WormMine

WS294

Intermine data mining platform for C. elegans and related nematodes

Gene :

WormBase Gene ID  ? WBGene00003039 Gene Name  mir-48
Sequence Name  ? F56A12.3 Brief Description  mir-48 encodes a microRNA (miRNA); mir-48 was identified in screens for new heterochronic loci required for the proper temporal control of specific postembryonic cell divisions; mutations in mir-48 result in precocious terminal differentiation of hypodermal seam cells and secretion of adult cuticle one stage too early.
Organism  Caenorhabditis elegans Automated Description  Involved in miRNA-mediated gene silencing by inhibition of translation and positive regulation of development, heterochronic. Expressed in P5.p hermaphrodite; P7.p hermaphrodite; RID; and seam cell. Used to study Parkinson's disease.
Biotype  SO:0001265 Genetic Position  V :6.27549 ±0.003412
Length (nt)  ? 98
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1 Organism

Name Taxon Id
Caenorhabditis elegans 6239

1 Synonyms

Value
WBGene00003039

Genomics

2 Transcripts

WormMine ID Sequence Name Length (nt) Chromosome Location
Transcript:F56A12.3b F56A12.3b 22   V: 14364435-14364456
Transcript:F56A12.3a F56A12.3a 23   V: 14364472-14364494
 

Other

0 CDSs

0 RNAi Result

13 Allele

Public Name
gk963271
gk963706
gk963301
gk964458
gk964459
gk963796
gk706175
gk728139
ve33
n4097
nDf51
ve12
gk603122

1 Chromosome

WormBase ID Organism Length (nt)
V Caenorhabditis elegans 20924180  

1 Chromosome Location


Feature . Primary Identifier 		Start End Strand
WBGene00003039 14364412 14364509 -1

3 Data Sets

Name URL
WormBaseAcedbConverter  
GO Annotation data set  
C. elegans genomic annotations (GFF3 Gene)  

1 Downstream Intergenic Region

WormBase ID Name Sequence Name Length (nt) Chromosome Location Organism
intergenic_region_chrV_14362452..14364411   1960 V: 14362452-14364411 Caenorhabditis elegans

33 Expression Clusters

Regulated By Treatment Description Algorithm Primary Identifier
  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 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
  Potental DAF-12 target genes identified by ChIP-chip analysis performed on strain ALF4 [daf-12 Affymetrix TAS software that computed for each probe estimates of fold enrichment (in linear scale) over hybridization with input DNA. At the same time, TAS calculated for each probe a p-value by applying a Wilcoxon signed rank test. A threshold of 2.5 was selected, which corresponds to probe intensities approximately 2.5 times stronger on the ChIP array than on the Input array. Additional TAS threshold parameters were MinRun=180 bp, MaxGap=300 bp. TAS analysis showed that the selected threshold of 2.5 corresponds approximately to a p-value of 0.01. WBPaper00040221:DAF-12_target_ALF4
  Transcripts that showed significantly decreased expression in mrps-5(RNAi) animals comparing to animals injected with empty vector. Differential expression was assessed using a Partial least-squares discriminant analysis (PLS-DA) using mixomics setting a variable of importance (VIP) score of greater than 1 as significant. WBPaper00059328:mrps-5(RNAi)_downregulated_mRNA
  miRNA with decreased 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_downregulated_adult
  Micro RNAs that showed significantly increased expression in day 8 adults comparing to in day 1 adults in intestine. 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_upregulated_intestine
  Potental DAF-12 target genes identified by ChIP-chip analysis performed on strain ALF9 [daf-12 Affymetrix TAS software that computed for each probe estimates of fold enrichment (in linear scale) over hybridization with input DNA. At the same time, TAS calculated for each probe a p-value by applying a Wilcoxon signed rank test. A threshold of 2.5 was selected, which corresponds to probe intensities approximately 2.5 times stronger on the ChIP array than on the Input array. Additional TAS threshold parameters were MinRun=180 bp, MaxGap=300 bp. TAS analysis showed that the selected threshold of 2.5 corresponds approximately to a p-value of 0.01. WBPaper00040221:DAF-12_target_ALF9
  MicroRNAs that showed significantly altered expression in hsf-1(+);+HS vs hsf-1(RNAi);+HS. Worms remained on RNAi plates until the L4 larval-stage before being heat shocked by submerging plates in a 33C water bath for 30 minutes. The Benjamini-Hochberg correction for multiple testing was then used to determine significantly altered miRNAs between each treatment condition. Micro RNAs with q-value < 0.05 was considered differentially expressed. WBPaper00052959:hsf-1(RNAi)_regulated_miRNA_HS-dependent
  miRNA with increased expression in N2 L2 larva comparing to in N2 L1 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_L2_vs_L1_upregulated_adult
  miRNAs that showed significantly increased expression in pry-1(mu38) comparing to in N2. Fold change > 2, FDR < 0.05 WBPaper00057033:pry-1(mu38)_upregulated
  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
  miRNA with decreased expression in N2 L1 larva comparing to in N2 embryo. 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_L1_vs_embryo_downregulated_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
  miRNA with decreased 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_downregulated_embryo
  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
  miRNA with increased expression in N2 L4 larva comparing to in N2 L3 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_L4_vs_L3_upregulated_adult
  miRNA with increased expression in prg-1(wm161) L1 larva comparing to in prg-1(wm161) embryo. 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_L1_vs_embryo_upregulated_adult
  miRNA with increased expression in prg-1(wm161) L3 larva comparing to in prg-1(wm161) L2 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_prg-1_L3_vs_L2_upregulated_adult
  miRNA with decreased expression in prg-1(wm161) L4 larva comparing to in prg-1(wm161) L3 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_prg-1_L4_vs_L3_downregulated_adult
  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_adult
  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
  MicroRNAs that showed significantly increased expression in alg-5(tm1163), comparing to in N2. DESeq2, Fold change > 1.5. WBPaper00051404:alg-5(tm1163)_upregulated_miRNA
  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
  Micro RNAs that showed significantly increased expression in drsh-1(ok369) comparing to in N2. Fold change > 1.5. WBPaper00055896:drsh-1(ok369)_upregulated
  miRNA with increased expression in prg-1(wm161) L4 larva comparing to in prg-1(wm161) L3 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_prg-1_L4_vs_L3_upregulated_adult

11 Expression Patterns

Remark Reporter Gene Primary Identifier Pattern Subcellular Localization
Reporter gene fusion type not specified. mir-48(del)::gfp gave a similar pattern.   Expr3769 gfp expression was detected in the lateral hypodermal seam and the vulva beginning during the L4 stage, when driven by a wild-type fragment extending 1.0 kb upstream from the miR-48 coding sequence (mir-48::gfp). A single head neuron, RID, also consistently expressed gfp, but did so in a nontemporally regulated fashion and served as an internal control.  
    Expr8455 Expressed from L1 to adulthood. Expression seen in vulval cells, seam cells, head and tail neurons.  
Picture: Fig 2A.   Expr8401 Northern blot temporal expression: L1 to adult.  
    Expr12250 Animals carrying the mir-48::gfp construct showed temporal expression in the hypodermal seam cells two stages earlier than its let-7 homologues at the L2 stage. mir-48 was not detected in the gonad at any stage. specific expression of mir-48 was observed in the P5.p and P7.p cells that will assume 2 vulval cell fates. It is interesting to note that expression of mir-237, mir-84, and mir-48 was absent in the P6.p cell during the mid- to late L3 stage, and expression of mir-237 and mir-84 but not mir-48 was present in the anchor cell.  
    Expr3740 Previous study reported that the let-7 family members, miR-84, miR-48, and miR-241, were expressed in a similar manner as the let-7 RNA, which was first detected during the L3 stage. However, this paper reveal that miR-241 and miR-48 both appeared one stage earlier than let-7 at eL2 with robust expression by L3. miR-84 appeared at low levels in the early L1 stage, was upregulated to an intermediate level in mid-L2, and had a high level of expression in early L4.  
Figure S4.   Expr12023 pri-mir-48 miRNA transcript levels oscillate during wild-type larval development, peaking once per larval stage.  
    Expr13378 In WT animals, miR-48, miR-241, and miR-237 miRNAs were expressed at very low levels during the L1, when LIN-14 is normally expressed, and increased in abundance 20- to 30-fold by the L3 when LIN-14 is down-regulated.  
Previous studies did not detect the four let-7 family members until the L3 stage, but earlier expression of all four microRNAs was detected by enhancing the sensitivity of detection.   Expr3772 When normalized to U6 expression, miR-48 reached half-maximal expression at about the L3 stage.  
    Expr2522 No signal detected in embryos, L1 and L2 larva. Intense signals detected in L3, L4 larva, adults, and glp-4(bn2) adults.  
    Expr12017    
    Expr10883    

3 GO Annotation

Annotation Extension Qualifier
  involved_in
  involved_in
  involved_in

0 Homologues

1 Locations


Feature . Primary Identifier 		Start End Strand
WBGene00003039 14364412 14364509 -1

3 Ontology Annotations

Annotation Extension Qualifier
  involved_in
  involved_in
  involved_in

0 Regulates Expr Cluster

1 Sequence

Length
98

1 Sequence Ontology Term