WormMine: Gene WBGene00000865

• WormBase Gene ID: WBGene00000865
• Gene Name: cyb-1
• Sequence Name: ZC168.4
• Brief Description: cyb-1 encodes a cyclin B homolog that appears to be required both for embryogenesis (via maternally encoded CYB-1) and for postembryonic development and fertility (via zygotically encoded CYB-1); removing maternal product in cyb-1(RNAi) embryos causes multiple nuclei, and affected embryos arrest development at an early embryonic stage.
• Organism: Caenorhabditis elegans
• Automated Description: Enables cyclin-dependent protein serine/threonine kinase regulator activity and ubiquitin protein ligase binding activity. Involved in mitotic cell cycle; oocyte maturation; and positive regulation of protein phosphorylation. Located in cytoplasm and nucleus. Expressed in germ cell; male gonad; and oocyte. Used to study cardiovascular system disease. Human ortholog(s) of this gene implicated in several diseases, including in situ carcinoma; renal cell carcinoma; and reproductive organ cancer (multiple). Is an ortholog of human CCNB1 (cyclin B1).
• Biotype: SO:0001217
• Genetic Position: IV :4.6818 ±0.002007
• Length (nt): 1962

1 Organism

• Name: Caenorhabditis elegans
• Taxon Id: 6239

1 Synonyms

• Value: WBGene00000865

Genomics

2 Transcripts

WormMine ID	Sequence Name	Length (nt)	Chromosome Location
Transcript:ZC168.4.2	ZC168.4.2	1691	IV: 10735216-10737177
Transcript:ZC168.4.1	ZC168.4.1	1521	IV: 10735442-10737173

Other

1 CDSs

WormMine ID	Sequence Name	Length (nt)	Chromosome Location
CDS:ZC168.4	ZC168.4	1086	IV: 10735456-10735515

6 RNAi Result

• WBRNAi00021586
• WBRNAi00106163
• WBRNAi00007847
• WBRNAi00058758
• WBRNAi00037964
• WBRNAi00085858

28 Allele

• gk964278
• gk964078
• gk964500
• gk962765
• gk963382
• WBVar02121996
• WBVar02021201
• gk946594
• gk622464
• gk546142
• gk364419
• gk891760
• gk341148
• gk400741
• tn1806
• gk866149
• gk511838
• gk433281
• WBVar01730902
• WBVar01730903
• gk35
• WBVar01730904
• gk649807
• gk327934
• gk855942
• WBVar01857341
• gk211375
• gk211374

1 Chromosome

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

1 Chromosome Location

• Feature . Primary Identifier: WBGene00000865
• Start: 10735216
• End: 10737177
• Strand: 1

4 Data Sets

• WormBaseAcedbConverter
• GO Annotation data set
• C. elegans genomic annotations (GFF3 Gene)
• Panther orthologue and paralogue predictions

1 Downstream Intergenic Region

• WormBase ID: intergenic_region_chrIV_10737178..10737473
• Length (nt): 296
• Chromosome Location: IV: 10737178-10737473
• Organism: Caenorhabditis elegans

238 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
	mRNAs that showed decreased expression in 1 cell mebryo comparing to in oocyte, according to RNAseq analysis.	Gaussian error propagation. As cutoff for the up-regulated genes authors used log2 fold change > 1 and P < 0.05 and as cutoff for the down-regulated genes authors used log2 fold change < -1 and P < 0.05.	WBPaper00045420:fertilization_downregulated_transcript
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
	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 expressed in NMDA neuron, according to PAT-Seq analysis using Pnmr-1-GFP-3XFLAG mRNA tagging.	Cufflinks FPKM value >=1.	WBPaper00050990:NMDA-neuron_expressed
	Transcripts expressed in pharynx, according to PAT-Seq analysis using Pmyo-2-GFP-3XFLAG mRNA tagging.	Cufflinks FPKM value >=1.	WBPaper00050990:pharynx_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 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 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 detected in germline isolated from day-1 adult hermaphrodite animals.	All three experiments have CPM >= 1.	WBPaper00067147:germline_expressed
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 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
starvation 12 hours	Transcripts that showed significantly increased expression in dissected intestines of N2 L1 larva that were starved for 12 hours, comparing to fed animals.	EdgeR, FDR < 0.05, fold change >= 2.	WBPaper00067259:starvation_upregulated_intestine
	Transcripts that showed significantly increased expression in animals exposed to 400uM tamoxifen from L1 to L4 larva stage.	DEseq2, fold change > 2	WBPaper00064505:tamoxifen_upregulated
	Transcripts that showed significantly increased expression after 24-hour exposure to 10uM benzyl butyl phthalate (BBP) in col-121(nx3) animals.	DESeq2v1.38.3, FDR < 0.05	WBPaper00067417:benzyl-butyl-phthalate_regulated
	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
	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
	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 detected in body muscle nuclei according to a nuclear FACS-based strategy.	Cufflinks	WBPaper00065120:body-muscle-transcriptome
	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 (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

14 Expression Patterns

• Primary Identifier: Expr1162177
• Pattern: Developmental gene expression time-course. Raw data can be downloaded from ftp://caltech.wormbase.org/pub/wormbase/datasets-published/hashimshony2015

• Primary Identifier: Expr1030532
• Pattern: Tiling arrays expression graphs

• Primary Identifier: Expr15887
• Subcellular Localization: CYB-1 and CYB-3 were detected in the nuclei of the mitotic proliferating region of the gonad.

• Primary Identifier: Expr15889
• Subcellular Localization: CYB-1 and CYB-3 remained diffusely distributed throughout the cytoplasm of the fertilized egg during meiosis.

• Primary Identifier: Expr2010646
• 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: Expr13283
• Pattern: mRNA levels of both cyb-1 and cyb-3 were high in young-adult and adult N2 hermaphrodites as well as in feminized fem-1(hc17lf) adult hermaphrodites. By contrast, cyb-1 mRNA, but not cyb-3 mRNA, was highly expressed in the L4 stage N2 hermaphrodites, adult N2 males, and masculinized fem-3(q20gf) adult hermaphrodites, in all of which spermatogenesis proceed specifically and robustly. On the other hand, mRNA levels of both cyb-1 and cyb-3 were negligible in germline proliferation-defective glp-1(q224lf) adult hermaphrodites. These results indicate that cyb-1 is the major B-type cyclin robustly expressed during spermatogenesis.

• Primary Identifier: Expr1014670
• Pattern: Developmental gene expression time-course. Raw data can be downloaded from ftp://caltech.wormbase.org/pub/wormbase/datasets-published/levin2012

• Primary Identifier: Expr13286
• Subcellular Localization: CYB-1 was expressed in most germ nuclei throughout male gonads. In particular, CYB-1 was robustly expressed in the proximal region, where CYB-3 was not expressed.

• Primary Identifier: Expr2028886
• 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: Expr12873

• Primary Identifier: Expr15885
• Pattern: The highest expression of CYB-1 and CYB-3 proteins was detected in embryos. CYB-1 and CYB-3 expression was virtually absent in developmentally arrested first stage and dauer larvae. Upon release from L1 arrest, sets of post-embryonic blast cells successively initiate cell division,37 and CYB-1 and CYB-3 levels were found to increase during this period. CYB-3 protein levels remained low during larval development, as compared to the levels in embryos, while CYB-1 levels were fairly constant in developing animals.

• Primary Identifier: Expr3273
• Remark: No GO_term assigned.
• Subcellular Localization: In 6/6 fertilized embryos, GFP-CYB-1 levels began to decrease dramatically soon after spermatheca exit. The fluorescence intensity did not always begin to decrease immediately, but in 2/6 embryos remained stable for several minutes, indicating that exit from the spermatheca is not the direct trigger for cyclin B degradation. GFP-CYB-1 fluorescence in fertilized embryos decreased for approximately 12 min and then remained fairly stable for approximately 10 min. These two periods of rapid GFP-CYB-1 turnover and of GFP-CYB-1 stability coincide with the timing of meiosis I and meiosis II, respectively. Twenty to twenty-four minutes after the start of GFP-CYB-1 proteolysis, at a time when meiosis II is expected to be completed, fluorescence levels decreased again and approached zero. Pronuclei were observed at the end of this period indicating that the embryos had entered interphase. In 9/9 unfertilized embryos, GFP-CYB-1 fluorescence decreased rapidly after exit from the spermatheca just as in fertilized embryos. This is consistent with the occurrence of anaphase I in unfertilized embryos, in contrast with unfertilized vertebrate eggs which arrest at metaphase with high levels of cyclin B. A significant difference was observed between the unfertilized and the fertilized embryos at the time that meiosis II was expected to be completed in fertilized embryos. The second phase of decreasing GFP-CYB-1 fluorescence intensity did not occur in unfertilized embryos to the extent observed in fertilized embryos. At 27 min after spermatheca exit, GFP-CYB-1 fluorescence intensity was 7 +/- 5% (n = 6) of the value in the proximal oocyte in fertilized embryos and 19 +/- 10% (n = 9) in unfertilized embryos. This difference was statistically significant (P = .001) indicating that cyclin B proteolysis is not complete in unfertilized embryos. Pronuclei were observed at the end of these time-lapse sequences, indicating that unfertilized embryos entered interphase with a residual, metaphase II level of cyclin B.

• Primary Identifier: Expr10984
• Pattern: In wild-type embryos, the GFP-CYB-1 signal accumulated in mature oocytes and immediately diminished as meiotic division progressed.

• Primary Identifier: Expr15177
• Pattern: CYB-1 is expressed in germ cells.

18 GO Annotation

19 Homologues

1 Locations

• Feature . Primary Identifier: WBGene00000865
• Start: 10735216
• End: 10737177
• Strand: 1

18 Ontology Annotations

0 Regulates Expr Cluster

1 Sequence

• Length: 1962

1 Sequence Ontology Term

• Name: gene

4 Strains

• WBStrain00035506
• WBStrain00035505
• WBStrain00054975
• WBStrain00054710

1 Upstream Intergenic Region

• WormBase ID: intergenic_region_chrIV_10734589..10735215
• Length (nt): 627
• Chromosome Location: IV: 10734589-10735215
• Organism: Caenorhabditis elegans