Accession ID: MIRT007363 [miRNA, hsa-miR-509-3p :: CFTR, target gene]
pre-miRNA Information
pre-miRNA ID hsa-mir-509-1LinkOut: [miRBase ]
Description Homo sapiens miR-509-1 stem-loop
Comment The mature sequence shown here represents the most commonly cloned form from large-scale cloning studies includes a 1 nt extension at the 3' end (A), which is incompatible with the genome sequence.
2nd Structure of pre-miRNA
Disease
Mature miRNA Information
Mature miRNA hsa-miR-509-3p
Mature Sequence 55| UGAUUGGUACGUCUGUGGGUAG |76
Evidence Experimental
Experiments Array-cloned
Putative hsa-miR-509-3p Targets LinkOut: [ TargetScanS 5.1 | MicroCosm | microRNA.org | miRecords | miRDB | miRo | miRNAMap 2.0 ]
Gene Information
Gene Symbol CFTR LinkOut: [ Entrez Gene | BioGPS | Wikipedia | iHop ]
Synonyms ABC35, ABCC7, CF, CFTR/MRP, MRP7, TNR-CFTR, dJ760C5.1
Description cystic fibrosis transmembrane conductance regulator (ATP-binding cassette sub-family C, member 7)
Transcript NM_0004    LinkOut: [ RefSeq ]
Expression LinkOut: [ BioGPS ]
Putative miRNA Targets on CFTR LinkOut: [ TargetScan 5.1 | MicroCosm | miRNAMap 2.0 ]
3'UTR of CFTR
(miRNA target sites are highlighted)
>CFTR|NM_0004|3'UTR
   1 TAGAGAGCAGCATAAATGTTGACATGGGACATTTGCTCATGGAATTGGAGCTCGTGGGACAGTCACCTCATGGAATTGGA
  81 GCTCGTGGAACAGTTACCTCTGCCTCAGAAAACAAGGATGAATTAAGTTTTTTTTTAAAAAAGAAACATTTGGTAAGGGG
 161 AATTGAGGACACTGATATGGGTCTTGATAAATGGCTTCCTGGCAATAGTCAAATTGTGTGAAAGGTACTTCAAATCCTTG
 241 AAGATTTACCACTTGTGTTTTGCAAGCCAGATTTTCCTGAAAACCCTTGCCATGTGCTAGTAATTGGAAAGGCAGCTCTA
 321 AATGTCAATCAGCCTAGTTGATCAGCTTATTGTCTAGTGAAACTCGTTAATTTGTAGTGTTGGAGAAGAACTGAAATCAT
 401 ACTTCTTAGGGTTATGATTAAGTAATGATAACTGGAAACTTCAGCGGTTTATATAAGCTTGTATTCCTTTTTCTCTCCTC
 481 TCCCCATGATGTTTAGAAACACAACTATATTGTTTGCTAAGCATTCCAACTATCTCATTTCCAAGCAAGTATTAGAATAC
 561 CACAGGAACCACAAGACTGCACATCAAAATATGCCCCATTCAACATCTAGTGAGCAGTCAGGAAAGAGAACTTCCAGATC
 641 CTGGAAATCAGGGTTAGTATTGTCCAGGTCTACCAAAAATCTCAATATTTCAGATAATCACAATACATCCCTTACCTGGG
 721 AAAGGGCTGTTATAATCTTTCACAGGGGACAGGATGGTTCCCTTGATGAAGAAGTTGATATGCCTTTTCCCAACTCCAGA
 801 AAGTGACAAGCTCACAGACCTTTGAACTAGAGTTTAGCTGGAAAAGTATGTTAGTGCAAATTGTCACAGGACAGCCCTTC
 881 TTTCCACAGAAGCTCCAGGTAGAGGGTGTGTAAGTAGATAGGCCATGGGCACTGTGGGTAGACACACATGAAGTCCAAGC
 961 ATTTAGATGTATAGGTTGATGGTGGTATGTTTTCAGGCTAGATGTATGTACTTCATGCTGTCTACACTAAGAGAGAATGA
1041 GAGACACACTGAAGAAGCACCAATCATGAATTAGTTTTATATGCTTCTGTTTTATAATTTTGTGAAGCAAAATTTTTTCT
1121 CTAGGAAATATTTATTTTAATAATGTTTCAAACATATATAACAATGCTGTATTTTAAAAGAATGATTATGAATTACATTT
1201 GTATAAAATAATTTTTATATTTGAAATATTGACTTTTTATGGCACTAGTATTTCTATGAAATATTATGTTAAAACTGGGA
1281 CAGGGGAGAACCTAGGGTGATATTAACCAGGGGCCATGAATCACCTTTTGGTCTGGAGGGAAGCCTTGGGGCTGATGCAG
1361 TTGTTGCCCACAGCTGTATGATTCCCAGCCAGCACAGCCTCTTAGATGCAGTTCTGAAGAAGATGGTACCACCAGTCTGA
1441 CTGTTTCCATCAAGGGTACACTGCCTTCTCAACTCCAAACTGACTCTTAAGAAGACTGCATTATATTTATTACTGTAAGA
1521 AAATATCACTTGTCAATAAAATCCATACATTTGTGTGAAA
Target sites Provided by authors  Predicted by miRanda
miRNA-target interactions (Predicted by miRanda)
IDDuplex structurePositionScoreMFE
1
miRNA  3' gaUGGGUG---UCUGCAUGGUUAGu 5'
            || |||   ||| | ||||||| 
Target 5' agACACACTGAAGAAGCACCAATCa 3'
1042 - 1066 164.00 -15.40
2
miRNA  3' gaugggugUCUG-CA---UGGUUAGu 5'
                  |||: ||   ||||:|| 
Target 5' tctgaagaAGATGGTACCACCAGTCt 3'
1413 - 1438 130.00 -14.40
3
miRNA  3' gauggguGUCUGCAUGGUUagu 5'
                 |||:: ||||||   
Target 5' tattgtcCAGGTCTACCAAaaa 3'
658 - 679 119.00 -10.72
Experimental Support 1 for Functional miRNA-Target Interaction
miRNA:Target hsa-miR-509-3p :: CFTR    [ Functional MTI ]
Validation Method Luciferase reporter assay
Conditions PANC-1 , HEK293
Location of target site 3'UTR
Tools used in this research PITA , RNAhybrid
Original Description (Extracted from the article) ... Validation of miRNA Target Sites in the CFTR 39UTR Functional validation of the 2 predicted miRNA target sites containing the identified genetic variants was performed using a dual-luciferase assay in HEK 293 and in Panc1 cell lines. A luciferase-reporter construct containing the wild-type 39UTR of CFTR was co-transfected with the miRNAs mimics of interest. As shown in Figure 3A, a statistically significant reduction of the luciferase activity was observed for both the miRNAs used (miR- 509-3p, miR-433) when compared with control mimics. The down regulation observed ranged from a reduction of the luciferase expression of about 50% in the case of miR-433, up to 60% for the miR-509-3p. A western blot analysis was performed to check the levels of CFTR protein in Panc1 cells transient transfected with the two miRNAs. Both miRNAs were able, although to a different extent, to significantly reduce the endogenous levels of CFTR protein (Figure 3B). To further validate and to mimic a more physiological context, where different miRNAs may be expressed at high levels from their genomic loci, we cloned the genes of miR- 433 and miR-509-3p in lentiviral vectors. We also constructed a lentiviral vector expressing a short hairpin RNA (shRNA) against the target region of both miR-433 and miR-509-3p (Figure 4A). Then, we produced lentiviral particles with which we transduced Panc 1 cells. So we obtained Panc 1 cells stably expressing each of the two miRNAs of interest or the shRNA (Panc-miR-433, Panc- miR-509-3p, Panc-sh-39UTR). Thus, we transient transfected each of these cell lines with the wild-type construct of CFTR 39UTR. The levels of luciferase in cells expressing high levels of miR-433 or miR-509 compared to not transduced cells were comparable to those obtained using the miRNA mimics (Figure 4B, white rectangles), the residual luciferase activity in Panc-sh-39UTR was close to 10% compared to the control. The same results were obtained in HEK293 cell line. ...

- Amato, F. Seia, M. Giordano, S. Elce, A. et al., 2013, PLoS One.

miRNA-target interactions (Provided by authors)
IDDuplex structurePosition
1
miRNA  3' gaUGGGUG---UCUGCAUGGUUAGu 5'
            || |||   ||| | ||||||| 
Target 5' -gACACACUGAAGAAGCACCAAUCa 3'
1 - 24
Article - Amato, F. Seia, M. Giordano, S. Elce, A. et al.
- PLoS One, 2013
Cystic fibrosis (CF) is the most frequent lethal genetic disorder among Caucasians. It depends on alterations of a chloride channel expressed by most epithelial cells and encoded by CFTR gene. Also using scanning techniques to analyze the whole coding regions of CFTR gene, mutations are not identified in up to 10% of CF alleles, and such figure increases in CFTR-related disorders (CFTR-RD). Other gene regions may be the site of causing-disease mutations. We searched for genetic variants in the 1500 bp of CFTR 3' untranslated region, typical target of microRNA (miRNA) posttranscriptional gene regulation, in either CF patients with the F508del homozygous genotype and different clinical expression (n = 20), CF (n = 32) and CFTR-RD (n = 43) patients with one or none mutation after CFTR scanning and in controls (n = 50). We identified three SNPs, one of which, the c.*1043A>C, was located in a region predicted to bind miR-433 and miR-509-3p. Such mutation was peculiar of a CFTR-RD patient that had Congenital Bilateral Absence of Vas Deferens (CBAVD), diffuse bronchiectasis, a borderline sweat chloride test and the heterozygous severe F508del mutation on the other allele. The expression analysis demonstrated that the c.*1043A>C increases the affinity for miR-509-3p and slightly decreases that for the miR-433. Both miRNAs cause in vitro a reduced expression of CFTR protein. Thus, the c.*1043A>C may act as a mild CFTR mutation enhancing the affinity for inhibitory miRNAs as a novel pathogenetic mechanism in CF.
LinkOut: [PMID: 23555973]
MiRNA-Target Expression Profile:

 
MiRNA-Target Interaction Network:
Strong evidence (reporter assay, western blot, qRT-PCR or qPCR)
Other evidence
2 hsa-miR-509-3p Target Genes:
ID Target Description Validation methods
Strong evidence Less strong evidence
MIRT004915 NTRK3 neurotrophic tyrosine kinase, receptor, type 3 2 2
MIRT007363 CFTR cystic fibrosis transmembrane conductance regulator (ATP-binding cassette sub-family C, member 7) 1 1