WormMine: Gene WBGene00003260

• WormBase Gene ID: WBGene00003260
• Gene Name: mir-1
• Sequence Name: T09B4.11
• Brief Description: mir-1 encodes a muscle-specific microRNA (miRNA) conserved in Caenorhabditis briggsae, Drosophila, mice, and humans; miR-1 activity is required for proper pre- and postsynaptic functions at neuromuscular junctions; postsynaptic targets of miR-1 include the UNC-29 and UNC-63 nicotinic acetylcholine receptors and the MEF-2 muscle transcription factor; miR-1 regulation of presynaptic function is mediated by a MEF-2-dependent retrograde signal that requires the RAB-3 synaptic vesicle GTPase; miR-1 is expressed at uniform levels throughout C. elegans development and is also detected in him-8 mutant animals as well as dauer and starved L1 larvae; a mir-1::gfp transcriptional fusion is expressed in pharyngeal and body wall muscle.
• Organism: Caenorhabditis elegans
• Automated Description: Expressed in body wall musculature; muscle cell; and pharyngeal muscle cell. Used to study Parkinson's disease.
• Biotype: SO:0001265
• Genetic Position: I :0.867368 ±0.006934
• Length (nt): 96

1 Organism

• Name: Caenorhabditis elegans
• Taxon Id: 6239

1 Synonyms

• Value: WBGene00003260

Genomics

2 Transcripts

WormMine ID	Sequence Name	Length (nt)	Chromosome Location
Transcript:T09B4.11b	T09B4.11b	21	I: 6172677-6172697
Transcript:T09B4.11a	T09B4.11a	22	I: 6172716-6172737

Other

0 CDSs

0 RNAi Result

12 Allele

• gk962858
• gk962706
• gk963902
• gk964505
• gk742558
• tm1635
• gk276
• n4101
• n4102
• gk314835
• zen208
• dev462

1 Chromosome

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

1 Chromosome Location

• Feature . Primary Identifier: WBGene00003260
• Start: 6172662
• End: 6172757
• Strand: -1

2 Data Sets

• WormBaseAcedbConverter
• C. elegans genomic annotations (GFF3 Gene)

1 Downstream Intergenic Region

• WormBase ID: intergenic_region_chrI_6171659..6172661
• Length (nt): 1003
• Chromosome Location: I: 6171659-6172661
• Organism: Caenorhabditis elegans

19 Expression Clusters

Regulated By Treatment	Description	Algorithm	Primary Identifier
	MicroRNAs that showed significantly decreased expression in alg-5(ram2), comparing to in N2.	DESeq2, Fold change > 1.5.	WBPaper00051404:alg-5(ram2)_downregulated_miRNA
	micro RNAs that exhibit changes in expression during adulthood (p-value < = 0.05).	Authors searched for targets with seed matches of perfect Watson-Crick base-pair complementarity to positions two-eight of the miRNAs (counting from the 5' end). In order to consider these seed matches as potential target sites, authors required a minimal cut-off for binding specificity of the remainder of the miRNA to the target. Recent evidence suggests that this is not required for function in humans, but 3' binding does occur in studies of C. elegans. Authors used the scoring algorithm from Robins et al. (2005). The binding cut-off is determined by creating a second-order Markov model of the background for the 3' UTRs. The cut off was p-value < = 0.05.	WBPaper00028344:adult_expr_change
	miRNAs that showed increased expression in 1 day post L4 adult hermaphrodite eat-2(ad1116) comparing to in N2.	A fold change >= 1.5 with a minimum read count of >= 10 were used to filter the differentially expressed miRNA. The p-value cutoff was set at p <= 0.05 based on Kals Z test statistical.	WBPaper00046156:eat-2(ad1116)_Day1_upregulated
	miRNA with increased expression in N2 1-day post L4 adult hermaphrodite comparing to in N2 L4 larva.	DEGseq and GFOLD were used to analyze miRNAs expression. Authors chose miRNAs which had more than two-fold difference in expression (P < 0.001, q < 0.01 of Storey) from DEGseq, and miRNAs which had more than two-fold difference in expression (GFOLD score > 0 for up-regulation and GFOLD score < 0 for down-regulation) from GFOLD outcomes. Then authors obtained the intersection of up-regulated miRNAs and down-regulated miRNAs for each stage from the chosen miRNAs, respectively.	WBPaper00045316:miRNA_N2_adult_vs_L4_upregulated_adult
	MicroRNAs that showed significantly increased expression in alg-2(ok304), comparing to in N2.	DESeq2, Fold change > 1.5.	WBPaper00051404:alg-2(ok304)_upregulated_miRNA
	MicroRNAs that showed significantly decreased expression in alg-5(tm1163), comparing to in N2.	DESeq2, Fold change > 1.5.	WBPaper00051404:alg-5(tm1163)_downregulated_miRNA
	miRNA with increased expression in prg-1(wm161) comparing to in N2.	DEGseq and GFOLD were used to analyze miRNAs expression. Authors chose miRNAs which had more than two-fold difference in expression (P < 0.001, q < 0.01 of Storey) from DEGseq, and miRNAs which had more than two-fold difference in expression (GFOLD score > 0 for up-regulation and GFOLD score < 0 for down-regulation) from GFOLD outcomes. Then authors obtained the intersection of up-regulated miRNAs and down-regulated miRNAs for each stage from the chosen miRNAs, respectively.	WBPaper00045316:miRNA_prg-1_upregulated_L2
	miRNAs with age dependent abundance in wild type animals.	Details available in Supplementary material of the paper. Diff Exp, is the approximate ratio of expression comparing Young to Old animals (11 day difference in age). The raw p-value is for the null hypothesis that the Diff exp Ratio = 1 (based on robust inference - see supplemental information) and the associated 95% CI of the ratio.	WBPaper00042527:age_dependent_miRNA
	miRNA with increased expression in prg-1(wm161) comparing to in N2.	DEGseq and GFOLD were used to analyze miRNAs expression. Authors chose miRNAs which had more than two-fold difference in expression (P < 0.001, q < 0.01 of Storey) from DEGseq, and miRNAs which had more than two-fold difference in expression (GFOLD score > 0 for up-regulation and GFOLD score < 0 for down-regulation) from GFOLD outcomes. Then authors obtained the intersection of up-regulated miRNAs and down-regulated miRNAs for each stage from the chosen miRNAs, respectively.	WBPaper00045316:miRNA_prg-1_upregulated_L1
	miRNA with increased expression in prg-1(wm161) comparing to in N2.	DEGseq and GFOLD were used to analyze miRNAs expression. Authors chose miRNAs which had more than two-fold difference in expression (P < 0.001, q < 0.01 of Storey) from DEGseq, and miRNAs which had more than two-fold difference in expression (GFOLD score > 0 for up-regulation and GFOLD score < 0 for down-regulation) from GFOLD outcomes. Then authors obtained the intersection of up-regulated miRNAs and down-regulated miRNAs for each stage from the chosen miRNAs, respectively.	WBPaper00045316:miRNA_prg-1_upregulated_L3
	miRNA with increased expression in prg-1(wm161) comparing to in N2.	DEGseq and GFOLD were used to analyze miRNAs expression. Authors chose miRNAs which had more than two-fold difference in expression (P < 0.001, q < 0.01 of Storey) from DEGseq, and miRNAs which had more than two-fold difference in expression (GFOLD score > 0 for up-regulation and GFOLD score < 0 for down-regulation) from GFOLD outcomes. Then authors obtained the intersection of up-regulated miRNAs and down-regulated miRNAs for each stage from the chosen miRNAs, respectively.	WBPaper00045316:miRNA_prg-1_upregulated_L4
	MicroRNAs that showed significantly increased expression in mir-71(n4115) comparing to in N2 at 4-days post L4 adult hermaphrodite.	Differential expression for both small RNA- and mRNA-seq data was tested using DESeq2; P-values were adjusted for multiple testing by Benjamini-Hochberg method.	WBPaper00053318:mir-71(n4115)_upregulated_miRNA
Bacteria infection: Pseudomonas aeruginosa PA14	miRNAs up regulated by Pseudomonas aeruginosa infection.	N.A.	WBPaper00046303:P.aeruginosa_upregulated_miRNA
	miRNAs in F1 generation up regulated by exposure to 20uM and 20mM nicotine during F0 generation.	Statistical analysis was based on t-test for independent samples via SPSS to compare each of the nicotine treatments with control (i.e. low vs. control and high vs. control). Welch test correction was performed to account for unequal variance in each of the compared groups (control and treatment). In addition, to increase the statistical stringency, miRNAs differential expression was deemed significant only if it fulfilled two criteria: p value , 0.05 and expression changed by at least 50% relative to control.	WBPaper00049006:nicotine_upregulated_F1
	MicroRNAs that showed significantly decreased expression after animals were exposed to 1 mg per liter multi-walled carbon nanotubes (MWCNTs) from L1 larva to young adult.	DESeq, cut-off of 2-fold change.	WBPaper00045019:MWCNT_downregulated
	MicroRNAs that showed significantly increased expression in alg-1(gk214), comparing to in N2.	DESeq2, Fold change > 1.5.	WBPaper00051404:alg-1(gk214)_upregulated_miRNA
	Micro RNAs that showed significantly decreased expression in day 8 adults comparing to in day 1 adults in neuron.	Differentially expressed miRNAs were identified using DEGseq based on unique molecular identifier (UMI). A minimum UMI sum of 10 in 3 replicates was set as the threshold of expression. MiRNAs with more than five reads were defined as expressed. Differential expression of miRNAs was analysed by t-test (P value < 0.05 and fold-change > 1.5 or < 0.67) after Box-Cox transformation. MiRNA targets were identified by TargetScanWorm (Release 6.2) and Pearson Correlation Coefficient smaller than -0.2.	WBPaper00066447:Day8_vs_Day1_downregulated_neuron
	miRNAs in F2 generation up regulated by exposure to 20uM and 20mM nicotine during F0 generation.	Statistical analysis was based on t-test for independent samples via SPSS to compare each of the nicotine treatments with control (i.e. low vs. control and high vs. control). Welch test correction was performed to account for unequal variance in each of the compared groups (control and treatment). In addition, to increase the statistical stringency, miRNAs differential expression was deemed significant only if it fulfilled two criteria: p value , 0.05 and expression changed by at least 50% relative to control.	WBPaper00049006:nicotine_upregulated_F2
	miRNAs that showed significantly increased expression after 48 hour treatment in 10uM sanguinarine.	Fold change > 2.	WBPaper00055663:sanguinarine_upregulated

6 Expression Patterns

• Primary Identifier: Expr13549
• Pattern: Muscle and pharynx.

• Primary Identifier: Expr8411
• Pattern: Expression detected from early embryos to adults specifically in pharynx and precursors.

• Primary Identifier: Expr8106
• Remark: Picture: Figure 1A.
• Pattern: This construct expressed GFP in both pharyngeal and body muscles, with no apparent expression in other tissues.

• Primary Identifier: Expr12251
• Pattern: For each of the mir::GFP-pest reporters (Plin-4::GFP-pest, Plet-7::GFP-pest, mir-1::GFP-pest) post-embryonic GFP-pest expression was first detected at approximately 14 hours post L1 arrest. Once transcriptionally activated, Plin-4::GFP-pest and Plet-7::GFP-pest reporters peak in expression by 18-20 hours and diminish with similar kinetics. For animals expressing the Plet-7::GFP-pest reporter GFP-pest expression was monitored for longer periods after release from L1 arrest. Consistent with the highly pulsatile nature of this expression pattern, GFP-pest expression was reinitiated at 30 hours, which correlates with the later portions of the L2 stage. While transcriptional activation of the Pmir-1::GFP-pest reporter was also initiated at 14 hours post-L1 arrest, the peak of Pmir-1::GFPpest expression occurred at a later time point, and diminished with slower kinetics, as compared to Plin-4::GFP-pest and Plet-7::GFP-pest expression.The majority of animals which harbor the Plin-4::GFP-pest transgene cease GFP-pest expression by L3 ecdysis and resume expression by the mid-L4 stage. The pulse of Plin-4::GFP-pest expression at the L4 stage extends through the early portion of young adulthood and completely overlaps with the lethargus period in all animals. Plet-7::GFP-pest expression followed a similar pattern. However, GFP-pest expression was more variable at the L3-to-L4 transition and L4-specific induction of this transgene was primarily restricted to the lethargus period. In contrast to the expression profiles of the lin-4 and let-7 reporters, induction of Pmir-1::GFP-pest expression began during, or immediately after, L3 ecdysis and persisted into the L4 stage. A second pulse of Pmir-1::GFP-pest expression completely overlapped with the L4 lethargus period and continued into early adulthood. Collectively, these results suggest that the expression patterns of lin-4, let-7 and mir-1 are dynamic throughout development and that the cyclical transcription of these miRNAs is mediated by their cognate promoter sequences.

• Primary Identifier: Expr2467
• Pattern: Faint signals were detected in embryos, larval stages (L1, L2, L3, L4), adults, and glp-4(bn2) adults.

• Primary Identifier: Expr1664
• Pattern: Expressed in embryo, L1, L2, L3, L4 and adults.

0 GO Annotation

0 Homologues

1 Locations

• Feature . Primary Identifier: WBGene00003260
• Start: 6172662
• End: 6172757
• Strand: -1

0 Ontology Annotations

4 Regulates Expr Cluster

Regulated By Treatment	Description	Algorithm	Primary Identifier
	Transcripts that showed significantly increased expression in mir-1(gk276) animals comparing to in N2 L4 larva.	Limma-voom, fold change > 2, FDR < 0.05.	WBPaper00058945:mir-1(gk276)_upregulated
	Transcripts that showed significantly decreased expression in mir-1(gk276) animals comparing to in N2 L4 larva.	Limma-voom, fold change > 2, FDR < 0.05.	WBPaper00058945:mir-1(gk276)_downregulated
	Proteins that showed significantly decreased expression in mir-1(gk276) comparing to in N2.	Fold change > 2, p-value < 0.05.	WBPaper00061740:mir-1(gk276)_downregulated_protein
	Proteins that showed significantly increased expression in mir-1(gk276) comparing to in N2.	Fold change > 2, p-value < 0.05.	WBPaper00061740:mir-1(gk276)_upregulated_protein

1 Sequence

• Length: 96

1 Sequence Ontology Term