WormMine: Gene WBGene00003048

• WormBase Gene ID: WBGene00003048
• Gene Name: lit-1
• Sequence Name: W06F12.1
• Brief Description: lit-1 encodes a serine threonine protein kinase homolog related to the Drosophila protein Nemo; lit-1 is required for embryonic viability and plays a central role in controlling the asymmetry of cell divisions during embryogenesis; lit-1 acts downstream of mom-2 with respect to polarity defects and mediates larval cell fate decisions that involve POP-1; lit-1 is also required for amphid channel morphogenesis and thus, also for normal morphology of the outer labial sensilla; specifically, lit-1 is required in sheath glia for positively regulating amphid sensory compartment expansion; lit-1 is expressed in most embryonic and larval cells, including the amphid sheath glia.
• Organism: Caenorhabditis elegans
• Automated Description: Enables beta-catenin binding activity and protein serine/threonine kinase activity. Involved in several processes, including cell fate commitment; polarity specification of proximal/distal axis; and positive regulation of nematode male tail tip morphogenesis. Located in cell cortex and nucleus. Part of serine/threonine protein kinase complex. Expressed in several structures, including hermaphrodite gonad; pharynx; tail hypodermis; and vulva. Is an ortholog of human NLK (nemo like kinase).
• Biotype: SO:0001217
• Genetic Position: III :21.3862 ±0.015644
• Length (nt): 22414

1 Organism

• Name: Caenorhabditis elegans
• Taxon Id: 6239

1 Synonyms

• Value: WBGene00003048

Genomics

7 Transcripts

WormMine ID	Sequence Name	Length (nt)	Chromosome Location
Transcript:W06F12.1d.2	W06F12.1d.2	2832	III: 13701991-13724403
Transcript:W06F12.1d.1	W06F12.1d.1	2868	III: 13701993-13724401
Transcript:W06F12.1d.3	W06F12.1d.3	2797	III: 13702141-13724403
Transcript:W06F12.1a.1	W06F12.1a.1	2846	III: 13714045-13724404
Transcript:W06F12.1b.1	W06F12.1b.1	2374	III: 13717965-13724401
Transcript:W06F12.1e.1	W06F12.1e.1	1365	III: 13718359-13723463
Transcript:W06F12.1c.1	W06F12.1c.1	2520	III: 13719396-13724401

Other

5 CDSs

WormMine ID	Sequence Name	Length (nt)	Chromosome Location
CDS:W06F12.1a	W06F12.1a	1905	III: 13714045-13714184
CDS:W06F12.1e	W06F12.1e	1365	III: 13718359-13718466
CDS:W06F12.1c	W06F12.1c	1314	III: 13719664-13719720
CDS:W06F12.1b	W06F12.1b	1389	III: 13718012-13718030
CDS:W06F12.1d	W06F12.1d	1806	III: 13702192-13702246

130 RNAi Result

• WBRNAi00114300
• WBRNAi00114065
• WBRNAi00114144
• WBRNAi00114223
• WBRNAi00091348
• WBRNAi00092512
• WBRNAi00099003
• WBRNAi00092553
• WBRNAi00080203
• WBRNAi00080204
• WBRNAi00098863
• WBRNAi00098996
• WBRNAi00110469
• WBRNAi00106738
• WBRNAi00101463
• WBRNAi00101819
• WBRNAi00110472
• WBRNAi00101818
• WBRNAi00113185
• WBRNAi00009260
• WBRNAi00106749
• WBRNAi00101402
• WBRNAi00054898
• WBRNAi00087872
• WBRNAi00027889
• WBRNAi00101962
• WBRNAi00099953
• WBRNAi00100483
• WBRNAi00068461
• WBRNAi00068463

321 Allele

• gk963887
• gk963715
• gk963904
• gk963552
• gk191041
• gk191042
• gk191040
• gk191045
• gk191046
• gk191043
• gk191044
• gk191048
• gk191049
• gk191047
• gk191052
• gk191053
• gk191050
• gk191051
• gk191056
• gk191054
• gk191055
• gk191057
• gk191060
• gk191061
• gk191058
• gk191059
• gk191064
• gk191065
• gk191062
• gk191063

1 Chromosome

• WormBase ID: III
• Organism: Caenorhabditis elegans
• Length (nt): 13783801

1 Chromosome Location

• Feature . Primary Identifier: WBGene00003048
• Start: 13701991
• End: 13724404
• 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_chrIII_13724405..13726632
• Length (nt): 2228
• Chromosome Location: III: 13724405-13726632
• Organism: Caenorhabditis elegans

155 Expression Clusters

Regulated By Treatment	Description	Algorithm	Primary Identifier
	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
	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 body muscle, according to PAT-Seq analysis using Pmyo-3-GFP-3XFLAG mRNA tagging.	Cufflinks FPKM value >=1.	WBPaper00050990:body-muscle_expressed
	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 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
	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 expressed in seam cells, according to PAT-Seq analysis using Pgrd-10-GFP-3XFLAG mRNA tagging.	Cufflinks FPKM value >=1.	WBPaper00050990:seam_expressed
	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)
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
	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
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 hrde-1(tm1200) animals, comparing to in N2, after growing at 25C for five generations (late generation).	CuffDiff2	WBPaper00051265:F4_hrde-1(tm1200)_upregulated
Bacteria infection: Staphylococcus aureus MW2. 4 hours of exposure.	Transcripts that showed significantly increased expression after N2 animals had 4 hours of infection by Staphylococcus aureus (MW2).	DEseq 1.18.0, adjusted p-value < 0.05.	WBPaper00056471:S.aureus-4h_upregulated_N2
	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 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
	Transcripts detected in body muscle nuclei according to a nuclear FACS-based strategy.	Cufflinks	WBPaper00065120:body-muscle-transcriptome
	Genes that showed oscillating mRNA expression level throughout the 16 hour time courses from L3 larva to young adult.	The following three lines of R code were used to perform the classification: increasing <-2*amplitude-PC1 < -1.7; oscillating <-!increasing & (amplitude > 0.55); flat <-!increasing & !oscillating; Note that the amplitude of a sinusoidal wave corresponds to only half the fold change between trough and peak.	WBPaper00044736:oscillating_dev_expression
	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 (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:excretory-cell_L2-larva_expressed
	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
	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
	Transcripts detected in germline isolated from day-1 adult hermaphrodite animals.	All three experiments have CPM >= 1.	WBPaper00067147:germline_expressed
	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
	Genes regulated by DAF-12, according to whole transcriptome profiling to compare genome-wide regulatory influences of DPY-21 and SET-4 to those of the key transcription factors controlling dauer arrest in eak-7;akt-1 animals, DAF-16 and DAF-12.	Authors identified genes differentially expressed between wild-type and eak-7;akt-1 double mutant animals [fold change >= 1.5 and false discovery rate (FDR) < 0.05]. Authors then compared the transcriptomes of eak-7;akt-1 double mutants to those of eak-7;akt-1 animals harboring mutations in dpy-21, set-4, daf-16, or daf-12, and identified genes that are differentially expressed in the opposite direction as in wild-type relative to eak-7;akt-1. Annotated gene expression data output from CuffDiff v2.2.1 was read into R version 3.2.1 for six comparisons: eak-7;akt-1 compared to (1) wild-type, (2) daf-16(mu86);eak-7;akt-1, (3) daf-12;eak-7;akt-1, (4) set-4(n4600);eak-7;akt-1, (5) set-4(dp268);eak-7;akt-1, and (6) dpy-21;eak-7;akt-1. Authors filtered genes by the following criteria: (1) status = OK for wild-type vs. eak-7;akt-1, (2) fold change (FC) >= 1.5 or FC <= 1/1.5 for wild-type vs. eak-7;akt-1 and (3) FDR < 0.05 for at least two separate comparisons.	WBPaper00050801:DAF-12_dauer_regulome
	Genes regulated by DAF-16, according to whole transcriptome profiling to compare genome-wide regulatory influences of DPY-21 and SET-4 to those of the key transcription factors controlling dauer arrest in eak-7;akt-1 animals, DAF-16 and DAF-12.	Authors identified genes differentially expressed between wild-type and eak-7;akt-1 double mutant animals [fold change >= 1.5 and false discovery rate (FDR) < 0.05]. Authors then compared the transcriptomes of eak-7;akt-1 double mutants to those of eak-7;akt-1 animals harboring mutations in dpy-21, set-4, daf-16, or daf-12, and identified genes that are differentially expressed in the opposite direction as in wild-type relative to eak-7;akt-1. Annotated gene expression data output from CuffDiff v2.2.1 was read into R version 3.2.1 for six comparisons: eak-7;akt-1 compared to (1) wild-type, (2) daf-16(mu86);eak-7;akt-1, (3) daf-12;eak-7;akt-1, (4) set-4(n4600);eak-7;akt-1, (5) set-4(dp268);eak-7;akt-1, and (6) dpy-21;eak-7;akt-1. Authors filtered genes by the following criteria: (1) status = OK for wild-type vs. eak-7;akt-1, (2) fold change (FC) >= 1.5 or FC <= 1/1.5 for wild-type vs. eak-7;akt-1 and (3) FDR < 0.05 for at least two separate comparisons.	WBPaper00050801:DAF-16_dauer_regulome

14 Expression Patterns

• Primary Identifier: Expr4599
• Pattern: The nuclear GFP::LIT-1, despite a low level, was detected in a dynamic pattern both temporally and spatially. GFP::LIT-1 was consistently enriched in the interphase nuclei of only a subset of early blastomeres. Comparison with the corresponding DIC images revealed that, at the eight-cell stage, nuclear GFP::LIT-1 was enriched in the interphase E blastomere but not in the MS blastomere. At the 12-cell stage, interphase nuclear GFP::LIT-1 was enriched in four of the great granddaughters of the AB blastomere (ABarp, ABalp, ABprp, and ABplp, all posterior daughters of A-P divisions) but not their anterior sister cells. Nuclear enrichment was also observed at the 14-cell stage in the posterior daughters of MS and E, MSp and Ep, respectively, but not their anterior daughters. After the 14-cell stage, the GFP signal was too low to continue evaluating.
• Subcellular Localization: The GFP::LIT-1 was detected, both cytoplasmic and nuclear, in every blastomere.

• Primary Identifier: Expr1031432
• Pattern: Tiling arrays expression graphs

• Primary Identifier: Expr9081
• Remark: Picture: Fig 4.
• Subcellular Localization: LIT-1::GFP localized to both cytoplasm and nucleus and was broadly expressed in a variety of cell types at post-embryonic stages, including in seam cells, vulva cells, neurons and pharyngeal muscles. In seam cells, LIT-1::GFP was present in both nucleus and cytoplasm and displayed a highly dynamic temporal pattern. LIT-1::GFP was barely detected in the early and middle stages of each larval stage. LIT-1::GFP was strongly detected at late period within each larval stage. Then, LIT-1::GFP formed punctate structure in the cytoplasm and levels of LIT-1::GFP in nucleus became weaker, followed by disappearance of LIT-1::GFP in seam cells. This periodic expression pattern of LIT-1::GFP was repeated at each larval stage. Seam cell expression of lit-1::gfp was not detectable at the young adult stage. Therefore, LIT-1::GFP oscillates in seam cells during each larval stage.

• Primary Identifier: Expr3448
• Pattern: LIT-1::GFP expression was observed in various tissues and developmental stages in N2 animals, notably in larval and adult pharynx.

• Primary Identifier: Expr11919
• Pattern: LIT-1::GFP is expressed in the developing tissues of the vulva, uterus, and spermatheca.

• Primary Identifier: Expr3201
• Pattern: GFP expression in the cells and nuclei of pharyngeal muscle cells.
• Subcellular Localization: cells and nuclei

• Primary Identifier: Expr9659
• Pattern: lit-1 is expressed in amphid sheath glia, among other cells. In addition, the expression pattern of this reporter partially overlaps with that of ptr-10, a gene expressed in ensheathing glia of other sensory organs.

• Primary Identifier: Expr11052
• Pattern: A strain expressing a LIT-1::GFP fusion protein shows nuclear expression in hyp9 and hyp10 but not in hyp8 or hyp11 prior to tail tip morphogenesis.

• Primary Identifier: Expr12652
• Pattern: The cct complex (cct-7) and six other genes- mep-1, a zinc finger TF; lit-1, an ortholog of NEMO-like kinase (NLK); cdc-37; T03F1.8, a guanylate kinase; and two uncharacterized conserved proteins, cacn-1 and T20B12.1-are up-regulated in the AC before or during the time of invasion (mid-to-late L3).

• Primary Identifier: Expr2013228
• 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: Expr1158438
• Pattern: Developmental gene expression time-course. Raw data can be downloaded from ftp://caltech.wormbase.org/pub/wormbase/datasets-published/hashimshony2015

• Primary Identifier: Expr2031459
• 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: Expr1027521
• Pattern: Developmental gene expression time-course. Raw data can be downloaded from ftp://caltech.wormbase.org/pub/wormbase/datasets-published/levin2012

• Primary Identifier: Expr3684
• Subcellular Localization: In the progeny of many cells, the nuclear level of WRM-1::GFP and GFP::LIT-1 was higher in the posterior daughters than in the anterior ones; this observation included hypodermal cells (T, V, and P cells), neuroblasts (QL and QR), and mesodermal cells (Mdr and Mvr). The asymmetric nuclear localization of LIT-1 is also reported in embryos. Weak punctate fluorescence was often detected at the anterior side of some cells before their division, for both GFP::LIT-1 and WRM-1::GFP. The asymmetric localization of GFP::LIT-1 and WRM-1::GFP was more clearly observed in seam cells (Vn.p), especially in the V5.p cell at the end of the L1 stage, when the expression of these genes was higher. Punctate fluorescence was clearly visible near the cell membrane in the anterior half of the cells. The asymmetric cortical localization was also observed during the mitosis of the V5.p cell. No asymmetry in the cytoplasmic localization of WRM-1 or LIT-1 was observed before or during cell division. At telophase, their localization near the anterior cortex and in the newly formed posterior nucleus was observed. Although WRM-1::GFP was nearly undetectable in the anterior nucleus after the V5.p division, it was clearly detected in the anterior nucleus at telophase, suggesting that the WRM-1 protein is exported out of the anterior nucleus during late telophase. These results indicate that WRM-1 and LIT-1 are asymmetrically localized to the anterior cortex before and during division and to the posterior nucleus after the division of many cells during post-embryonic development.

57 GO Annotation

10 Homologues

1 Locations

• Feature . Primary Identifier: WBGene00003048
• Start: 13701991
• End: 13724404
• Strand: 1

57 Ontology Annotations

0 Regulates Expr Cluster

1 Sequence

• Length: 22414

1 Sequence Ontology Term

• Name: gene

7 Strains

• WBStrain00035938
• WBStrain00040429
• WBStrain00007762
• WBStrain00007769
• WBStrain00007293
• WBStrain00007328
• WBStrain00008483

1 Upstream Intergenic Region

• WormBase ID: intergenic_region_chrIII_13693812..13701990
• Length (nt): 8179
• Chromosome Location: III: 13693812-13701990
• Organism: Caenorhabditis elegans