WormMine: Gene WBGene00006974

• WormBase Gene ID: WBGene00006974
• Gene Name: zen-4
• Sequence Name: M03D4.1
• Brief Description: zen-4 encodes a kinesin-like protein that is a member of the kinesin-6 subfamily of plus-end-directed microtubule motors; loss-of-function mutations and RNAi experiments indicate that ZEN-4 is required for polar body extrusion after meiotic divisions, for completion of cytokinesis after mitosis, and for formation and/or maintenance of spindle midzone microtubules; in addition, zen-4 functions together with cyk-1 to regulate pronuclear migration; during mitosis, ZEN-4 is detected at the spindle midzone where it co-localizes with spindle microtubules, and ZEN-4 persists at the midbody remnant once cell division is complete; ZEN-4 is also occasionally seen at centrosomes in interphase cells; initial localization of ZEN-4 to the spindle midzone requires activity of the Aurora-related kinase AIR-2 which physically interacts with ZEN-4 in vitro.
• Organism: Caenorhabditis elegans
• Automated Description: Enables several functions, including identical protein binding activity; microtubule binding activity; and plus-end-directed microtubule motor activity. Involved in several processes, including nuclear division; pronuclear migration; and regulation of actomyosin contractile ring contraction. Located in cleavage furrow; microtubule cytoskeleton; and midbody. Part of centralspindlin complex. Expressed in germ cell and gonad. Human ortholog(s) of this gene implicated in congenital dyserythropoietic anemia type III. Is an ortholog of human KIF23 (kinesin family member 23).
• Biotype: SO:0001217
• Genetic Position: IV :3.00419 ±0.004471
• Length (nt): 3563

1 Organism

• Name: Caenorhabditis elegans
• Taxon Id: 6239

1 Synonyms

• Value: WBGene00006974

Genomics

9 Transcripts

WormMine ID	Sequence Name	Length (nt)	Chromosome Location
Transcript:M03D4.1c.1	M03D4.1c.1	2682	IV: 6118215-6121775
Transcript:M03D4.1f.1	M03D4.1f.1	2876	IV: 6118215-6121777
Transcript:M03D4.1d.1	M03D4.1d.1	2882	IV: 6118215-6121777
Transcript:M03D4.1e.1	M03D4.1e.1	2992	IV: 6118217-6121749
Transcript:M03D4.1a.1	M03D4.1a.1	2674	IV: 6118217-6121775
Transcript:M03D4.1b.2	M03D4.1b.2	2976	IV: 6118219-6121741
Transcript:M03D4.1b.1	M03D4.1b.1	3258	IV: 6118219-6121777
Transcript:M03D4.1f.2	M03D4.1f.2	3118	IV: 6118219-6121777
Transcript:M03D4.1d.2	M03D4.1d.2	3119	IV: 6118220-6121773

Other

6 CDSs

WormMine ID	Sequence Name	Length (nt)	Chromosome Location
CDS:M03D4.1a	M03D4.1a	2328	IV: 6118224-6118666
CDS:M03D4.1b	M03D4.1b	2319	IV: 6118224-6118666
CDS:M03D4.1d	M03D4.1d	2364	IV: 6118224-6118666
CDS:M03D4.1f	M03D4.1f	2358	IV: 6118224-6118666
CDS:M03D4.1c	M03D4.1c	2334	IV: 6118224-6118666
CDS:M03D4.1e	M03D4.1e	2325	IV: 6118224-6118666

47 RNAi Result

• WBRNAi00034401
• WBRNAi00078443
• WBRNAi00064012
• WBRNAi00086669
• WBRNAi00086682
• WBRNAi00099939
• WBRNAi00100452
• WBRNAi00087252
• WBRNAi00088837
• WBRNAi00110353
• WBRNAi00063891
• WBRNAi00100826
• WBRNAi00101228
• WBRNAi00101266
• WBRNAi00101285
• WBRNAi00099333
• WBRNAi00099535
• WBRNAi00099737
• WBRNAi00101247
• WBRNAi00101127
• WBRNAi00080585
• WBRNAi00050865
• WBRNAi00004982
• WBRNAi00009000
• WBRNAi00025983
• WBRNAi00114571
• WBRNAi00111830
• WBRNAi00065742
• WBRNAi00100078
• WBRNAi00100265

51 Allele

• gk964500
• gk963722
• gk963417
• gk963375
• gk963416
• px47
• gk962781
• gk962782
• WBVar00189313
• gk930988
• gk557722
• gk809795
• gk572834
• gk521102
• gk454942
• gk863406
• gk629797
• gk573922
• gk518931
• gk798644
• gk740190
• gk667753
• gk473164
• gk791820
• gk925934
• gk566113
• gk489674
• gk636815
• gk440848
• gk349634

1 Chromosome

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

1 Chromosome Location

• Feature . Primary Identifier: WBGene00006974
• Start: 6118215
• End: 6121777
• 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

210 Expression Clusters

Regulated By Treatment	Description	Algorithm	Primary Identifier
	oocyte proteins identified by two or more unique peptides during proteomics study.	In the pooled data set, 1453 C. elegans proteins were identified with a probability >= 0.9 according to ProteinProphet, of which 1165 proteins were identified by more than one unique peptide.	WBPaper00038289:oocyte_protein
	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
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
	Proteins interacting with NHR-49-GFP according to co-IP and LC-MS.	N.A.	WBPaper00064071:NHR-49_interacting
	Transcripts expressed in intestine, according to PAT-Seq analysis using Pges-1-GFP-3XFLAG mRNA tagging.	Cufflinks FPKM value >=1.	WBPaper00050990:intestine_expressed
	Transcripts expressed in seam cells, according to PAT-Seq analysis using Pgrd-10-GFP-3XFLAG mRNA tagging.	Cufflinks FPKM value >=1.	WBPaper00050990:seam_expressed
	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 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 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 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 infection: Photorhabdus luminescens	Genes down-regulated in animals infected with Photorhabdus luminescens compared to the E. coli OP50 control after 24h of infection.	MAANOVA and BRB-Array-Tools.	WBPaper00030985:Photorhabdus_luminescens_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 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
Transgeneration hypoxia treatment.	Transcripts that are significantly upregulated in F1 animals after P0 parents were exposed to 0.1% oxygen for 16 hours at L4 larva stage.	For calling the significant differentially expressed genes (DEGs),the false discovery rate (FDR) after multiple testing correction was set as 0.05 and analyzed in edgeR.	WBPaper00064871:hypoxia_upregulated_F1
	Transcripts that showed significantly altered expression after 24 hour exposure to stavudine (d4T) starting at L1 lava stage.	DESeq	WBPaper00053302:stavudine_24h_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
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
	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
	Proteins interacting with HA-PPM-1.D.	N.A.	WBPaper00062498:PPM-1.D_interacting

15 Expression Patterns

• Primary Identifier: Expr8629
• Remark: Picture: Figure 2A. To confirm the specificity of the phospho-CeMKLP1 antibody, authors performed immunofluorescence experiments on C. elegans embryos in the presence of cognate peptides. The phospho-CeMKLP1 antibody was preincubated either with phospho- or nonphosphopeptides. Phosphorylated ZEN-4 was detected at anaphase on the central spindle after preincubation with the nonphosphopeptide with no significant reduction of signal intensity, whereas preincubation of the phospho-CeMKLP1 antibody with the phosphopeptide abolished central spindle staining.
• Subcellular Localization: The phospho-CeMKLP1 antibody shows a similar staining pattern. Phosphorylated ZEN-4 localizes to the anaphase spindle and persists into telophase, when midbody formation occurs. Aurora B and ZEN-4 have partially overlapping localization on the central spindle, and both become concentrated in the midbody and remnants. Thus, ZEN-4 is phosphorylated on the central spindle, midbody, and early remnant when it colocalizes with aurora B, consistent with ZEN-4 being an aurora B substrate. ZEN-4 localizes to a restricted region, which likely corresponds to the zone of microtubule overlap, on the central spindle in anaphase. It becomes concentrated in the midbody at telophase and persists at the remnant after sister-cell separation.

• Primary Identifier: Expr2036262
• 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: Expr1032979
• Pattern: Tiling arrays expression graphs

• Primary Identifier: Expr8005
• Remark: Picture: Figure 2. Similar results were obtained using an anti-ZEN-4 antibody.
• Pattern: During mid-embryogenesis, ZEN-4::GFP is expressed in all dividing cells, consistent with its role in cell division. However, at the onset of dorsal intercalation, when epidermal precursors have ceased dividing, ZEN-4::GFP becomes undetectable in the epidermis. ZEN-4::GFP is expressed for a correspondingly longer period, and is visible in spindle mid-bodies as ventral enclosure begins and before it completes. By the end of enclosure, little or no ZEN::GFP is detectable. As elongation of the embryo begins, virtually no ZEN-4::GFP can be detected, although occasional bright spots can be observed. By the 1.5- to 2-fold stage of elongation, no ZEN-4::GFP can be detected.

• Primary Identifier: Expr10989
• Subcellular Localization: GFP::ZEN-4 localized specifically to the subregion of the germ cell membranes that separates each germ cell from the rachis, i.e., the rachis bridge. Localization to the rachis bridge was maintained throughout the gonad and into the proximal region until the point where the oocyte is formed and the rachis disappears. GFP::ZEN-4 also appeared on or in nuclei as the transition to oogenesis was initiated and remained associated with oocyte nuclei in the proximal gonad. CYK-4::GFP has the same localization pattern as GFP::ZEN-4.

• Primary Identifier: Expr1024491
• Pattern: Developmental gene expression time-course. Raw data can be downloaded from ftp://caltech.wormbase.org/pub/wormbase/datasets-published/levin2012

• Primary Identifier: Expr1154560
• Pattern: Developmental gene expression time-course. Raw data can be downloaded from ftp://caltech.wormbase.org/pub/wormbase/datasets-published/hashimshony2015

• Primary Identifier: Expr2018125
• 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: Expr12579
• Subcellular Localization: Centralspindlin, a complex containing ZEN-4 and the GTPase activating protein (GAP) CYK-4 (Mishima et al., 2002), localizes near the ingressing cleavage furrow as well as the spindle midzone.

• Primary Identifier: Expr12795
• Subcellular Localization: In wild type, ZEN-4-GFP localized to microtubule bundles in the spindle midzone early in anaphase and then to the spindle midbody.

• Primary Identifier: Expr1999
• Subcellular Localization: In wild-type embryos, ZEN-4 localizes to the central spindle early during cytokinesis and persists at the division remnant. In icp-1(RNAi) embryos, ZEN-4 initially associated with the central spindle but, after 12 min, ZEN-4 disappeared from the central spindle.

• Primary Identifier: Expr1412
• Remark: No detailed description about cellular localization.
• Subcellular Localization: ZEN-4 localizes to the spindle midbody of all dividing cells. Low levels of protein appear to localize to the region of the chromosomes of the metaphase mitotic spindle. In anaphase cells, the antigen localizes in discrete lines along the equatorial region of the spindle. As mitosis progresses, the antigen condenses into a disk shape at the midzone of the intercellular bridge between daughter cells. Midbody staining intensifies during cytokinesis and gradually contracts to form an intense spot at the midzone of the mitotic spindle. After the completion of cell division, staining persists at the remnant of the midbody. ZEN-4 staining in the remnant is intense and persists well after the midbody microtubules have dissociated. In interphase cells, ZEN-4 can occasionally be seen localized to centrosomes, but protein does not appear to stain the centrosomes in dividing cells.

• Primary Identifier: Expr1200342
• Pattern: Data from the TransgeneOme project

• Primary Identifier: Expr16183
• Subcellular Localization: CYK-4 and ZEN-4 colocalize on the central spindle.

• Primary Identifier: Expr13887
• Subcellular Localization: During anaphase, ZEN-4 and SPD-1 both become enriched in a short region at the center of the spindle, with similar though non-identical localization.

45 GO Annotation

4 Homologues

1 Locations

• Feature . Primary Identifier: WBGene00006974
• Start: 6118215
• End: 6121777
• Strand: 1

45 Ontology Annotations

0 Regulates Expr Cluster

1 Sequence

• Length: 3563

1 Sequence Ontology Term

• Name: gene

9 Strains

• WBStrain00026489
• WBStrain00034581
• WBStrain00034110
• WBStrain00007290
• WBStrain00007286
• WBStrain00007291
• WBStrain00007301
• WBStrain00000061
• WBStrain00000062

1 Upstream Intergenic Region

• WormBase ID: intergenic_region_chrIV_6117877..6118214
• Length (nt): 338
• Chromosome Location: IV: 6117877-6118214
• Organism: Caenorhabditis elegans