WormMine: Gene WBGene00003052

• WormBase Gene ID: WBGene00003052
• Gene Name: lmn-1
• Sequence Name: DY3.2
• Brief Description: lmn-1 encodes the sole C. elegans nuclear lamin; lmn-1 is an essential gene that is required for a number of nuclear processes, including chromatin organization, cell cycle progression, chromosome segregation, and nuclear pore complex spacing; LMN-1 is also required for nuclear envelope localization of EMR-1/Emerin during early development; LMN-1 localizes to the nuclear periphery of all cell types except sperm, and in embryonic and some adult cells is visible in the nuclear interior; LMN-1 binds mitotic chromosomes and histone H2A in a manner that requires its predicted nuclear localization signal, KRRR.
• Organism: Caenorhabditis elegans
• Automated Description: Enables histone binding activity; identical protein binding activity; and structural molecule activity. Involved in several processes, including determination of adult lifespan; nuclear pore localization; and regulation of cell cycle. Located in nuclear envelope and nuclear periphery. Expressed in several structures, including ventral cord blast cell. Used to study Emery-Dreifuss muscular dystrophy; congenital muscular dystrophy; and progeria. Human ortholog(s) of this gene implicated in several diseases, including Charcot-Marie-Tooth disease type 2B1; autosomal dominant Emery-Dreifuss muscular dystrophy 2; autosomal recessive Emery-Dreifuss muscular dystrophy 3; brain disease (multiple); congenital muscular dystrophy due to LMNA mutation; and intrinsic cardiomyopathy (multiple). Is an ortholog of human LMNA (lamin A/C).
• Biotype: SO:0001217
• Genetic Position: I :3.07104 ±0.005882
• Length (nt): 2591

1 Organism

• Name: Caenorhabditis elegans
• Taxon Id: 6239

1 Synonyms

• Value: WBGene00003052

Genomics

1 Transcripts

WormMine ID	Sequence Name	Length (nt)	Chromosome Location
Transcript:DY3.2.1	DY3.2.1	2163	I: 8763041-8765631

Other

1 CDSs

WormMine ID	Sequence Name	Length (nt)	Chromosome Location
CDS:DY3.2	DY3.2	1701	I: 8763056-8763153

42 RNAi Result

• WBRNAi00070490
• WBRNAi00101829
• WBRNAi00059925
• WBRNAi00077202
• WBRNAi00106198
• WBRNAi00080942
• WBRNAi00063143
• WBRNAi00024969
• WBRNAi00108136
• WBRNAi00074076
• WBRNAi00085386
• WBRNAi00072401
• WBRNAi00074075
• WBRNAi00074074
• WBRNAi00074077
• WBRNAi00074079
• WBRNAi00074078
• WBRNAi00074080
• WBRNAi00080941
• WBRNAi00116674
• WBRNAi00087593
• WBRNAi00087592
• WBRNAi00080579
• WBRNAi00074081
• WBRNAi00024970
• WBRNAi00115677
• WBRNAi00115676
• WBRNAi00080936
• WBRNAi00080938
• WBRNAi00080940

48 Allele

• gk962858
• gk962706
• gk963902
• gk963849
• gk964316
• gk963349
• gk963350
• WBVar01432364
• gk411523
• gk330888
• gk430221
• gk642616
• gk362185
• gk642617
• gk398563
• gk528604
• gk710260
• gk602630
• gk615330
• gk362184
• gk787693
• gk893773
• gk492483
• gk764380
• gk413240
• gk440409
• WBVar01391938
• gk117465
• gk117466
• gk555045

1 Chromosome

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

1 Chromosome Location

• Feature . Primary Identifier: WBGene00003052
• Start: 8763041
• End: 8765631
• 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_8765632..8765744
• Length (nt): 113
• Chromosome Location: I: 8765632-8765744
• Organism: Caenorhabditis elegans

149 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
	Transcripts that showed significantly increased expression in L1 neural cells comparing to in adult neural cells.	DESeq2 (v1.18.1) fold change > 2, P-adj<0.05, using BenjaminiHochberg correction.	WBPaper00060811:L1_vs_adult_upregulated_neural
	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
	Proteins interacting with NHR-49-GFP according to co-IP and LC-MS.	N.A.	WBPaper00064071:NHR-49_interacting
	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
	Genes significantly enriched in NSM neurons (isolated by FACS) versus the reference, according to RNAseq analysis towards total RNA.	Gene expression quantification and differential expression was analyzed using cufflinks v2.2.1. Enriched contains only genes significantly enriched (differentially expressed >= 2.4 fold in total RNA or >= 3.2 fold in DSN treated total RNA) in the NSM neurons versus the reference.	WBPaper00045974:NSM_enriched_totalRNA_RNAseq
	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
	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 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 L3 larva and Late reproduction stage (96 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_developing
	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 L3 larva and Late reproduction stage (96 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_developing
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 altered expression after 24 hour exposure to stavudine (d4T) starting at L1 lava stage.	DESeq	WBPaper00053302:stavudine_24h_regulated
	Transcripts detected in body muscle nuclei according to a nuclear FACS-based strategy.	Cufflinks	WBPaper00065120:body-muscle-transcriptome
	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:coelomocytes_L2-larva_expressed
	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 (embryonic 0hr 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:germline-precursors_blastula-embryo_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:glr-1(+)-neurons_L2-larva_expressed
	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
	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
	Proteins identified in extracellular vesicle.	N.A.	WBPaper00062669:extracellular-vesicle_protein
Bacteria infection: Enterococcus faecalis OG1RF. Exposure for 16 hours.	Transcripts that showed significantly decreased expression in hpx-2(dg047) after animals were exposed to E. faecalis OG1RF for 16 hours comparing to exposure to E. Coli OP50.	Cuffcompare and Cuffdiff	WBPaper00056090:E.faecalis_downregulated_hpx-2(dg047)

13 Expression Patterns

• Primary Identifier: Expr1031433
• Pattern: Tiling arrays expression graphs

• Primary Identifier: Marker9
• Remark: Picture: Figure 1.
• Subcellular Localization: nuclear lamina

• Primary Identifier: Expr955
• Pattern: Antibodies to Ce-lamin stained the nuclear envelope at all developmental stages and in essentially every region where the Ce-lamin antibodies penetrated, including embryos, all larval stages, and adults. Nuclear envelope staining of Ce-lamin was also detected in all cells in the gonad, with one exception: antibody staining was not detected in cells undergoing spermiogenesis that had condensed chromatin.
• Subcellular Localization: nuclear envelope at all developmental stages

• Primary Identifier: Expr956
• Remark: data derived from more than one GFP construct.
• Reporter Gene: Three different lmn-1-GFP constructs were used. The construct pDRNL1, contains a GFP-Ce-lamin fusion with GFP fused to the N-terminus of lmn-1: a 6.5-kb HindIISalI genomic fragment positioned between 7.95 kb and 1.45 kb upstream to the lmn-1 coding region, was cloned into the pPD95.77 vector. A 1.45-kb fragment, just 5' to the lmn-1 coding region, was amplified by PCR with a novel NcoI cloning site introduced at its 3' end, and inserted 3' to the 6.5-kb genomic fragment. The 0.75-kb KpnISmaI fragment of the GFP gene was PCR amplified from pEGFP and inserted into the NcoI and SmaI sites. A 2.2-kb KpnISmaI fragment of the lmn-1 genomic region, containing the complete lamin coding region, was PCR amplified and inserted 3' in frame to the GFP gene. The second construct is a fusion of GFP to the C-terminus of Ce-lamin. To prepare this construct, termed pJKL380.4, long-range PCR was used to amplify from wild-type genomic DNA a 9.6-kb lamin genomic fragment, containing 4.7 kb of 5' sequence, the entire coding sequence plus introns, and 2.8 kb of 3' sequence. This 9.6-kb fragment was engineered such that unique NotI and SmaI sites were present at its ends and used for cloning into the pBluescript II SK vector. The resulting plasmid, in which the BamHI site in the vector backbone was destroyed, contained a single BamHI site 12 amino acids before the stop codon of lamin. This site was used to insert GFP (from pPD102.33) in frame into the lmn-1 gene. A third construct, termed pDRCL2, contained 7.95 kb of 5' promoter sequence of lmn-1, the first three exons, and two introns of lmn-1 fused in frame to the GFP gene. --precise ends.
• Pattern: With the exception of mature sperm, Ce-lamin-GFP fusion protein was localized to the nuclear periphery of all cells throughout the development of the nematode. The Ce-lamin-GFP expression in these lines reproduced the antibody staining pattern of the native protein, including the presence of subregions in the nuclear envelope with higher fluorescence intensity.
• Subcellular Localization: nuclear periphery of all cells

• Primary Identifier: Expr13171
• Subcellular Localization: Both LMN-1 GFP fusion proteins localized to the periphery of nearly all nuclei in a pattern similar to anti-LMN-1 antibodies (Liu et al., 2000). However, LMN-1::GFP was significantly fainter than GFP::LMN-1. GFP::LMN-1 localized around the nuclear volume of P cells prior to and during nuclear migration. During nuclear migration, GFP::LMN-1 was visible around both the lateral and ventral volumes of the nucleus and in the constricted space.

• Primary Identifier: Expr2013234
• 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: Expr2031465
• 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: Expr1069
• Remark: Ce-lamin(author) = lam-1 (wjc). The specificity of antibody staining for Ce-lamin was confirmed by the lack of signal in preimmune controls and by the 40-fold loss of the rim stain signal in nematodes disrupted for Ce-lamin expression). No detailed description on cellular localization.
• Subcellular Localization: In both early and later embryos, lamins maintained a nearly complete rim-staining pattern during metaphase and early anaphase. The exception to rim staining was near the spindle poles, where Ce-lamin staining became progressively weaker starting in prometaphase, with a large gap at both poles during early anaphase. This local disruption of lamina integrity was consistent with mechanical puncturing by spindle microtubules, as seen in other organisms. Elsewhere, the lamina remained apparently intact through early anaphase and was removed only during mid-late anaphase. In later embryos (30 cells), the lamina appeared to disassemble more extensively at earlier stages (e.g., prometaphase), as deduced from higher levels of cytoplasmic staining at earlier stages of mitosis. The intensity of lamin antibody staining during mitosis was always higher than in interphase.

• Primary Identifier: Expr1200239
• Pattern: Data from the TransgeneOme project

• Primary Identifier: Expr2364
• Subcellular Localization: Ce-lamin is shown mostly localized underneath the inner nuclear membrane. Additional gold labeling was observed in the nuclear interior, but not the cytoplasm. When the nuclear membranes were removed with detergent, Ce-lamin remained associated with the peripheral chromatin.

• Primary Identifier: Expr1147541
• Pattern: Developmental gene expression time-course. Raw data can be downloaded from ftp://caltech.wormbase.org/pub/wormbase/datasets-published/hashimshony2015

• Primary Identifier: Chronogram1204
• Remark: Original chronogram file: chronogram.2328.xml
• Reporter Gene: [DY3.2:gfp] transcriptional fusion.

• Primary Identifier: Expr1016830
• Pattern: Developmental gene expression time-course. Raw data can be downloaded from ftp://caltech.wormbase.org/pub/wormbase/datasets-published/levin2012

33 GO Annotation

16 Homologues

1 Locations

• Feature . Primary Identifier: WBGene00003052
• Start: 8763041
• End: 8765631
• Strand: 1

33 Ontology Annotations

4 Regulates Expr Cluster

Regulated By Treatment	Description	Algorithm	Primary Identifier
	Genes that were down regulated as the result of the lmn-1(L535P) mutation.	Differential expression was calculated with cuffdiff, using a count threshold (-c parameter) of at least 15 for statistical significance testing. Significantly differentially expressed genes were defined as ones with at least 1 FPKM level of expression in at least one of the conditions and a q-value less than 0.05.	WBPaper00050182:lmn-1(L535P)_downregulated
	Genes that were up regulated as the result of the lmn-1(L535P) mutation.	Differential expression was calculated with cuffdiff, using a count threshold (-c parameter) of at least 15 for statistical significance testing. Significantly differentially expressed genes were defined as ones with at least 1 FPKM level of expression in at least one of the conditions and a q-value less than 0.05.	WBPaper00050182:lmn-1(L535P)_upregulated
	Transcripts that showed significantly decreased expression in ygIs2[baf-1p-GFP-lmn-1(Y59C)] comparing to in WT control ygIs1[baf-1p-GFP-lamin wt].	edgeR v3.24, FDR < 0.01, fold change >= 1.5.	WBPaper00059378:lmn-1(Y59C)_downregulated
	Transcripts that showed significantly increased expression in ygIs2[baf-1p-GFP-lmn-1(Y59C)] comparing to in WT control ygIs1[baf-1p-GFP-lamin wt].	edgeR v3.24, FDR < 0.01, fold change >= 1.5.	WBPaper00059378:lmn-1(Y59C)_upregulated

1 Sequence

• Length: 2591

1 Sequence Ontology Term