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MIR21 (microRNA 21)

Written2007-03Sadan Duygu Selcuklu, Mustafa Cengiz Yakicier, Ayse Elif Erson
Biology Department, Room: 141, Middle East Technical University, Ankara 06531, Turkey

(Note : for Links provided by Atlas : click)

Identity

Alias_namesMIRN21
Alias_symbol (synonym)hsa-mir-21
MIR-21
Other aliasMIRN21 (microRNA 21)
miR-21
HGNC (Hugo) MIR21
LocusID (NCBI) 406991
Atlas_Id 44019
Location 17q23.1  [Link to chromosome band 17q23]
Location_base_pair Starts at 59841266 and ends at 59841337 bp from pter ( according to hg19-Feb_2009)  [Mapping MIR21.png]
Local_order Based on Mapviewer, genes flanking MIRN21 oriented from centromere to telomere on 17q23 are:
  • TMEM49, transmembrane protein 49, 17q23.1 .
  • MIRN21, microRNA 21, 17q23.1 .
  • TUBD1, tubulin, delta 1, 17q23.1 .
  • LOC729565 ,similar to NADH dehydrogenase (ubiquinone) 1 beta subcomplex, 8, 19kDa, 17q23.1 .
  • RPS6KB1, ribosomal protein S6 kinase, 70kDa, polypeptide 1, 17q23.1 .
  • Fusion genes
    (updated 2016)
    MIR21 (17q23.1) / WDR53 (3q29)

    DNA/RNA

     
      A: Characterization of the full-length about 3433 nt pri-MIRN21.
    Open Reading frame analysis within the 3433 nucleotides identified a potential 124 amino acids long peptide. This uncharacterized ORF is located near the transcription start site (+114).
    This potential peptide sequence shows homology to a 180-amino-acid human protein. However, it is not clear yet if pri-MIRN21 functions as an mRNA as well.
    B: Stem-loop structure of MIRN21.
    Description The gene is located in an intergenic region. The length of MIRN21 gene is reported as 3433 nucleotides long. It overlaps with the 3' UTR end of the Transmembrane Protein 49 (TMEM 49) (also known as Human Vacuole Membrane Protein 1, VMP-1).
    Transcription RNA Pol II is suggested to be the most likely enzyme involved in miRNA transcription. However, current studies also provide evidences for RNA Pol III dependent transcription of few miRNAs interspersed among repetitive Alu elements.
    For MIRN21, the major RNA polymerase is likely to be RNA Pol II due to the presence of 5' cap and 3' poly (A) tail of the pri-MIRN21. Chromatin immunoprecipitation (ChIP) analysis of upstream sequences of MIRN21 showed enrichment for Pol II but not Pol III.
    MIRN21 gene was shown to harbor a 5' promoter element. 1008 bp DNA fragment for MIRN21 gene was cloned (-959 to +49 relative to T1 transcription site, see Figure 1; A). Analysis of the sequence showed a candidate "CCAAT" box transcription control element located approximately about 200 nt upstream of the T1 site. T1 transcription site was found to be located in a sequence similar to "TATA" box (ATAAACCAAGGCTCTTACCATAGCTG). To test the activity of the element, about 1kb DNA fragment was inserted into the 5' end of firefly luciferase indicator gene and transfected into 293T cells. The sense orientation insert, unlike antisense, induced luciferase activity.
    pri-MIRN21 gene was reported to have two transcription sites, T1 and T2. T1 (identified by RACE, +1 start site) was reported as the minor transcription site and T2 (identified by RACE, +27 start site) as the major transcription start site. Based on the data of pmiR-21-luc expression plasmid, the endogenous pri-MIRN21 was suggested to utilize T1 and T2 sites for initiation of transcription (Figure 1; A).

    The maturation of miRNA gene involves sequential process.

    Pri-miRNA
    The miRNA genes are first transcribed in nucleus as long primary transcripts called pri-miRNA. The primary transcript for MIRN21 is found to be 3433-nt long.
    For localization of the pri-MIRN21 transcript, total, nuclear and cytoplasmic RNA fractions from HeLa cells were oligo-dT primed and reverse transcribed into cDNA. pri-MIRN21 transcript was found mainly in the nucleus as well as modest levels in the cytoplasm.
    Sequence: NCBI cDNA clone: BC053563.
    Length: 3389bp

    Pre-miRNA
    The primary transcripts of microRNAs are processed by enzymatic microprocessor Drosha (RNase III enzyme) and DGCR8 (dsRNA binding protein) from their 3' and 5' cleavage sites into an intermediate stem-loop precursor or pre-miRNA in the nucleus.
    The precursor of MIRN21 is 72 bases long (pre-MIRN21), forms a secondary structure, and contains the mature miRNA sequence, stem and terminal loop structures with 2-nt 3'overhang (Figure 1; B). The precursor is then transferred from nucleus to cytoplasm by the enzyme Exportin 5. In cytoplasm, a second RNase III enzyme, Dicer, removes terminal loop generating about 20-bp RNA duplex.
    Length: 72 bases
    Sequence: UGUCGGGUAGCUUAUCAGACUGAUGUUGACUGUUGAAUCUCAUGGCAACACCAGUCGAUGGGCUGUCUGACA (Figure 1; B).

    Mature MIRN21
    The mature miRNA forms one strand of the RNA duplex. One strand is degraded and other is incorporated in to a protein complex, RNA induced silencing complex (RISC), targeting a partially complementary target mRNA.
    MIRN21 is 22 nucleotides long.
    Sequence: UAGCUUAUCAGACUGAUGUUGA .

    Pseudogene No reported pseudogenes.

    Protein

    Note miRNAs are not translated into amino acids.

    Mutations

    Note In a panel of 91 human cancer cell lines representing several human cancers, sequencing showed no sequence variations in mature miRNAs.
    In HCT-15 colon cancer cell line, pri-MIRN21 showed a A+29G (A/G) heterozygous variation (Figure 2).
    It was suggested that sequence variations in pri-miRNAs may cause structural alterations. However, the variation was not found to be affecting pri-MIRN21 processing when it was compared to the wild type.
     
      Localization of sequence variation in pri-MIRN21 in HTC-15 colon cancer cell line.

    Implicated in

    Note
      
    Entity Human neoplasms.
    Note Overexpression was fist shown in glioblastoma and then in papillary thyroid carcinoma (PTC), breast tumors and other various tumors (e.g. colorectal carcinoma, lung tumors, pancreatic tumors, prostate tumors, stomach tumors cholangiocarcinomas, neuroblastoma, hepatocellular carcinoma and uterine leiomyomas) and cervical adenocarcinoma cell line, HeLa.
    Relatively low expression was seen in cell lines HL-60 (promyelocytic leukemia), K562 (chronic myelogenous leukemia) and prostatic adenocarcinoma cell line.
    miRNA microarray data from 540 samples from 6 solid cancers (lung, stomach, prostate, colon, pancreatic and breast) showed overexpression of MIRN21 gene compared to normal cells.
      
      
    Entity Glioblastoma
    Disease Overexpression of MIRN21 was first shown in malignant human brain tumor cells. When, human glioblastoma tumor tissues, 12 early passage cultures (passage 3) from high grade gliomas and 6 glioblastoma cell lines (A172, U87, U373, LN229, LN428 and LN308) were compared to non-neoplastic glial cells and a variety of mammalian tissues, MIRN21 was found to be strongly overexpressed in the neoplastic samples. Moreover, oligonucleotide microarrays specific for 180 human and mouse miRNAs and Northern blotting methods were used to profile expression of MIRN21.In glioblastoma tissues its expression showed 5 to 100 fold increase compared to non-neoplastic brain sample and 5 to 30 fold increase in cell lines compared to normal.
    Oncogenesis Apoptosis: Loss-of-function approach was used to identify the biological significance of MIRN21 in glioblastoma cells. Sequence specific inhibitors (2'-O-methyl-oligonucleotides) were used to knock-down MIRN21 transcript and apoptosis activity (caspase-3 and caspase-7 enzymatic activities) was measured. 48 hours post-transfection, caspase activity increased 3-folds suggesting that MIRN21 acted as an anti-apoptotic factor in glioblastoma cells through blocking expression of key apoptosis-enabling genes.
      
      
    Entity Breast Cancer.
    Disease RNAs from 76 breast cancer tumors and 14 cell lines were analyzed by using miRNA microarray and Northern blotting (10 normal samples were used for comparison and normalization). MIRN21 was up-regulated and the results were confirmed by Northern blotting.
    Consistent with other studies, MIRN21 overexpression in breast tumors compared to matched normal breast tissues was verified by stem-loop RT real-time PCR and miRNA microarrays containing 157 mature human miRNAs.
    Oncogenesis Apoptosis: Inhibition of MIRN21 in breast cancer cell line MCF-7 by transfection of anti-mir-21 inhibitors (chemically modified oligonucleotides) showed growth inhibition. Treatment of transfected MCF-7 cell line with anticancer drug topotecan (TPT) caused cell growth inhibition by 40%. The results suggested suppression of MIRN21 gene could sensitize tumor cells to anticancer drugs. Inhibition of MIRN21 in a xenograft carcinoma mouse model verified tumor growth suppression.
    Transfection results of MCF-7 cells with a general caspase inhibitor suggested MIRN21 role in regulation of bcl-2 gene expression indirectly, possibly controlling expression of genes involved in apoptosis pathways including bcl-2.
      
      
    Entity Pancreatic cancer.
    Disease 16 pancreatic adenocarcinomas and 10 adjacent benign tissues compared to 6 normal pancreas samples were analyzed for MIRN21 precursor expression and compared to mature MIRN21 by using real-time PCR assay. The results were consistent between precursor and mature MIRN21 showing overexpression.
      
      
    Entity Neuroblastoma.
    Disease Neuroblastoma cell line, SH-SY5Y, was treated with a tumor promoting agent (12-O-tetradecanoyl phorbol 13-acetate (TPA)) to induce differentiation into a neuronal phenotype. Following stimulation, microarray analysis of stem-loop precursors was performed and MIRN21 showed 7-8 times higher expression compared to other up-regulated miRNAs showing 2-4 times relative increase.
      
      
    Entity Lung cancer.
    Disease Analysis of 104 pairs of primary lung cancers and non-cancerous lung tissues by microRNA microarray showed differential expression of mature MIRN21 among phenotypical and histological classifications. The results were confirmed by solution hybridization and RT-PCR. The results verified up-regulation of MIRN21 in lung cancer tissues compared to normals. Moreover, real time RT-PCR results for stem-loop precursor of MIRN21 showed at least 2-fold up-regulation in 66% of 32 cases.
      
      
    Entity Other cancers.
    Disease In other miRNA microarray studies, MIRN21 was found to be overexpressed in papillary thyroid cancer, hepatocellular carcinoma, cholangiocarcinomas and uterine leiomyomas. A study suggested that MIRN21 inhibition in a cervical adenocarcinoma cell line, HeLa, caused increase in cell growth.
    Prognosis MIRN21 (as well as 7 other miRNAs) expresion was correlated with adenocarcinoma patients' survival. Patients that have high expression of MIRN21 were found to have worse prognosis. Thus, in addition to potential role of MIRN21 in lung carcinogenesis through apoptosis pathway, it was suggested that expression profiles could be informative in adenocarcinoma patient survival.
    Cytogenetics Genomic amplification of chromosome band 17q23.2 in neuroblastoma, breast cancer, colon cancer, lung cancer is known.
    Oncogenesis Apoptosis: MIRN21 was found to be highly over-expressed in malignant cholangiocytes. In cholangiocarcinoma cells it was shown that one of the targets of MIRN21 was PTEN encoding phosphatase that inhibited the survival and growth promoting activity of PI 3-kinase (phosphoinositole 3-kinase) signaling.
    In another report, inhibiton of MIRN21 showed increased sensitivity to gemcitabine. The results suggested that MIRN21 regulated gemcitabine-induced apoptosis by PTEN (phosphatase and tensin homolog) dependent activation of PI 3-kinase and AKT/mTOR signaling. These studies suggested anti-apoptotic role for the MIRN21 gene.
      

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    Citation

    This paper should be referenced as such :
    Erson, AE ; Yakicier, MC ; Selcuklu, SD
    MIRN21 (microRNA 21)
    Atlas Genet Cytogenet Oncol Haematol. 2007;11(3):232-236.
    Free journal version : [ pdf ]   [ DOI ]
    On line version : http://AtlasGeneticsOncology.org/Genes/MIRN21ID44019ch17q23.html


    Other Leukemias implicated (Data extracted from papers in the Atlas) [ 1 ]
      Aggressive natural killer leukemia (ANKL)


    Other Solid tumors implicated (Data extracted from papers in the Atlas) [ 1 ]
      Lung: Translocations in Squamous Cell Carcinoma


    External links

    Nomenclature
    HGNC (Hugo)MIR21   31586
    Cards
    AtlasMIRN21ID44019ch17q23
    Entrez_Gene (NCBI)MIR21  406991  microRNA 21
    AliasesMIRN21; hsa-mir-21; miR-21; miRNA21
    GeneCards (Weizmann)MIR21
    Ensembl hg19 (Hinxton)ENSG00000199004 [Gene_View]
    Ensembl hg38 (Hinxton)ENSG00000199004 [Gene_View]  chr17:59841266-59841337 [Contig_View]  MIR21 [Vega]
    ICGC DataPortalENSG00000199004
    TCGA cBioPortalMIR21
    AceView (NCBI)MIR21
    Genatlas (Paris)MIR21
    WikiGenes406991
    SOURCE (Princeton)MIR21
    Genetics Home Reference (NIH)MIR21
    miRBaseMIR21
    dbDEMCMIR21
    Genomic and cartography
    GoldenPath hg38 (UCSC)MIR21  -     chr17:59841266-59841337 +  17q23.1   [Description]    (hg38-Dec_2013)
    GoldenPath hg19 (UCSC)MIR21  -     17q23.1   [Description]    (hg19-Feb_2009)
    EnsemblMIR21 - 17q23.1 [CytoView hg19]  MIR21 - 17q23.1 [CytoView hg38]
    Mapping of homologs : NCBIMIR21 [Mapview hg19]  MIR21 [Mapview hg38]
    OMIM611020   
    Gene and transcription
    Genbank (Entrez)AF480502 AF480524 AF480557 AJ421741 AY699265
    RefSeq transcript (Entrez)
    RefSeq genomic (Entrez)
    Consensus coding sequences : CCDS (NCBI)MIR21
    Cluster EST : UnigeneHs.444569 [ NCBI ]
    CGAP (NCI)Hs.444569
    Alternative Splicing GalleryENSG00000199004
    Gene ExpressionMIR21 [ NCBI-GEO ]   MIR21 [ EBI - ARRAY_EXPRESS ]   MIR21 [ SEEK ]   MIR21 [ MEM ]
    Gene Expression Viewer (FireBrowse)MIR21 [ Firebrowse - Broad ]
    SOURCE (Princeton)Expression in : [Datasets]   [Normal Tissue Atlas]  [carcinoma Classsification]  [NCI60]
    BioGPS (Tissue expression)406991
    GTEX Portal (Tissue expression)MIR21
    Protein : pattern, domain, 3D structure
    Domain families : Pfam (Sanger)
    Domain families : Pfam (NCBI)
    Conserved Domain (NCBI)MIR21
    DMDM Disease mutations406991
    Blocks (Seattle)MIR21
    Human Protein AtlasENSG00000199004
    Protein Interaction databases
    FunCoupENSG00000199004
    BioGRIDMIR21
    STRING (EMBL)MIR21
    ZODIACMIR21
    Ontologies - Pathways
    Huge Navigator MIR21 [HugePedia]
    snp3D : Map Gene to Disease406991
    BioCentury BCIQMIR21
    ClinGenMIR21
    Clinical trials, drugs, therapy
    Chemical/Protein Interactions : CTD406991
    Chemical/Pharm GKB GenePA164722590
    Clinical trialMIR21
    Miscellaneous
    canSAR (ICR)MIR21 (select the gene name)
    Probes
    Litterature
    PubMed499 Pubmed reference(s) in Entrez
    GeneRIFsGene References Into Functions (Entrez)
    CoreMineMIR21
    EVEXMIR21
    GoPubMedMIR21
    iHOPMIR21
    REVIEW articlesautomatic search in PubMed
    Last year publicationsautomatic search in PubMed

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