pre-miRNA Information | |
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pre-miRNA | hsa-mir-4283-1 |
Genomic Coordinates | chr7: 56955785 - 56955864 |
Description | Homo sapiens miR-4283-1 stem-loop |
Comment | None |
RNA Secondary Structure | |
pre-miRNA | hsa-mir-4283-2 |
Genomic Coordinates | chr7: 63621090 - 63621169 |
Description | Homo sapiens miR-4283-2 stem-loop |
Comment | None |
RNA Secondary Structure |
Mature miRNA Information | |||||||||||||||||||||||||||||||
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Mature miRNA | hsa-miR-4283 | ||||||||||||||||||||||||||||||
Sequence | 11| UGGGGCUCAGCGAGUUU |27 | ||||||||||||||||||||||||||||||
Evidence | Experimental | ||||||||||||||||||||||||||||||
Experiments | SOLiD | ||||||||||||||||||||||||||||||
SNPs in miRNA |
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Putative Targets |
miRNA Expression profile | |
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miRNAs in Extracellular Vesicles |
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Circulating MicroRNA Expression Profiling |
Gene Information | |||||||||||||||||||||
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Gene Symbol | STRN4 | ||||||||||||||||||||
Synonyms | PPP2R6C, ZIN, zinedin | ||||||||||||||||||||
Description | striatin 4 | ||||||||||||||||||||
Transcript | NM_001039877 | ||||||||||||||||||||
Other Transcripts | NM_013403 | ||||||||||||||||||||
Expression | |||||||||||||||||||||
Putative miRNA Targets on STRN4 | |||||||||||||||||||||
3'UTR of STRN4 (miRNA target sites are highlighted) |
>STRN4|NM_001039877|3'UTR 1 TGCCCACCTGGCCCTGCCCTGGCCGCCACGCTGGCTGGGGTGTAGGGCCGGGCAGGTGGGGCTGAGGGGACTCCCAGCCT 81 CGCTGGAGGTGCAGAGGCCTGGCCTCTGTCTGTTTGCCATGGAGCCTGGTGGTGCTAACGGCCCTTTCCCCAGGAATCCC 161 TCCCCAACGGCTGCCTTCCCCAAGCATCCAGCCTGGGGATGGGCCCCTTTCAGGAATCACCCCCGAGGATGGCCTCGGGG 241 TTTCCCCCTGTGCCCTGACAGCCGCTCCTGGTATCAGAGCTGCTTTCCAGAGGGCAGCACAGCCAGGGCCGGGTGTCTTT 321 AGGGATCAGTTTTTCCAAGACTCCAGAAGGTGCCAGGTTCTCCCCTTGAGCTCCTGCTCCCCCATCCCCCATCCTCCCAG 401 ACCTGGGCAGGAGCTGTGCTGGGAGAAAGGGTGGCAGCCGGGAGCCTCAGAGCTGAGCCCCGGCCTGGCTGCCCCTCCCC 481 TCCGGCCCTCTCCACTGCTTTCCAGACACTAACCAAGGCTTCCAGGCCAGGGATTGCCCAACACTCCTAGGGCAGCCCTC 561 CCAGCGCCCCATGGGGTCGCCCATGGGTAGAGACGGCTTTCTTGTGCCCCTCCCTGGGGCATGGAGGGTGGAGTGGGCCT 641 CGGGTCCCCCTGAACTCCCTGTATATCTGTATAAATAACGGGATTTTCATGGCGCCGCCCCACCCGCATTATCACTGTGT 721 GATGGTCTCAGTCAGTCTCCTCCCTGTCTCCACTCTTTCCCTCTATTTATTTCACTCTCTTGTTTGGTTCTACCCTGCAC 801 CCTCGGTCCCCTTCCAGGTTCCTGTTTATAAGCCCCAACCCCTCTGTCCCCATCTTGTATGTGAAAACTTGTCTCAATAA 881 ACCCTTTGGAGTAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA 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 GSM4903836 | |
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Method / RBP | HITS-CLIP / AGO |
Cell line / Condition | Dermal fibroblasts / 124_TD_21_a |
Location of target site | NM_001039877 | 3UTR | CUGUUUAUAAGCCCCAACCCCUCUGUCCCCAUCUUGUAUGUGAAAACUU |
Tools used in this analysis | TargetScan, miRTarCLIP, and Piranha |
Accession Series | GSE161239 |
CLIP-seq Viewer | Link |
CLIP-seq Support 2 for dataset GSM1462572 | |
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Method / RBP | PAR-CLIP / AGO2 |
Cell line / Condition | C8166 / C8166 NL4-3 |
Location of target site | ENST00000263280.6 | 3UTR | CGGCCUGGCUGCCCCUC |
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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53 hsa-miR-4283 Target Genes:
Functional analysis:
ID | Target | Description | Validation methods | |||||||||
Strong evidence | Less strong evidence | |||||||||||
MIRT083347 | E2F1 | E2F transcription factor 1 | 2 | 4 | ||||||||
MIRT120466 | U2SURP | U2 snRNP associated SURP domain containing | 2 | 4 | ||||||||
MIRT266892 | HDGF | heparin binding growth factor | 2 | 2 | ||||||||
MIRT445166 | TFPI | tissue factor pathway inhibitor | 2 | 2 | ||||||||
MIRT445906 | SLC10A3 | solute carrier family 10 member 3 | 2 | 2 | ||||||||
MIRT455530 | GJB1 | gap junction protein beta 1 | 2 | 2 | ||||||||
MIRT460172 | UNK | unkempt family zinc finger | 2 | 6 | ||||||||
MIRT461728 | SLC27A1 | solute carrier family 27 member 1 | 2 | 2 | ||||||||
MIRT465219 | TRIP10 | thyroid hormone receptor interactor 10 | 2 | 2 | ||||||||
MIRT468911 | RPS6KA4 | ribosomal protein S6 kinase A4 | 2 | 2 | ||||||||
MIRT469691 | RAB5B | RAB5B, member RAS oncogene family | 2 | 2 | ||||||||
MIRT471050 | PIM3 | Pim-3 proto-oncogene, serine/threonine kinase | 2 | 2 | ||||||||
MIRT472526 | NACC1 | nucleus accumbens associated 1 | 2 | 2 | ||||||||
MIRT474932 | KCTD15 | potassium channel tetramerization domain containing 15 | 2 | 2 | ||||||||
MIRT486980 | STEAP3 | STEAP3 metalloreductase | 2 | 4 | ||||||||
MIRT487483 | BANP | BTG3 associated nuclear protein | 2 | 4 | ||||||||
MIRT488263 | HSP90AB1 | heat shock protein 90 alpha family class B member 1 | 2 | 8 | ||||||||
MIRT490733 | SRCIN1 | SRC kinase signaling inhibitor 1 | 2 | 2 | ||||||||
MIRT490896 | BARHL1 | BarH like homeobox 1 | 2 | 6 | ||||||||
MIRT490909 | STRN4 | striatin 4 | 2 | 2 | ||||||||
MIRT493812 | FSCN1 | fascin actin-bundling protein 1 | 2 | 2 | ||||||||
MIRT509030 | PALM2-AKAP2 | PALM2-AKAP2 readthrough | 2 | 2 | ||||||||
MIRT509049 | AKAP2 | A-kinase anchoring protein 2 | 2 | 2 | ||||||||
MIRT509404 | MCM7 | minichromosome maintenance complex component 7 | 2 | 6 | ||||||||
MIRT523303 | HIST1H1B | histone cluster 1 H1 family member b | 2 | 2 | ||||||||
MIRT529487 | TPD52L3 | tumor protein D52 like 3 | 2 | 2 | ||||||||
MIRT529825 | ARGFX | arginine-fifty homeobox | 2 | 4 | ||||||||
MIRT542941 | GIGYF1 | GRB10 interacting GYF protein 1 | 2 | 2 | ||||||||
MIRT543668 | PUM1 | pumilio RNA binding family member 1 | 2 | 4 | ||||||||
MIRT546994 | PPP2CA | protein phosphatase 2 catalytic subunit alpha | 2 | 2 | ||||||||
MIRT560377 | TIMM8A | translocase of inner mitochondrial membrane 8A | 2 | 2 | ||||||||
MIRT561752 | PLAGL2 | PLAG1 like zinc finger 2 | 2 | 2 | ||||||||
MIRT568966 | CACNA1C | calcium voltage-gated channel subunit alpha1 C | 2 | 2 | ||||||||
MIRT569892 | ROBO4 | roundabout guidance receptor 4 | 2 | 2 | ||||||||
MIRT570097 | SCN2B | sodium voltage-gated channel beta subunit 2 | 2 | 2 | ||||||||
MIRT576503 | Slc35e2 | solute carrier family 35, member E2 | 2 | 3 | ||||||||
MIRT623795 | GK5 | glycerol kinase 5 (putative) | 2 | 2 | ||||||||
MIRT625142 | ITPRIPL1 | inositol 1,4,5-trisphosphate receptor interacting protein-like 1 | 2 | 2 | ||||||||
MIRT631438 | HSPA14 | heat shock protein family A (Hsp70) member 14 | 2 | 2 | ||||||||
MIRT633973 | SLC35E2 | solute carrier family 35 member E2 | 2 | 3 | ||||||||
MIRT634811 | ASB6 | ankyrin repeat and SOCS box containing 6 | 2 | 2 | ||||||||
MIRT640520 | TET3 | tet methylcytosine dioxygenase 3 | 2 | 2 | ||||||||
MIRT644446 | ALDOC | aldolase, fructose-bisphosphate C | 2 | 2 | ||||||||
MIRT644767 | TXNRD3NB | thioredoxin reductase 3 neighbor | 2 | 2 | ||||||||
MIRT648809 | ZNF689 | zinc finger protein 689 | 2 | 2 | ||||||||
MIRT654912 | POMGNT1 | protein O-linked mannose N-acetylglucosaminyltransferase 1 (beta 1,2-) | 2 | 2 | ||||||||
MIRT670832 | SFT2D2 | SFT2 domain containing 2 | 2 | 2 | ||||||||
MIRT675826 | UBE2D4 | ubiquitin conjugating enzyme E2 D4 (putative) | 2 | 2 | ||||||||
MIRT684020 | FOLR1 | folate receptor 1 | 2 | 2 | ||||||||
MIRT698589 | TEX261 | testis expressed 261 | 2 | 2 | ||||||||
MIRT703208 | GOLGA3 | golgin A3 | 2 | 2 | ||||||||
MIRT703492 | FNDC3B | fibronectin type III domain containing 3B | 2 | 2 | ||||||||
MIRT710754 | GRID1 | glutamate ionotropic receptor delta type subunit 1 | 2 | 2 |
miRNA-Drug Associations | ||||||||||||||||||
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miRNA-Drug Resistance Associations | ||||||||||||||||||||||||||||||
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