WormMine: Gene WBGene00003163

• WormBase Gene ID: WBGene00003163
• Gene Name: mdl-1
• Sequence Name: R03E9.1
• Brief Description: mdl-1 encodes a basic helix-loop-helix (bHLH) protein similar to the vertebrate MAD transcriptional regulators; in vitro, MDL-1 can heterodimerize, and bind an E-box DNA sequence, with MXL-1, a C. elegans MAX-like bHLH protein; when expressed in rat embryonic fibroblasts, MDL-1 is able to suppress c-MYC/RAS-induced cell transformation, in a manner dependent upon an intact, predicted SIN3 interaction domain; mdl-1::gfp promoter fusions are expressed in a number of different tissues, including the posterior intestine, anterior and ventral cord neurons, pharyngeal and body wall muscles, somatic gonad precursors, and hypodermal cells; yeast one-hybrid and ChIP experiments indicate that DAF-3/Smad can bind the mdl-1 promoter; in addition, mdl-1 pharyngeal expression is specifically increased in daf-3(RNAi) animals, suggesting that DAF-3 directly negatively regulates mdl-1 transcription in pharyngeal tissue during dauer formation.
• Organism: Caenorhabditis elegans
• Automated Description: Enables protein heterodimerization activity. Contributes to sequence-specific DNA binding activity. Involved in determination of adult lifespan and regulation of cell differentiation. Located in nucleus. Part of transcription regulator complex. Expressed in body wall musculature; neurons; pharynx; and somatic nervous system. Used to study Parkinson's disease. Human ortholog(s) of this gene implicated in neurofibrosarcoma and prostate cancer. Is an ortholog of human MXI1 (MAX interactor 1, dimerization protein).
• Biotype: SO:0001217
• Genetic Position: X :-2.50858 ±0.015767
• Length (nt): 1549

1 Organism

• Name: Caenorhabditis elegans
• Taxon Id: 6239

1 Synonyms

• Value: WBGene00003163

Genomics

1 Transcripts

WormMine ID	Sequence Name	Length (nt)	Chromosome Location
Transcript:R03E9.1.1	R03E9.1.1	1211	X: 6742351-6743899

Other

1 CDSs

WormMine ID	Sequence Name	Length (nt)	Chromosome Location
CDS:R03E9.1	R03E9.1	846	X: 6742486-6742639

15 RNAi Result

• WBRNAi00000455
• WBRNAi00001392
• WBRNAi00051181
• WBRNAi00017355
• WBRNAi00026016
• WBRNAi00026017
• WBRNAi00034559
• WBRNAi00092029
• WBRNAi00115661
• WBRNAi00027425
• WBRNAi00092068
• WBRNAi00115865
• WBRNAi00115631
• WBRNAi00092010
• WBRNAi00063190

35 Allele

• gk964260
• gk962713
• tm10572
• gk963451
• gk963910
• gk853891
• gk634530
• gk793294
• gk848581
• gk691561
• gk315565
• gk720996
• gk890819
• gk883108
• gk412296
• gk368287
• gk673642
• gk765991
• gk869355
• gk811184
• gk774242
• gk828714
• tm311
• WBVar00034556
• WBVar00034561
• WBVar00034551
• h3683
• WBVar00080075
• WBVar00080076
• ok5897

1 Chromosome

• WormBase ID: X
• Organism: Caenorhabditis elegans
• Length (nt): 17718942

1 Chromosome Location

• Feature . Primary Identifier: WBGene00003163
• Start: 6742351
• End: 6743899
• 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_chrX_6743900..6743977
• Length (nt): 78
• Chromosome Location: X: 6743900-6743977
• Organism: Caenorhabditis elegans

234 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 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
	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
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 glp-1(e2141); TU3401 animals comparing to in TU3401 animals.	Fold change > 2, FDR < 0.01.	WBPaper00065993:glp-1(e2141)_upregulated
	Transcripts that showed significantly increased expression after animals were treated with 50uM Rifampicin from day 1 to day 3 adult hermaphradite.	DESeq2(v1.14.1), fold change > 2, p-value < 0.05	WBPaper00055354:Rifampicin_upregulated
Fungi infection: Myzocytiopsis humicola	Transcripts that showed significantly altered expression 12 hours after animals were infected by M. humicola.	Differentially expressed genes as determined by Kallisto and Sleuth (pval<0.01, qval<0.1).	WBPaper00060871:M.humicola-infection_12h_regulated
	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 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
	Genes up regulated in alg-1(gk214) comparing to in N2.	Differential expression was assessed using an empirical Bayes statistics using the eBayes function.	WBPaper00040823:alg-1(gk214)_upregulated
	Transcripts expressed in pharynx, according to PAT-Seq analysis using Pmyo-2-GFP-3XFLAG mRNA tagging.	Cufflinks FPKM value >=1.	WBPaper00050990:pharynx_expressed
	Transcripts that showed significantly increased expression in day 1 adult hermaphrodite comparing to in L4 larva daf-16(mu86);glp-1(e2141) animals.	Fold change > 2, FDR < 0.05	WBPaper00064088:Day-1-adult_vs_L4_upregulated_daf-16(mu86);glp-1(e2141)
	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 increased expression in day 1 adult hermaphrodite comparing to in L4 larva glp-1(e2141) animals.	Fold change > 2, FDR < 0.05	WBPaper00064088:Day-1-adult_vs_L4_upregulated_glp-1(e2141)
	Transcripts that showed significantly increased expression after four-day-old young adult worms were placed on NGM plates seeded with OP50 in the presence 5% Agaro-oligosaccharides(AGO) for 24 h, comparing to animals grown in the absence of AGO.	Fold change > 2.	WBPaper00064306:Agaro-oligosaccharides_upregulated
	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
Dietary restriction	Transcripts that showed significantly decreased expression after N2 animals were under dietary restriction (DR, OP50 OD = 0.1) from 3-day post L4 till 6-day post L4 adult hermaphrodite stage, comparing to under ad libtum (AL, OP50 OD = 3) condition.	Bioconductor package edgeR, p < 0.05.	WBPaper00056443:DietaryRestriction_downregulated
	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
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
	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
	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 increased expression in daf-2(e1370) comparing to in control animals.	NOIseq(v2.34.0), fold change > = 1.5, Differentially expressed genes (DEGs) were defined as having a probability of differentialexpression > 95%.	WBPaper00064727:daf-2(e1370)_upregulated

12 Expression Patterns

• Primary Identifier: Expr1031498
• Pattern: Tiling arrays expression graphs

• Primary Identifier: Expr696
• Remark: Reporter gene fusion type not specified. This information was extracted from published material (Archana Sharma-Oates, Andrew Mounsey and Ian A. Hope). mdl-1 coexpressed with mxl-1 in posterior intestinal cells.
• Pattern: Expression begins at midpoint of the animal and continues to the posterior intestinal cells. GFP detected in all larval stages but most strongly from late L1 to L4. Strongly detected in posterior 8 intestinal cells, late L1 just prior to their division near the end of L1. No expression observed in anterior cells. GFP detected in intestinal cells after L1 although only in some of the divided binucleated posterior intestinal cells. Expression also detected in many neurons during all larval stages (CEPDR and CEPVR). Expression observed in posterior pharyngeal bulb muscle cells and ventral cord motorneurons in all larval stages, as well as in several hypodermal cells and body wall muscles. Expression detected in Z1 and Z4 cells in L1 larva but not in their daughters. 8 posterior intestinal cells at late L1. posterior pharyngeal bulb muscle cells. CEPDR, CEPVR at L1-L4. Hypodermal cells at L1-L4. Z1 and Z4 at L1. ventral cord motorneurons at L1-L4. Body wall muscles. Hypodermis at L1-L4.

• Primary Identifier: Expr15753

• Primary Identifier: Expr11547
• Pattern: Expressed in head and tail neurons, ventral and dorsal NC neurons, pharynx.

• Primary Identifier: Expr7628
• Remark: Clone: pUL#JRH/AC3
• Pattern: Strong expression, particularly through mid larval stages. Quite general. Strongest throughout pharynx, then in nervous system, particularly nerve cord, then in hypodermis, apart from seam cells which show up as shadows.

• Primary Identifier: Expr7629
• Remark: Clone: pUL#JRH/AC3
• Pattern: Expression is seen in the ventral and dorsal nerve cords and commissures running between them, from late embryo to adult. Some, presumably background pharyngeal expression is also seen and a very few individuals show more generalised expression.

• Primary Identifier: Expr1200006
• Pattern: Data from the TransgeneOme project

• Primary Identifier: Expr14850
• Pattern: mdl-1 is expressed in D-type motor neurons.

• Primary Identifier: Expr2013467
• 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: Expr1154889
• Pattern: Developmental gene expression time-course. Raw data can be downloaded from ftp://caltech.wormbase.org/pub/wormbase/datasets-published/hashimshony2015

• Primary Identifier: Expr1026588
• Pattern: Developmental gene expression time-course. Raw data can be downloaded from ftp://caltech.wormbase.org/pub/wormbase/datasets-published/levin2012

• Primary Identifier: Expr2031701
• 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).

16 GO Annotation

14 Homologues

1 Locations

• Feature . Primary Identifier: WBGene00003163
• Start: 6742351
• End: 6743899
• Strand: 1

16 Ontology Annotations

0 Regulates Expr Cluster

1 Sequence

• Length: 1549

1 Sequence Ontology Term