remark: Original chronogram file: chronogram.131.xml
• Reporter Gene: [F08C6.7:gfp] transcriptional fusion.

• Primary Identifier: Expr2017924
• 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: Expr1015982
• Pattern: Developmental gene expression time-course. Raw data can be downloaded from ftp://caltech.wormbase.org/pub/wormbase/datasets-published/levin2012

• Primary Identifier: Expr1147957
• Pattern: Developmental gene expression time-course. Raw data can be downloaded from ftp://caltech.wormbase.org/pub/wormbase/datasets-published/hashimshony2015

• Primary Identifier: Expr2578
• Remark: EU131 staining was undetectable in the muscle of each of the unc-98 mutants, consistent with the absence of the 37-kDa polypeptide on Western blots, and thus demonstrating the specificity of the antibodies for UNC-98 protein.
• Subcellular Localization: In wild-type muscle fixed with methanol and paraformaldehyde on whole worms, or alternatively, ethanol or methanol on worm frozen sections, anti-UNC-98 staining was only found at the M-line; no staining was observed at the dense bodies or in nuclei. However, when frozen sections were fixed with n-heptane, staining of M-lines and, in addition, the muscle cell nuclei was observed. Thus, it would seem that there is indeed UNC-98 in the nucleus, but the epitopes detected by these antibodies are inactivated by the usual fixatives. UNC-98 antibodies were used to stain animals genotypically unc-98(su130) that were rescued with a transgenic array carrying the 8.1-kb unc-98rescuing fragment and rol-6 marker DNA. Because extrachromosomal arrays contain multiple expressed copies of an introduced gene, these unc-98-rescued animals are likely to express higher than wildtype levels of UNC-98. In these unc-98-rescued animals, anti-UNC-98 antibodies localize to all three structures labeled with UNC-98-GFP: M-lines, nuclei, and dense bodies. When used against wild-type embryos, these antibodies stain filamentous structures, presumably myofibrils, as early as the 1.5- to 2-fold stage. In wild-type adult animals fixed with methanol and paraformaldehyde, these antibodies stain the M-line region, colocalizing with UNC-89, a previously described component of the M-line region.

20 GO Annotation

0 Homologues

1 Locations

• Feature . Primary Identifier: WBGene00006827
• Start: 7570374
• End: 7573619
• Strand: -1

20 Ontology Annotations

0 Regulates Expr Cluster

1 Sequence

• Length: 3246

1 Sequence Ontology Term

• Name: gene

6 Strains

• WBStrain00029994
• WBStrain00035296
• WBStrain00035295
• WBStrain00035294
• WBStrain00007704
• WBStrain00008391

0 Upstream Intergenic Region