WormMine: Gene WBGene00004043

• WormBase Gene ID: WBGene00004043
• Gene Name: plk-2
• Sequence Name: Y71F9B.7
• Brief Description: plk-2 encodes one of three C. elegans polo-like kinases; in the developing germ line, PLK-2 activity is required for regulation of chromosome dynamics that result in recruitment and attachment of meiotic chromosomes to the nuclear envelope and cytoskeleton; in the early embryo, PLK-2 activity is required for regulating the function of MEX-5/6, zinc-finger proteins essential for embryonic polarity and with which PLK-2 interacts, via its polo box domain, in yeast two-hybrid assays; PLK-2 is expressed in the meiotic germ line where it initially localizes to pairing centers and later localizes to synaptonemal complexes and in early embryos where it localizes asymmetrically to the cytoplasm of somatic blastomeres; in the mitotic germline faint PLK-2 is seen faintly centrosomes and kinetochores.
• Organism: Caenorhabditis elegans
• Automated Description: Predicted to enable protein serine/threonine kinase activity. Involved in regulation of meiosis I. Located in cytoplasm. Expressed in germ line. Human ortholog(s) of this gene implicated in several diseases, including breast carcinoma; reproductive organ cancer (multiple); and urinary bladder cancer. Is an ortholog of human PLK1 (polo like kinase 1).
• Biotype: SO:0001217
• Genetic Position: I :-7.26598 ±0.016083
• Length (nt): 2665

1 Organism

• Name: Caenorhabditis elegans
• Taxon Id: 6239

1 Synonyms

• Value: WBGene00004043

Genomics

1 Transcripts

WormMine ID	Sequence Name	Length (nt)	Chromosome Location
Transcript:Y71F9B.7.1	Y71F9B.7.1	2177	I: 2755540-2758204

Other

1 CDSs

WormMine ID	Sequence Name	Length (nt)	Chromosome Location
CDS:Y71F9B.7	Y71F9B.7	1899	I: 2755818-2756120

5 RNAi Result

• WBRNAi00058184
• WBRNAi00108302
• WBRNAi00062543
• WBRNAi00037783
• WBRNAi00116534

78 Allele

• gk963902
• gk964159
• gk962616
• gk964303
• WBVar01712859
• WBVar01712862
• WBVar01712863
• WBVar01712860
• WBVar01712861
• WBVar02102564
• WBVar02102563
• me107
• WBVar00025726
• WBVar01622639
• WBVar00025731
• WBVar00025736
• WBVar00025741
• WBVar00151062
• tm1395
• WBVar00025746
• WBVar00151069
• WBVar00151070
• WBVar00025751
• WBVar00025756
• WBVar00025761
• WBVar00025766
• WBVar00025771
• WBVar00025776
• WBVar01249250
• WBVar02016299

1 Chromosome

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

1 Chromosome Location

• Feature . Primary Identifier: WBGene00004043
• Start: 2755540
• End: 2758204
• 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_chrI_2745119..2755539
• Length (nt): 10421
• Chromosome Location: I: 2745119-2755539
• Organism: Caenorhabditis elegans

134 Expression Clusters

Regulated By Treatment	Description	Algorithm	Primary Identifier
	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
	Transcripts that showed significantly decreased expression in AGP22 [nhr-49(nr2041)I;glp-1(e2141)III] comparing to in CF1903 [glp-1(e2144)III] at Day 2 adults.	Fold change > 2, p Value of < 0.05 and a false discovery rate (FDR) of < 0.05.	WBPaper00061530:nhr-49(e2144)_downregulated
	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
	Proteins interacting with NHR-49-GFP according to co-IP and LC-MS.	N.A.	WBPaper00064071:NHR-49_interacting
	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
	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
	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)
	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
	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
	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 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 mbl-1(syb4318), referred to as mbl-1short(ex7-), comparing to in N2 at L4 larva stage.	DESeq2, Fold change > 2 and FDR < 0.05	WBPaper00066410:mbl-1(syb4318)_upregulated
	Transcripts that showed significantly altered expression at URX, AQR, and PQR neurons in camt-1(ok515) animals comparing to in wild type AX1888-1 strain.	RNA-seq data were mapped using PRAGUI - a Python 3-based pipeline for RNA-seq data analysis.	WBPaper00061902:camt-1(ok515)_regulated_URX-AQR-PQR
	Transcripts that showed significantly decreased expression in rbr-2(tm3141) comparing to in N2 animals.	Mapped reads were analyzed for transcript assembly and differential expression using Cufflinks 2.1.1 with a filter of twofold difference and FDR correction (P < 0.05).	WBPaper00050080:rbr-2(tm3141)_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
	Transcriptions that showed significantly increased expression in skn-1(RNAi) comparing to empty vector injection into rrf-3(pk1426);daf-2(e1368) animals.	Genes with an absolute fold changeof at least 2 and standard p-values below 0.05 were considered as differentially expressed.	WBPaper00062193:skn-1(RNAi)_upregulated
	Transcripts that showed significantly increased expression in hda-1(RNAi) embryos comparing to control animals.	DESeq2, fold change > 2, FDR < 0.05.	WBPaper00067044:hda-1(RNAi)_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
	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
Starvation	Transcripts that showed significantly altered expression by starvation with 100 mM salt (NaCl)	DESeq(version 1.10.1), FDR < 0.05.	WBPaper00050726:starvation_regulated_LowSalt

9 Expression Patterns

• Primary Identifier: Expr1031943
• Pattern: Tiling arrays expression graphs

• Primary Identifier: Expr7874
• Remark: Picture: Figure 2M, 2N.
• Subcellular Localization: A similar, albeit much fainter, asymmetric staining pattern to Expr7873.

• Primary Identifier: Expr9849
• Subcellular Localization: Antibodies that specifically recognize PLK-2 revealed a dynamic localization pattern in the germline. Premeiotic nuclei undergoing mitosis showed faint staining at centrosomes and kinetochores. By contrast, transition zone nuclei showed strong patches of PLK-2 staining at the nuclear envelope that colocalized with all four pairing centers ZnF proteins and the associated patches of SUN-1 and ZYG-12. By mid to late pachytene PLK-2 staining was no longer detected at pairing centers, but appeared along the synaptonemal complexes and disassembled with synaptonemal complex central region components at diplotene.

• Primary Identifier: Expr9847
• Subcellular Localization: In the mitotically dividing nuclei of the distal region of the germ-line, PLK-2 is first detectable at the centrosomes. However, upon entry into meiotic prophase, PLK-2 then localizes to approximately three to five chromosome-associated aggregates at the nuclear periphery of leptotene-zygotene nuclei; these aggregates disappear as synapsis initiates, and PLK-2 then colocalizes with the synapsed chromosomes of pachytene nuclei. PLK-2 colocalizes with PLK-1 to the nuclear periphery in some NE-associated patches but is undetectable in others.

• Primary Identifier: Expr2014959
• 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: Expr1028150
• Pattern: Developmental gene expression time-course. Raw data can be downloaded from ftp://caltech.wormbase.org/pub/wormbase/datasets-published/levin2012

• Primary Identifier: Expr2033194
• 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: Expr14834
• Subcellular Localization: As previously reported (HARPER et al. 2011; LABELLA et al. 2011), PLK-2 became concentrated in bright foci and patches at the nuclear envelope (NE) upon entry into meiotic prophase; these NE-associated foci and patches illustrate the localization of PLK-2 at chromosome-NE attachment sites, where PLK-2 promotes PC-led chromosome movements that are important for homolog pairing and synapsis. NE localization of PLK-2 was lost by the end of early pachytene, and PLK-2 subsequently became localized to the SCs. In addition to these previously reported localization patterns, however, we also detected a strong nucleoplasmic localization of PLK-2 in premeiotic germ cell nuclei As previously reported (HARPER et al. 2011; LABELLA et al. 2011), PLK-2 became concentrated in bright foci and patches at the nuclear envelope (NE) upon entry into meiotic prophase; these NE-associated foci and patches illustrate the localization of PLK-2 at chromosome-NE attachment sites, where PLK-2 promotes PC-led chromosome movements that are important for homolog pairing and synapsis. NE localization of PLK-2 was lost by the end of early pachytene, and PLK-2 subsequently became localized to the SCs. In addition to these previously reported localization patterns, however, we also detected a strong nucleoplasmic localization of PLK-2 in premeiotic germ cell nuclei.

• Primary Identifier: Expr1161603
• Pattern: Developmental gene expression time-course. Raw data can be downloaded from ftp://caltech.wormbase.org/pub/wormbase/datasets-published/hashimshony2015

32 GO Annotation

6 Homologues

1 Locations

• Feature . Primary Identifier: WBGene00004043
• Start: 2755540
• End: 2758204
• Strand: -1

32 Ontology Annotations

0 Regulates Expr Cluster

1 Sequence

• Length: 2665

1 Sequence Ontology Term

• Name: gene

2 Strains

• WBStrain00032279
• WBStrain00047219

1 Upstream Intergenic Region

• WormBase ID: intergenic_region_chrI_2758205..2758297
• Length (nt): 93
• Chromosome Location: I: 2758205-2758297
• Organism: Caenorhabditis elegans