pre-miRNA Information | |
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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 | ||||||||||||||||
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Mature miRNA | hsa-miR-569 | |||||||||||||||
Sequence | 61| AGUUAAUGAAUCCUGGAAAGU |81 | |||||||||||||||
Evidence | Experimental | |||||||||||||||
Experiments | SAGE | DRVs in miRNA |
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SNPs in miRNA |
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Putative Targets |
Gene Information | |||||||||||||||||||||
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Gene Symbol | ZFP36 | ||||||||||||||||||||
Synonyms | G0S24, GOS24, NUP475, RNF162A, TIS11, TTP, zfp-36 | ||||||||||||||||||||
Description | ZFP36 ring finger protein | ||||||||||||||||||||
Transcript | NM_003407 | ||||||||||||||||||||
Expression | |||||||||||||||||||||
Putative miRNA Targets on ZFP36 | |||||||||||||||||||||
3'UTR of ZFP36 (miRNA target sites are highlighted) |
>ZFP36|NM_003407|3'UTR 1 CAAAGTGACTGCCCGGTCAGATCAGCTGGATCTCAGCGGGGAGCCACGTCTCTTGCACTGTGGTCTCTGCATGGACCCCA 81 GGGCTGTGGGGACTTGGGGGACAGTAATCAAGTAATCCCCTTTTCCAGAATGCATTAACCCACTCCCCTGACCTCACGCT 161 GGGGCAGGTCCCCAAGTGTGCAAGCTCAGTATTCATGATGGTGGGGGATGGAGTGTCTTCCGAGGTTCTTGGGGGAAAAA 241 AAATTGTAGCATATTTAAGGGAGGCAATGAACCCTCTCCCCCACCTCTTCCCTGCCCAAATCTGTCTCCTAGAATCTTAT 321 GTGCTGTGAATAATAGGCCTTCACTGCCCCTCCAGTTTTTATAGACCTGAGGTTCCAGTGTCTCCTGGTAACTGGAACCT 401 CTCCTGAGGGGGAATCCTGGTGCTCAAATTACCCTCCAAAAGCAAGTAGCCAAAGCCGTTGCCAAACCCCACCCATAAAT 481 CAATGGGCCCTTTATTTATGACGACTTTATTTATTCTAATATGATTTTATAGTATTTATATATATTGGGTCGTCTGCTTC 561 CCTTGTATTTTTCTTCCTTTTTTTGTAATATTGAAAACGACGATATAATTATTATAAGTAGACTATAATATATTTAGTAA 641 TATATATTATTACCTTAAAAGTCTATTTTTGTGTTTTGGGCATTTTTAAATAAACAATCTGAGTGTAAGCTGG Target sites
Provided by authors
Predicted by miRanda
DRVs
SNPs
DRVs & SNPs
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miRNA-target interactions (Predicted by miRanda) |
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DRVs in gene 3'UTRs | |||||||||||||||||||||
SNPs in gene 3'UTRs |
Experimental Support 1 for Functional miRNA-Target Interaction | |||||||
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miRNA:Target | ---- | ||||||
Validation Method |
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Conditions | C8166 | ||||||
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 GSM1462572. RNA binding protein: AGO2. Condition:C8166 NL4-3
... - Whisnant AW; Bogerd HP; Flores O; Ho P; et al., 2013, mBio. |
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miRNA-target interactions (Provided by authors) |
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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]
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CLIP-seq Support 1 for dataset GSM1462572 | |
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Method / RBP | PAR-CLIP / AGO2 |
Cell line / Condition | C8166 / C8166 NL4-3 |
Location of target site | ENST00000597629.1 | 3UTR | AUGCAUUAACCCACUCCCCUG |
Tools used in this analysis | TargetScan, miRTarCLIP, and Piranha |
Article / Accession Series | PMID: 23592263 / GSE59944 |
CLIP-seq Viewer | Link |
MiRNA-Target Expression Profile | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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MiRNA-Target Expression Profile (TCGA) | |||||||
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58 hsa-miR-569 Target Genes:
Functional analysis:
ID![]() |
Target | Description | Validation methods |
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Strong evidence | Less strong evidence | |||||||||||
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MIRT004827 | SPI1 | Spi-1 proto-oncogene | ![]() |
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2 | 1 | ||||||
MIRT086537 | HSPE1-MOB4 | HSPE1-MOB4 readthrough | ![]() |
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2 | 2 | ||||||
MIRT086545 | MOB4 | MOB family member 4, phocein | ![]() |
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2 | 2 | ||||||
MIRT154349 | PARD6B | par-6 family cell polarity regulator beta | ![]() |
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2 | 4 | ||||||
MIRT182174 | POU2F1 | POU class 2 homeobox 1 | ![]() |
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2 | 2 | ||||||
MIRT190452 | EIF5 | eukaryotic translation initiation factor 5 | ![]() |
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2 | 2 | ||||||
MIRT191410 | NAA30 | N(alpha)-acetyltransferase 30, NatC catalytic subunit | ![]() |
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2 | 2 | ||||||
MIRT199846 | CSNK1G2 | casein kinase 1 gamma 2 | ![]() |
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2 | 2 | ||||||
MIRT208376 | SLC25A36 | solute carrier family 25 member 36 | ![]() |
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2 | 2 | ||||||
MIRT275677 | CARKD | NAD(P)HX dehydratase | ![]() |
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2 | 2 | ||||||
MIRT275764 | TFDP1 | transcription factor Dp-1 | ![]() |
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2 | 2 | ||||||
MIRT280470 | UBR7 | ubiquitin protein ligase E3 component n-recognin 7 (putative) | ![]() |
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2 | 2 | ||||||
MIRT296592 | FAM217B | family with sequence similarity 217 member B | ![]() |
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2 | 4 | ||||||
MIRT306847 | FYTTD1 | forty-two-three domain containing 1 | ![]() |
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2 | 2 | ||||||
MIRT443764 | HLF | HLF, PAR bZIP transcription factor | ![]() |
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2 | 2 | ||||||
MIRT448026 | GSR | glutathione-disulfide reductase | ![]() |
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2 | 2 | ||||||
MIRT448659 | NCALD | neurocalcin delta | ![]() |
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2 | 2 | ||||||
MIRT449142 | UQCRB | ubiquinol-cytochrome c reductase binding protein | ![]() |
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2 | 2 | ||||||
MIRT449225 | RAD51B | RAD51 paralog B | ![]() |
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2 | 2 | ||||||
MIRT462421 | TWISTNB | TWIST neighbor | ![]() |
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2 | 2 | ||||||
MIRT468478 | SESN3 | sestrin 3 | ![]() |
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2 | 4 | ||||||
MIRT478170 | DENND5B | DENN domain containing 5B | ![]() |
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2 | 2 | ||||||
MIRT478577 | VSIG2 | V-set and immunoglobulin domain containing 2 | ![]() |
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2 | 2 | ||||||
MIRT481300 | ATP5G3 | ATP synthase, H+ transporting, mitochondrial Fo complex subunit C3 (subunit 9) | ![]() |
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2 | 16 | ||||||
MIRT485894 | ZFP36 | ZFP36 ring finger protein | ![]() |
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2 | 2 | ||||||
MIRT497242 | FITM2 | fat storage inducing transmembrane protein 2 | ![]() |
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2 | 2 | ||||||
MIRT500282 | ZNF703 | zinc finger protein 703 | ![]() |
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2 | 8 | ||||||
MIRT509536 | RSBN1L | round spermatid basic protein 1 like | ![]() |
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2 | 4 | ||||||
MIRT511835 | GPATCH8 | G-patch domain containing 8 | ![]() |
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2 | 4 | ||||||
MIRT522437 | MON1B | MON1 homolog B, secretory trafficking associated | ![]() |
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2 | 2 | ||||||
MIRT523538 | GLO1 | glyoxalase I | ![]() |
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2 | 4 | ||||||
MIRT527631 | MYBPC1 | myosin binding protein C, slow type | ![]() |
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2 | 4 | ||||||
MIRT528059 | OLAH | oleoyl-ACP hydrolase | ![]() |
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2 | 2 | ||||||
MIRT532549 | TXNL1 | thioredoxin like 1 | ![]() |
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2 | 2 | ||||||
MIRT545503 | NAP1L1 | nucleosome assembly protein 1 like 1 | ![]() |
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2 | 2 | ||||||
MIRT546724 | RNF6 | ring finger protein 6 | ![]() |
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2 | 2 | ||||||
MIRT546737 | RNF141 | ring finger protein 141 | ![]() |
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2 | 2 | ||||||
MIRT550889 | ACTA1 | actin, alpha 1, skeletal muscle | ![]() |
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2 | 2 | ||||||
MIRT554180 | SLC35E2B | solute carrier family 35 member E2B | ![]() |
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2 | 2 | ||||||
MIRT555878 | PAFAH1B2 | platelet activating factor acetylhydrolase 1b catalytic subunit 2 | ![]() |
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2 | 2 | ||||||
MIRT558458 | DCUN1D1 | defective in cullin neddylation 1 domain containing 1 | ![]() |
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2 | 2 | ||||||
MIRT560375 | TIMM8A | translocase of inner mitochondrial membrane 8A | ![]() |
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2 | 2 | ||||||
MIRT562672 | AKT3 | AKT serine/threonine kinase 3 | ![]() |
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2 | 2 | ||||||
MIRT563810 | TUBA1B | tubulin alpha 1b | ![]() |
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2 | 2 | ||||||
MIRT564607 | ZNF711 | zinc finger protein 711 | ![]() |
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2 | 2 | ||||||
MIRT564881 | YWHAE | tyrosine 3-monooxygenase/tryptophan 5-monooxygenase activation protein epsilon | ![]() |
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2 | 2 | ||||||
MIRT566724 | MSL2 | MSL complex subunit 2 | ![]() |
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2 | 2 | ||||||
MIRT566900 | CSRP3 | cysteine and glycine rich protein 3 | ![]() |
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2 | 2 | ||||||
MIRT570002 | COL1A2 | collagen type I alpha 2 chain | ![]() |
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2 | 2 | ||||||
MIRT612300 | ZFP14 | ZFP14 zinc finger protein | ![]() |
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2 | 2 | ||||||
MIRT618334 | ZNF813 | zinc finger protein 813 | ![]() |
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2 | 2 | ||||||
MIRT627658 | RSBN1 | round spermatid basic protein 1 | ![]() |
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2 | 2 | ||||||
MIRT630660 | PLAG1 | PLAG1 zinc finger | ![]() |
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2 | 2 | ||||||
MIRT640802 | MYCL1 | MYCL proto-oncogene, bHLH transcription factor | ![]() |
1 | 1 | |||||||
MIRT651370 | ZBTB21 | zinc finger and BTB domain containing 21 | ![]() |
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2 | 2 | ||||||
MIRT709227 | GPSM2 | G protein signaling modulator 2 | ![]() |
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2 | 2 | ||||||
MIRT712058 | ZBTB34 | zinc finger and BTB domain containing 34 | ![]() |
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2 | 2 | ||||||
MIRT725006 | ZPBP | zona pellucida binding protein | ![]() |
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2 | 2 |
miRNA-Drug Resistance Associations | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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