WormMine: Gene WBGene00003165

• WormBase Gene ID: WBGene00003165
• Gene Name: mec-1
• Sequence Name: T07H8.4
• Brief Description: mec-1 encodes proteins with multiple disulfide-linked EGF and Kunitz domains; MEC-1 activity is required for normal mechanosensory behavior, and specifically for: 1) localization of the touch receptor degenerin channel complex, 2) accumulation of MEC-5/collagen into the extracellular matrix surrounding touch receptor neurons, and 3) attachment of touch receptor processes to the body wall; mec-1 promoter-GFP fusions indicate that, in addition to the six touch receptors, mec-1 can be expressed in many lateral neurons, the PVT interneuron, and the intestinal muscle; mec-1 expression in the touch receptors is, however, sufficient to rescue touch sensitivity in mec-1 mutant animals; MEC-1 appears to be an extracellular protein that: 1) binds to touch receptor processes uniformly and in a punctate pattern and 2) colocalizes with MEC-5 and degenerin channel puncta on these processes; while localization of MEC-1 into puncta requires the activity of mec-5 and mec-9, uniform MEC-1 localization requires the activity of him-4; in addition, proper organization and distribution of MEC-1, MEC-5, and the degenerin channel complex puncta appears to be regulated by interactions with adjacent epidermal tissue.
• Organism: Caenorhabditis elegans
• Automated Description: Predicted to enable serine-type endopeptidase inhibitor activity. Involved in detection of mechanical stimulus involved in sensory perception of touch; extracellular structure organization; and mechanosensory behavior. Predicted to be located in extracellular space. Expressed in PVT; cholinergic neurons; intestinal muscle; and touch receptor neurons.
• Biotype: SO:0001217
• Genetic Position: V :0.482741 ±0.000385
• Length (nt): 9889

1 Organism

• Name: Caenorhabditis elegans
• Taxon Id: 6239

1 Synonyms

• Value: WBGene00003165

Genomics

11 Transcripts

WormMine ID	Sequence Name	Length (nt)	Chromosome Location
Transcript:T07H8.4a.1	T07H8.4a.1	6150	V: 6956537-6966425
Transcript:T07H8.4d.1	T07H8.4d.1	6090	V: 6956537-6966401
Transcript:T07H8.4d.2	T07H8.4d.2	5989	V: 6956637-6966352
Transcript:T07H8.4j.1	T07H8.4j.1	768	V: 6956638-6957968
Transcript:T07H8.4i.1	T07H8.4i.1	2865	V: 6956638-6960653
Transcript:T07H8.4c.1	T07H8.4c.1	3504	V: 6956638-6961338
Transcript:T07H8.4b.1	T07H8.4b.1	5280	V: 6956638-6965058
Transcript:T07H8.4h.1	T07H8.4h.1	6021	V: 6956638-6966352
Transcript:T07H8.4f.1	T07H8.4f.1	5945	V: 6956736-6966352
Transcript:T07H8.4e.1	T07H8.4e.1	5865	V: 6957078-6966352
Transcript:T07H8.4g.1	T07H8.4g.1	4815	V: 6958798-6966352

Other

10 CDSs

WormMine ID	Sequence Name	Length (nt)	Chromosome Location
CDS:T07H8.4d	T07H8.4d	5988	V: 6956638-6956778
CDS:T07H8.4j	T07H8.4j	768	V: 6956638-6956778
CDS:T07H8.4i	T07H8.4i	2865	V: 6956638-6956778
CDS:T07H8.4c	T07H8.4c	3504	V: 6956638-6956778
CDS:T07H8.4e	T07H8.4e	5865	V: 6957078-6957398
CDS:T07H8.4f	T07H8.4f	5457	V: 6957565-6957601
CDS:T07H8.4a	T07H8.4a	6024	V: 6956638-6956778
CDS:T07H8.4b	T07H8.4b	5058	V: 6956638-6956778
CDS:T07H8.4g	T07H8.4g	4815	V: 6958798-6959517
CDS:T07H8.4h	T07H8.4h	6021	V: 6956638-6956778

4 RNAi Result

• WBRNAi00052813
• WBRNAi00018412
• WBRNAi00089153
• WBRNAi00103515

159 Allele

• gk963301
• gk963553
• gk964259
• gk964351
• gk963850
• gk964527
• gk962860
• gk964528
• WBVar01973969
• gk633957
• gk238337
• gk238336
• WBVar01973970
• gk238358
• gk238357
• gk238361
• gk238360
• gk238359
• gk238339
• gk238338
• gk238346
• gk238345
• gk238344
• gk238343
• gk238342
• gk238341
• gk238340
• gk238350
• gk238349
• gk238348

1 Chromosome

• WormBase ID: V
• Organism: Caenorhabditis elegans
• Length (nt): 20924180

1 Chromosome Location

• Feature . Primary Identifier: WBGene00003165
• Start: 6956537
• End: 6966425
• Strand: 1

4 Data Sets

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

0 Downstream Intergenic Region

158 Expression Clusters

Regulated By Treatment	Description	Algorithm	Primary Identifier
	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 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
	TGF- Dauer pathway adult transcriptional targets. Results obtained by comparing the microarray results of the dauer-constitutive mutants daf-7(e1372), daf-7(m62), and daf-1(m40) with dauer-defective mutants daf-3(mgDf90), daf-5(e1386), and daf-7(e1372);daf-3(mgDf90) double mutants at the permissive temperature, 20C, on the first day of adulthood.	SAM	WBPaper00031040:TGF-beta_adult_upregulated
	Neuronally enriched transcripts according to a comparison of neuronal nuclei IP samples to total nuclei using isolation of nuclei from tagged specific cell types (INTACT) technology.	DESEQ2, fold change > 2 and FDR < 0.01.	WBPaper00062103:neuron_enriched
	Transcripts that showed significantly increased expression glp-1(e2141); TU3401 animals comparing to in TU3401 animals.	Fold change > 2, FDR < 0.01.	WBPaper00065993:glp-1(e2141)_upregulated
Bacteria infection: Enterococcus faecalis	Genes with increased expression after 24 hours of infection by E.faecalis Fold changes shown are pathogen vs OP50.	For RNA-seq and tiling arrays, log2 fold changes between gene expression values of infected versus uninfected nematodes were calculated. For log2 fold changes > 0.00001 the values > 81.25th percentile were defined as up-regulated and for log2 fold changes < -0.00001 the values < 18.75th percentile were defined as down-regulated.	WBPaper00038438:E.faecalis_24hr_upregulated_TilingArray
	Genes that are significantly up regulated in tdp-1(ok803) poly(A) RNA-seq verses in N2.	DESeq v1.14, with cut-off p-value < 0.05 and FDR < 0.1.	WBPaper00046012:tdp-1(ok803)_upregulated
	Transcripts that showed significantly decreased expression in atfs-1(cmh15) (null allele) animals comparing to in N2 animals at L4 larva stage.	edgeR, fold change > 2, FDR < 0.05	WBPaper00060909:atfs-1(cmh15)_downregulated
	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
	Genes with expression level regulated by genotype (N2 vs CB4856) 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_regulated_aging
	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 sin-3(tm1276) comparing to in N2.	DESeq2, fold change > 2, p-value < 0.01.	WBPaper00061203:sin-3(tm1276)_upregulated
	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
	Transcripts that showed significantly increased expression in aak-1(tm1944);aak-2(ok524) animals comparing to in N2.	DEseq 1.18.0, adjusted p-value < 0.05.	WBPaper00056471:aak-1(tm1944);aak-2(ok524)_upregulated
	Genes that showed significantly increased expression in daf-2(e1370);hel-1(gk148684) comparing to in hel-1(gk148684)	To identify DEGs, Students t test and the log2 median ratio test were performed to compute t values and median ratios for all the annotated genes. The adjusted P values from each test were computed using an empirical distribution of the null hypothesis, which was obtained from random permutations of the samples. Finally, the adjusted P values from the individual tests were combined to compute the overall P values using Stouffers method , and genes with overall P < 0.05 and fold change > 1.5 were selected as DEGs.	WBPaper00047131:daf-2(e1370)_upregulated_hel-1(gk148684)-background
	Genes that showed significantly increased expression in daf-2(e1370) comparing to in N2.	To identify DEGs, Students t test and the log2 median ratio test were performed to compute t values and median ratios for all the annotated genes. The adjusted P values from each test were computed using an empirical distribution of the null hypothesis, which was obtained from random permutations of the samples. Finally, the adjusted P values from the individual tests were combined to compute the overall P values using Stouffers method , and genes with overall P < 0.05 and fold change > 1.5 were selected as DEGs.	WBPaper00047131:daf-2(e1370)_upregulated_N2-background
	Transcripts that showed significantly decreased expression in N2 animals exposed to 0.1mM Paraquat from hatching to reaching adult stage.	DESeq2 version 1.22.2, p < 0.05	WBPaper00064716:paraquat_downregulated
	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 that showed significantly increased expression in hpk-1(pk1393) comparing to in N2 at adult day 2.	DESeq 2, fold change > 2, FDR < 0.05.	WBPaper00065581:hpk-1(pk1393)_upregulated
	Transcripts that showed significantly increased expression in hda-1(ne4752[3xFLAG-Degron-HDA-1]) in gonads dissected from 1-day old adult animals.	Salmon was used to map the mRNA-seq reads with the worm database WS268, and its output files were imported to DESeq2 in R. The differentially expressed genes were filtered by fold change more than 2 and adjusted p-value < 0.05. The scatter plots were generated by the plot function in R.	WBPaper00061479:hda-1(ne4752)_upregulated
	Transcripts that showed significantly increased expression in mep-1(ne4629[MEP-1-GFP-Degron]) in gonads dissected from 1-day old adult animals.	Salmon was used to map the mRNA-seq reads with the worm database WS268, and its output files were imported to DESeq2 in R. The differentially expressed genes were filtered by fold change more than 2 and adjusted p-value < 0.05. The scatter plots were generated by the plot function in R.	WBPaper00061479:mep-1(ne4629)_upregulated
	Transcripts that showed significantly increased expression in wdr-23(mac32) embryos from parents fed with E. coliHB101, comparing to N2 embryos parents fed with E. coli HB101.	DESeq2, Fold Change > 2 or < 0.5.	WBPaper00059566:wdr-23(mac32)_upregulated
	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
	Transcripts that showed significantly increased expression in mut-16(pk710), comparing to in N2 animals.	DESeq2 v. 1.22.2, adjusted p-value <= 0.05.	WBPaper00059605:mut-16(pk710)_upregulated
	Transcripts that showed significantly increased expression in hda-2(ok1479) comparing to in N2 animals.	DESeq2 (version 1.28.1), FDR < 0.01, fold change > 2.	WBPaper00062159:hda-2(ok1479)_upregulated
	Transcripts that showed significantly increased expression in npr-15(tm12539) comparing to in N2 at L4 larva stage.	Fold change > 2, FDR < 0.05.	WBPaper00066608:npr-15(tm12539)_upregulated

6 Expression Patterns

• Primary Identifier: Expr1031500
• Pattern: Tiling arrays expression graphs

• Primary Identifier: Expr3463
• Remark: Because of the expression in non-touch receptor neurons, mec-1 (also tagged with gfp) was tested whether could rescue the Mec phenotype when expressed from the touch receptor neurons-specific mec-18 promoter. Touch receptor expression was sufficient for rescue (three strains produced 90% +/- 5% touch-sensitive animals; N = 70). LacZ expression was used to test protein topology with respect to the plasma membrane, because cytoplasmic, but not extracellular, beta-galactosidase is active . When lacZ was fused directly after the DNA for the predicted signal sequence, no beta-galactosidase activity was found, suggesting that the resulting fusion protein is extracellular. Insertion of an artificial transmembrane domain after the signal sequence restored activity. beta-galactosidase activity was also absent when lacZ was fused at codon 45, directly after sequence for the weakly predicted transmembrane domain. As before, insertion of a sequence encoding an artificial transmembrane domain before lacZ restored activity. These results suggest that MEC-1 does not contain a transmembrane domain between residues 21 and 41.
• Pattern: The mec-1 promoter expressed GFP in the touch receptor neurons, many lateral neurons (the SDQ, PLN, and ALN neurons and two neurons of the dorsal sublateral cord), the PVT neuron, and the intestinal muscle.
• Subcellular Localization: Expression of a full-length MEC-1::GFP protein fusion from the mec-1 promoter rescued the mec-1(e1496) null phenotype and revealed that MEC-1 was processed differently in touch receptor neurons. The fusion protein was visible in the ER of the same non-touch cells seen with the promoter fusion and in some neurons of the ventral cord, but it was not seen along their processes. In contrast, MEC-1::GFP was consistently visible in the ER and along the processes of the touch receptor neurons. In addition, MEC-1::GFP was sometimes seen along the edge of the body wall muscles. Since these cells did not express the promoter fusion, this muscle fluorescence suggests that MEC-1 is a secreted protein.

• Primary Identifier: Expr1156414
• Pattern: Developmental gene expression time-course. Raw data can be downloaded from ftp://caltech.wormbase.org/pub/wormbase/datasets-published/hashimshony2015

• Primary Identifier: Expr2013495
• 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: Expr1026744
• Pattern: Developmental gene expression time-course. Raw data can be downloaded from ftp://caltech.wormbase.org/pub/wormbase/datasets-published/levin2012

• Primary Identifier: Expr2031729
• 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).

20 GO Annotation

12 Homologues

1 Locations

• Feature . Primary Identifier: WBGene00003165
• Start: 6956537
• End: 6966425
• Strand: 1

20 Ontology Annotations

0 Regulates Expr Cluster

1 Sequence

• Length: 9889

1 Sequence Ontology Term

• Name: gene

2 Strains

• WBStrain00004236
• WBStrain00004291

1 Upstream Intergenic Region

• WormBase ID: intergenic_region_chrV_6956144..6956536
• Length (nt): 393
• Chromosome Location: V: 6956144-6956536
• Organism: Caenorhabditis elegans