WormMine: Gene WBGene00002994

• WormBase Gene ID: WBGene00002994
• Gene Name: lin-5
• Sequence Name: T09A5.10
• Brief Description: lin-5 encodes a novel protein with a centrally located alpha-helical coiled-coil domain and ten potential proline-directed kinase phosphorylation sites; LIN-5 activity is required for mitosis and cytokinesis at all stages of development and specifically, for spindle positioning, chromosome alignment and segregation, and perhaps also for blocking exit from mitosis when chromosome segregation fails; LIN-5, which is expressed maternally, embryonically, and during larval stages, localizes to the cell periphery and, in a microtubule-dependent manner, to the meiotic spindle and the asters and kinetochore microtubules of the mitotic spindle; in regulating spindle function, LIN-5 interacts with two G protein regulators, GPR-1 and GPR-2, which require LIN-5 activity for localization to the spindle and cell cortex; additionally, LIN-5 interacts in vitro with itself, the coiled-coil protein LFI-1, GEI-16, and several other novel proteins; genetic studies indicate that in regulating embryonic spindle function, lin-5 acts downsteam of par-2, par-3, mes-1, and src-1 and upstream of gpr-1, gpr-2, goa-1, and gpa-16.
• Organism: Caenorhabditis elegans
• Automated Description: Enables dynein complex binding activity. Involved in several processes, including gonad development; microtubule cytoskeleton organization; and regulation of protein localization. Located in cell cortex; condensed chromosome; and spindle.
• Biotype: SO:0001217
• Genetic Position: II :0.586677 ±0.000809
• Length (nt): 2990

1 Organism

• Name: Caenorhabditis elegans
• Taxon Id: 6239

1 Synonyms

• Value: WBGene00002994

Genomics

2 Transcripts

WormMine ID	Sequence Name	Length (nt)	Chromosome Location
Transcript:T09A5.10.1	T09A5.10.1	2689	II: 7860574-7863563
Transcript:T09A5.10.2	T09A5.10.2	2598	II: 7860659-7863557

Other

1 CDSs

WormMine ID	Sequence Name	Length (nt)	Chromosome Location
CDS:T09A5.10	T09A5.10	2466	II: 7860660-7860799

25 RNAi Result

• WBRNAi00063515
• WBRNAi00079154
• WBRNAi00063516
• WBRNAi00079118
• WBRNAi00009141
• WBRNAi00061024
• WBRNAi00063510
• WBRNAi00052915
• WBRNAi00063506
• WBRNAi00111687
• WBRNAi00008059
• WBRNAi00026246
• WBRNAi00065756
• WBRNAi00079146
• WBRNAi00079131
• WBRNAi00079136
• WBRNAi00079141
• WBRNAi00079156
• WBRNAi00063508
• WBRNAi00063519
• WBRNAi00062798
• WBRNAi00062805
• WBRNAi00069338
• WBRNAi00069339
• WBRNAi00114440

47 Allele

• gk963801
• gk963053
• gk962682
• WBVar01438607
• WBVar01438605
• WBVar01438606
• WBVar01438603
• WBVar01438604
• h3060
• e1348
• WBVar01241817
• e1457
• WBVar00173711
• WBVar00173712
• tm7982
• WBVar01626772
• n3066
• WBVar00226018
• gk742076
• gk730048
• n3070
• gk548535
• gk402037
• gk592543
• WBVar00226020
• gk898957
• ev571
• gk570262
• gk147762
• gk147768

1 Chromosome

• WormBase ID: II
• Organism: Caenorhabditis elegans
• Length (nt): 15279421

1 Chromosome Location

• Feature . Primary Identifier: WBGene00002994
• Start: 7860574
• End: 7863563
• 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_chrII_7863564..7864506
• Length (nt): 943
• Chromosome Location: II: 7863564-7864506
• Organism: Caenorhabditis elegans

158 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
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 increased expression after animals were treated with 100uM Psora and 250uM Allantoin from day 1 to day 3 adult hermaphradite.	DESeq2(v1.14.1), fold change > 2, p-value < 0.05	WBPaper00055354:Psora-Allantoin_upregulated
	Transcripts that showed significantly increased expression after animals were treated with 100uM Rapamycin and 50mM Metformin from day 1 to day 3 adult hermaphradite.	DESeq2(v1.14.1), fold change > 2, p-value < 0.05	WBPaper00055354:Rapamycin-Metformin_upregulated
	Transcripts expressed in the epithelial tissues surrounding the pharynx that includes the arcade and intestinal valve (AIV) cells, according to PAT-Seq analysis using Pbath-15-GFP-3XFLAG mRNA tagging.	Cufflinks FPKM value >=1.	WBPaper00050990:arcade_intestinal-valve_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 expressed in NMDA neuron, according to PAT-Seq analysis using Pnmr-1-GFP-3XFLAG mRNA tagging.	Cufflinks FPKM value >=1.	WBPaper00050990:NMDA-neuron_expressed
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 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 10 mix) vs BT407 6h), according to RNAseq.	Cuffdiff, ajusted p-value < 0.01.	WBPaper00046497:B.thuringiensis_0.1mix_downregulated_6h
Bacteria infection: Bacillus thuringiensis	mRNAs that showed significantly decreased expression after pathogenic bacteria Bacillus thuringiensis infections comparing to non pathogenic BT (BT247(1 to 10 mix) vs BT407 12h), according to RNAseq.	Cuffdiff, ajusted p-value < 0.01.	WBPaper00046497:B.thuringiensis_0.1mix_downregulated_12h
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 6h), according to RNAseq.	Cuffdiff, ajusted p-value < 0.01.	WBPaper00046497:B.thuringiensis_0.5mix_downregulated_6h
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 increased expression in enriched nuclei of daf-2(e1370) comparing to in wild type nuclei.	edgeR, fold change > 2, FDR < 0.05	WBPaper00067267:daf-2(e1370)_upregulated_nuclei
	Transcripts that showed significantly altered expression after 24 hour exposure to stavudine (d4T) starting at L1 lava stage.	DESeq	WBPaper00053302:stavudine_24h_regulated
	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
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 increased expression in sftb-1(cer6) deletion homozygous comparing to to in N2 animals at L4 larva stage.	DESeq2, fold change > 2	WBPaper00058725:sftb-1(cer6)_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
	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
	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:A-class-motor-neurons_L2-larva_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:all-neurons_L2-larva_expressed
	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

11 Expression Patterns

• Primary Identifier: Expr1031392
• Pattern: Tiling arrays expression graphs

• Primary Identifier: Expr7893
• Remark: Picture: Fig. 1.
• Subcellular Localization: During prophase of the first mitosis in centration and rotation stage embryos, LIN-5 did not appear enriched at the cortex relative to the underlying cytoplasm. However, the anterior cortex and cytoplasm stained more intensely for LIN-5. Although both cortical and cytoplasmic LIN-5 intensities were somewhat discontinuous, most prophase embryos exhibited clear asymmetries overall: The highest levels of cortical LIN-5 staining were at the anterior from 0% to 30% egg length (33/38 cortices, n = 19 embryos; note that in some embryos the upper and lower cortex showed different patterns and thus the number of cortices, rather than embryos, was scored). In these embryos, LIN-5 staining intensities began to decrease at about 40% egg length. LIN-5 cytoplasmic intensities showed similar anterior enrichment and the traces closely matched those of cortical levels in most cases (30/38 traces). The differences between anterior and posterior intensities are statistically significant. The averaged plot also shows a bipolar appearance rather than a simple anterior to posterior gradient: the region from 50% to 70% egg length had the lowest average staining intensities.

• Primary Identifier: Expr8527
• Remark: Picture: Fig. 2aa, Fig. 3a; Supplementary Information, Fig. S1a.
• Subcellular Localization: LIN-5 and ASPM-1 were found to co-localize at the meiotic spindle and mitotic spindle poles. LIN-5 also localizes diffusely between the poles of the metaphase spindle and at the cell cortex. These latter locations sometimes stained weakly with anti-ASPM-1 antibodies; however, this staining was probably non-specific because the intensity was similar in wild-type and in aspm-1(RNAi) embryos.

• Primary Identifier: Expr2564
• Remark: The close sequence identity of gpr-1 and gpr-2 prevented distinguishing between them in the experiments.
• Subcellular Localization: During all mitotic divisions examined, GPR-1/GPR-2 and LIN-5 were present at the cell cortex and spindle asters. GPR-1/GPR-2 and LIN-5 were detected at the spindle asters and at the membranes between germ-precursor nuclei in the distal gonad arms. During the formation and maturation of oocytes, GPR-1/GPR-2 and LIN-5 localized diffusely to the cytoplasm and more prominently to the nuclear and cytoplasmic membranes, in particular to membranes between adjacent oocytes. Following fertilization and meiosis, GPR-1/GPR-2 and LIN-5 appeared at the duplicated centrosomes associated with the sperm pronucleus. GPR-1/GPR-2 and LIN-5 both became progressively more abundant at the spindle asters during the formation of the first mitotic spindle. Both proteins also localized diffusely around the kinetochore MTs in metaphase. Although the latter localization disappeared in early anaphase, GPR-1/GPR-2 and LIN-5 persisted at the spindle asters until chromosome decondensation in telophase. On completion of cell cleavage, GPR-1/GPR-2 and LIN-5 were detected only at the cell cortex and cytoplasm. This pattern of spindle-associated localizations was repeated during subsequent mitotic divisions. The cortical localization appeared enriched between blastomeres, especially the cortical staining of LIN-5. No other asymmetries in localization were detected until the four-cell stage. At that stage, both LIN-5 and GPR-1/GPR-2 showed significant accumulation at the boundary between the EMS and P2 blastomeres. Similar asymmetries were detected during some of the subsequent divisions. Unlike LIN-5, GPR-1/GPR-2 were not detected at the meiotic spindle. In 15/18 embryos, GPR-1/GPR-2 antiserum diffusely stained the maternal pronucleus or condensed meiotic chromosomes. However, this staining is likely not specific, as similar staining was seen in 9/16 gpr-1/gpr-2(RNAi) embryos. In contrast, LIN-5 was abundantly present at the polar regions of the meiotic spindle.

• Primary Identifier: Expr1156517
• Pattern: Developmental gene expression time-course. Raw data can be downloaded from ftp://caltech.wormbase.org/pub/wormbase/datasets-published/hashimshony2015

• Primary Identifier: Expr2013196
• 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: Expr1022273
• Pattern: Developmental gene expression time-course. Raw data can be downloaded from ftp://caltech.wormbase.org/pub/wormbase/datasets-published/levin2012

• Primary Identifier: Expr13459
• Subcellular Localization: To explore the relative cortical localization patterns of LIN-5 and dynein, egfp::lin-5; mcherry::dhc-1 embryos were imaged by SDCM. In late metaphase, eGFP::LIN-5 became modestly enriched at the cortex as compared with the adjacent cytoplasm, both in the anterior and posterior. Although this was not observed for dynein, both LIN-5 and dynein showed higher cytoplasmic levels in the anterior compared with the posterior during all mitotic stages. This gradient affected the relative cortex/cytoplasm ratios calculated for the anterior and posterior and caused the increase of cortical levels observed in the posterior, which was not observed when a mean cytoplasmic value was used for normalization of all points instead.During anaphase, cortical enrichment of eGFP::LIN-5 increased substantially, most noticeably in the posterior. When averaging fluorescence intensities from multiple embryos, mCherry::DHC-1 did not show clear enrichment at the cortex above local cytoplasmic levels during anaphase. This reflects the patchy appearance of cortical dynein enrichment along the A-P axis. Importantly, side-by- side comparison of nonnormalized cortical line scans revealed a strong cross-correlation between cortical eGFP::LIN-5 and mCherry::DHC-1. This indicates that both proteins follow a similar cortical distribution, in agreement with LIN-5-dependent dynein localization. These protein localization patterns can account for force asymmetries in anaphase, but not during metaphase spindle displacement.

• Primary Identifier: Expr988
• Pattern: LIN-5 was present at the meiotic spindles in the fertilized egg during meiosis I and II. Staining associated with the maternal pronucleus disappeared after completion of meiosis and LIN-5 became localized at the duplicated centrosomes that adjoined the paternal pronucleus. LIN-5 remained localized at the centrosomes until completion of the first mitotic division. In all subsequent mitoses, LIN-5 was associated with the centrosomes and detectable after separation of the centrosomes in prophase until decondensation of chromosomes in telophase. LIN-5 was also diffusely present in the cytoplasm and at two other locations; LIN-5 appeared microtubule-associated in cells with metaphase-aligned chromosomes. This localization was limited to the region between the poles and did not overlap with DNA staining. Therefore, it appeared to reflect specific association of LIN-5 with kinetochore microtubules. LIN-5 was diffusely present at the cell cortex in most embryonic cells from the two-cell stage onward. During the larval stages, LIN-5 localized to the centrosomes from prophase to telophase and to the cell periphery in late mitosis. In adult hermaphrodites, mitosis is restricted to germ presursor cells in the distal ends of the gonad. LIN-5 was detected at the centrosomes of such cells and, in addition, diffuse cytoplasmic LIN-5 staining was detected in oocytes. Strong membrane-associated staining was detected in the gonad at all stages of development.
• Subcellular Localization: cytoplasmic, membrane-associated or chromosome associated (nuclei).

• Primary Identifier: Expr15123

• Primary Identifier: Expr2031428
• 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).

32 GO Annotation

2 Homologues

1 Locations

• Feature . Primary Identifier: WBGene00002994
• Start: 7860574
• End: 7863563
• Strand: 1

32 Ontology Annotations

0 Regulates Expr Cluster

1 Sequence

• Length: 2990

1 Sequence Ontology Term

• Name: gene

7 Strains

• WBStrain00024322
• WBStrain00034592
• WBStrain00034590
• WBStrain00034597
• WBStrain00034599
• WBStrain00034598
• WBStrain00004404

1 Upstream Intergenic Region

• WormBase ID: intergenic_region_chrII_7859754..7860573
• Length (nt): 820
• Chromosome Location: II: 7859754-7860573
• Organism: Caenorhabditis elegans