pre-miRNA Information
pre-miRNA hsa-mir-569   
Genomic Coordinates chr3: 171106664 - 171106759
Synonyms MIRN569, hsa-mir-569, MIR569
Description Homo sapiens miR-569 stem-loop
Comment None
RNA Secondary Structure
Associated Diseases

Mature miRNA Information
Mature miRNA hsa-miR-569
Sequence 61| AGUUAAUGAAUCCUGGAAAGU |81
Evidence Experimental
Experiments SAGE
DRVs in miRNA
Mutant ID Mutant Position Mutant Source
COSN23021417 4 COSMIC
COSN1083370 8 COSMIC
COSN30455038 12 COSMIC
COSN24300323 13 COSMIC
COSN32068274 16 COSMIC
SNPs in miRNA
Mutant ID Mutant Position Mutant Source
rs752673293 5 dbSNP
rs1218920077 8 dbSNP
rs745722313 12 dbSNP
rs1368837885 14 dbSNP
Putative Targets

Gene Information
Gene Symbol VSIG2   
Synonyms 2210413P10Rik, CTH, CTXL
Description V-set and immunoglobulin domain containing 2
Transcript NM_014312   
Expression
Putative miRNA Targets on VSIG2
3'UTR of VSIG2
(miRNA target sites are highlighted)
>VSIG2|NM_014312|3'UTR
   1 CTTCTCCCGATCCCTGAGGGCGGTGAGGGGGAATATCAATAATTAAAGTCTGTGGGTACCATAAAAAAAAAAAAAAAAAA
  81 AAAAAAAAAAAAAAAAA
Target sites Provided by authors   Predicted by miRanda    DRVs    SNPs    DRVs & SNPs
DRVs in gene 3'UTRs
Mutant ID Mutant Position Mutant Source
COSN30492998 9 COSMIC
COSN1128299 14 COSMIC
COSN30448162 14 COSMIC
COSN30152350 16 COSMIC
COSN13308404 22 COSMIC
COSN1128296 24 COSMIC
COSN31556533 34 COSMIC
COSN31556489 36 COSMIC
COSN20059937 58 COSMIC
SNPs in gene 3'UTRs
Mutant ID Mutant Position Mutant Source
rs757986971 3 dbSNP
rs752723202 4 dbSNP
rs749970589 6 dbSNP
rs963596656 7 dbSNP
rs1246718846 9 dbSNP
rs764610806 14 dbSNP
rs1469138187 15 dbSNP
rs756762832 22 dbSNP
rs1207655694 24 dbSNP
rs1016114468 25 dbSNP
rs754352723 27 dbSNP
rs764649445 29 dbSNP
rs571472276 32 dbSNP
rs961435977 36 dbSNP
rs370596267 39 dbSNP
rs1363029602 46 dbSNP
rs546624160 48 dbSNP
rs199561614 54 dbSNP
rs886195853 58 dbSNP
Experimental Support 1 for Functional miRNA-Target Interaction
miRNA:Target ----
Validation Method
Conditions TZM-bl
Location of target site 3'UTR
Tools used in this research TargetScan , miRTarCLIP , Piranha
Original Description (Extracted from the article) ... PAR-CLIP data was present in GSM1462574. RNA binding protein: AGO2. Condition:TZM-bl ami BaL ...

- Whisnant AW; Bogerd HP; Flores O; Ho P; et al., 2013, mBio.

miRNA-target interactions (Provided by authors)
ID Duplex structure Position
1
miRNA  3' ugaAAGGUCCUAA------GUAAUUGa 5'
             ||||   |||      ||||||| 
Target 5' auaUUCCUACAUUAUGUGACAUUAACc 3'
1 - 27
Article - Whisnant AW; Bogerd HP; Flores O; Ho P; et al.
- mBio, 2013
UNLABELLED: The question of how HIV-1 interfaces with cellular microRNA (miRNA) biogenesis and effector mechanisms has been highly controversial. Here, we first used deep sequencing of small RNAs present in two different infected cell lines (TZM-bl and C8166) and two types of primary human cells (CD4(+) peripheral blood mononuclear cells [PBMCs] and macrophages) to unequivocally demonstrate that HIV-1 does not encode any viral miRNAs. Perhaps surprisingly, we also observed that infection of T cells by HIV-1 has only a modest effect on the expression of cellular miRNAs at early times after infection. Comprehensive analysis of miRNA binding to the HIV-1 genome using the photoactivatable ribonucleoside-induced cross-linking and immunoprecipitation (PAR-CLIP) technique revealed several binding sites for cellular miRNAs, a subset of which were shown to be capable of mediating miRNA-mediated repression of gene expression. However, the main finding from this analysis is that HIV-1 transcripts are largely refractory to miRNA binding, most probably due to extensive viral RNA secondary structure. Together, these data demonstrate that HIV-1 neither encodes viral miRNAs nor strongly influences cellular miRNA expression, at least early after infection, and imply that HIV-1 transcripts have evolved to avoid inhibition by preexisting cellular miRNAs by adopting extensive RNA secondary structures that occlude most potential miRNA binding sites. IMPORTANCE: MicroRNAs (miRNAs) are a ubiquitous class of small regulatory RNAs that serve as posttranscriptional regulators of gene expression. Previous work has suggested that HIV-1 might subvert the function of the cellular miRNA machinery by expressing viral miRNAs or by dramatically altering the level of cellular miRNA expression. Using very sensitive approaches, we now demonstrate that neither of these ideas is in fact correct. Moreover, HIV-1 transcripts appear to largely avoid regulation by cellular miRNAs by adopting an extensive RNA secondary structure that occludes the ability of cellular miRNAs to interact with viral mRNAs. Together, these data suggest that HIV-1, rather than seeking to control miRNA function in infected cells, has instead evolved a mechanism to become largely invisible to cellular miRNA effector mechanisms.
LinkOut: [PMID: 23592263]
CLIP-seq Support 1 for dataset GSM1462574
Method / RBP PAR-CLIP / AGO2
Cell line / Condition TZM-bl / TZM-bl ami BaL
Location of target site ENST00000411986.2 | 3UTR | AUAUUCCUACAUUAUGUGACAUUAACCUAUAUUCCUG
Tools used in this analysis TargetScan, miRTarCLIP, and Piranha
Article / Accession Series PMID: 23592263 / GSE59944
CLIP-seq Viewer Link
MiRNA-Target Expression Profile
Dataset Pearson Correlation P-value for Pearson Correlation Spearman Correlation P-value for Spearman Correlation Samples Chart
GSE28260 Renal cortex and medulla -0.776 9.1e-4 -0.753 1.5e-3 13 Click to see details
GSE21849 B cell lymphoma -0.353 3.0e-2 -0.186 1.7e-1 29 Click to see details
GSE17306 Multiple myeloma -0.255 3.9e-2 0.410 1.7e-3 49 Click to see details
GSE42095 Differentiated embryonic stem cells -0.21 1.7e-1 -0.043 4.2e-1 23 Click to see details
GSE26953 Aortic valvular endothelial cells 0.158 2.3e-1 0.177 2.0e-1 24 Click to see details
GSE21687 Ependynoma primary tumors -0.086 2.5e-1 -0.061 3.2e-1 64 Click to see details
GSE38974 Chronic obstructive pulmonary disease -0.14 2.5e-1 -0.223 1.4e-1 25 Click to see details
GSE28544 Breast cancer -0.115 3.0e-1 -0.202 1.7e-1 24 Click to see details
GSE14794 Lymphoblastoid cells -0.052 3.1e-1 0.005 4.8e-1 90 Click to see details
GSE38226 Liver fibrosis 0.059 4.0e-1 0.087 3.5e-1 21 Click to see details
GSE34608 Pulmonary tuberculosis and sarcoidosis -0.038 4.4e-1 0.102 3.3e-1 20 Click to see details
GSE32688 Pancreatic cancer 0.024 4.5e-1 -0.031 4.3e-1 32 Click to see details
GSE27834 Pluripotent stem cells -0.022 4.7e-1 -0.200 2.3e-1 16 Click to see details
GSE27834 Pluripotent stem cells -0.022 4.7e-1 -0.200 2.3e-1 16 Click to see details
GSE27834 Pluripotent stem cells -0.022 4.7e-1 -0.200 2.3e-1 16 Click to see details
GSE27834 Pluripotent stem cells -0.022 4.7e-1 -0.200 2.3e-1 16 Click to see details
MiRNA-Target Expression Profile (TCGA)
Tumor Pearson Correlation P-value for Pearson Correlation Spearman Correlation P-value for Spearman Correlation Samples Chart
58 hsa-miR-569 Target Genes:
Functional analysis:
ID Target Description Validation methods
Strong evidence Less strong evidence
MIRT004827 SPI1 Spi-1 proto-oncogene 2 1
MIRT086537 HSPE1-MOB4 HSPE1-MOB4 readthrough 2 2
MIRT086545 MOB4 MOB family member 4, phocein 2 2
MIRT154349 PARD6B par-6 family cell polarity regulator beta 2 4
MIRT182174 POU2F1 POU class 2 homeobox 1 2 2
MIRT190452 EIF5 eukaryotic translation initiation factor 5 2 2
MIRT191410 NAA30 N(alpha)-acetyltransferase 30, NatC catalytic subunit 2 2
MIRT199846 CSNK1G2 casein kinase 1 gamma 2 2 2
MIRT208376 SLC25A36 solute carrier family 25 member 36 2 2
MIRT275677 CARKD NAD(P)HX dehydratase 2 2
MIRT275764 TFDP1 transcription factor Dp-1 2 2
MIRT280470 UBR7 ubiquitin protein ligase E3 component n-recognin 7 (putative) 2 2
MIRT296592 FAM217B family with sequence similarity 217 member B 2 4
MIRT306847 FYTTD1 forty-two-three domain containing 1 2 2
MIRT443764 HLF HLF, PAR bZIP transcription factor 2 2
MIRT448026 GSR glutathione-disulfide reductase 2 2
MIRT448659 NCALD neurocalcin delta 2 2
MIRT449142 UQCRB ubiquinol-cytochrome c reductase binding protein 2 2
MIRT449225 RAD51B RAD51 paralog B 2 2
MIRT462421 TWISTNB TWIST neighbor 2 2
MIRT468478 SESN3 sestrin 3 2 4
MIRT478170 DENND5B DENN domain containing 5B 2 2
MIRT478577 VSIG2 V-set and immunoglobulin domain containing 2 2 2
MIRT481300 ATP5G3 ATP synthase, H+ transporting, mitochondrial Fo complex subunit C3 (subunit 9) 2 16
MIRT485894 ZFP36 ZFP36 ring finger protein 2 2
MIRT497242 FITM2 fat storage inducing transmembrane protein 2 2 2
MIRT500282 ZNF703 zinc finger protein 703 2 8
MIRT509536 RSBN1L round spermatid basic protein 1 like 2 4
MIRT511835 GPATCH8 G-patch domain containing 8 2 4
MIRT522437 MON1B MON1 homolog B, secretory trafficking associated 2 2
MIRT523538 GLO1 glyoxalase I 2 4
MIRT527631 MYBPC1 myosin binding protein C, slow type 2 4
MIRT528059 OLAH oleoyl-ACP hydrolase 2 2
MIRT532549 TXNL1 thioredoxin like 1 2 2
MIRT545503 NAP1L1 nucleosome assembly protein 1 like 1 2 2
MIRT546724 RNF6 ring finger protein 6 2 2
MIRT546737 RNF141 ring finger protein 141 2 2
MIRT550889 ACTA1 actin, alpha 1, skeletal muscle 2 2
MIRT554180 SLC35E2B solute carrier family 35 member E2B 2 2
MIRT555878 PAFAH1B2 platelet activating factor acetylhydrolase 1b catalytic subunit 2 2 2
MIRT558458 DCUN1D1 defective in cullin neddylation 1 domain containing 1 2 2
MIRT560375 TIMM8A translocase of inner mitochondrial membrane 8A 2 2
MIRT562672 AKT3 AKT serine/threonine kinase 3 2 2
MIRT563810 TUBA1B tubulin alpha 1b 2 2
MIRT564607 ZNF711 zinc finger protein 711 2 2
MIRT564881 YWHAE tyrosine 3-monooxygenase/tryptophan 5-monooxygenase activation protein epsilon 2 2
MIRT566724 MSL2 MSL complex subunit 2 2 2
MIRT566900 CSRP3 cysteine and glycine rich protein 3 2 2
MIRT570002 COL1A2 collagen type I alpha 2 chain 2 2
MIRT612300 ZFP14 ZFP14 zinc finger protein 2 2
MIRT618334 ZNF813 zinc finger protein 813 2 2
MIRT627658 RSBN1 round spermatid basic protein 1 2 2
MIRT630660 PLAG1 PLAG1 zinc finger 2 2
MIRT640802 MYCL1 MYCL proto-oncogene, bHLH transcription factor 1 1
MIRT651370 ZBTB21 zinc finger and BTB domain containing 21 2 2
MIRT709227 GPSM2 G protein signaling modulator 2 2 2
MIRT712058 ZBTB34 zinc finger and BTB domain containing 34 2 2
MIRT725006 ZPBP zona pellucida binding protein 2 2
miRNA-Drug Resistance Associations
miRNA Drug Name CID NSC FDA Effect/Pattern Detection Method Level Phenotype Condition
hsa-miR-569 Doxorubicin 31703 NSC123127 approved resistant High Breast Cancer cell line (MCF-7)
hsa-miR-569 Verapamil 2520 NSC272366 approved resistant High Breast Cancer cell line (MCF-7)
hsa-miR-569 Trametinib 11707110 NSC758246 approved sensitive High Melanoma cell line (M14) (50nM)
hsa-miR-569 Vemurafenib 42611257 NSC761431 approved sensitive High Melanoma cell line (M14) (50nM)
hsa-mir-569 Fluorouracil 3385 NSC19893 approved sensitive cell line (OE19)
hsa-mir-569 Cisplatin 5460033 NSC119875 approved sensitive cell line (BxPC3)
hsa-miR-569 Tamoxifen 2733525 NSC180973 approved resistant cell line (LCC2)
hsa-miR-569 Fluorouracil 3385 NSC19893 approved resistant cell line (KM12C) (72 h)
hsa-miR-569 Sunitinib 5329102 NSC750690 approved resistant tissue (CardB)
hsa-miR-569 Paclitaxel 36314 NSC125973 approved sensitive cell line (SKOV3)
hsa-miR-569 Cisplatin 5460033 NSC119875 approved sensitive cell line (A549)
hsa-miR-569 Cisplatin 5460033 NSC119875 approved sensitive cell line (A2780)
hsa-miR-569 Paclitaxel/Docetaxel/Vinorelbine/Doxorubicin/Etoposide/Methotrexate/Gemcitabine resistant cell line (Bats-72)

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