pre-miRNA Information
pre-miRNA hsa-mir-3678   
Genomic Coordinates chr17: 75406069 - 75406162
Description Homo sapiens miR-3678 stem-loop
Comment None
RNA Secondary Structure

Mature miRNA Information
Mature miRNA hsa-miR-3678-3p
Sequence 69| CUGCAGAGUUUGUACGGACCGG |90
Evidence Experimental
Experiments Illumina
SNPs in miRNA
Mutant ID Mutant Position Mutant Source
rs988363493 1 dbSNP
rs753118178 5 dbSNP
rs1424776090 14 dbSNP
rs1475188526 15 dbSNP
rs1163369708 17 dbSNP
rs1174219930 19 dbSNP
rs915488824 20 dbSNP
rs1273558782 21 dbSNP
rs755095016 22 dbSNP
Putative Targets

miRNA Expression profile
Human miRNA Tissue Atlas
Circulating MicroRNA Expression Profiling
Gene Information
Gene Symbol CCDC64
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 GSM1462573. RNA binding protein: AGO2. Condition:TZM-bl 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' ggccaGGCAUGUUUGA-GACGUc 5'
               |||  |   || || || 
Target 5' --cagCCGCCCCUCCUCCUCCAc 3'
1 - 21
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 GSM1462573
Method / RBP PAR-CLIP / AGO2
Cell line / Condition TZM-bl / TZM-bl BaL
Location of target site ENST00000397558.2 | 3UTR | CAGCCGCCCCUCCUCCUCCACCCAGGC
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
MiRNA-Target Expression Profile (TCGA)
Tumor Pearson Correlation P-value for Pearson Correlation Spearman Correlation P-value for Spearman Correlation Samples Chart
LUSC 0.972 0.01 0.800 0.1 4 Click to see details
LIHC -0.543 0.07 -0.500 0.09 9 Click to see details
HNSC -0.015 0.48 0.209 0.27 11 Click to see details
HNSC -0.015 0.48 0.209 0.27 11 Click to see details
HNSC -0.015 0.48 0.209 0.27 11 Click to see details
HNSC -0.015 0.48 0.209 0.27 11 Click to see details
HNSC -0.015 0.48 0.209 0.27 11 Click to see details
HNSC -0.015 0.48 0.209 0.27 11 Click to see details
HNSC -0.015 0.48 0.209 0.27 11 Click to see details
HNSC -0.015 0.48 0.209 0.27 11 Click to see details
HNSC -0.015 0.48 0.209 0.27 11 Click to see details
HNSC -0.015 0.48 0.209 0.27 11 Click to see details
86 hsa-miR-3678-3p Target Genes:
Functional analysis:
ID Target Description Validation methods
Strong evidence Less strong evidence
MIRT074327 TNRC6A trinucleotide repeat containing 6A 2 10
MIRT107705 CLTA clathrin light chain A 2 2
MIRT114113 AGO1 argonaute 1, RISC catalytic component 2 2
MIRT155293 IFNAR2 interferon alpha and beta receptor subunit 2 2 4
MIRT159171 NRBP1 nuclear receptor binding protein 1 2 2
MIRT185795 ZNF678 zinc finger protein 678 2 2
MIRT282672 SYNM synemin 2 2
MIRT294386 ZNF264 zinc finger protein 264 2 2
MIRT295818 CHMP4B charged multivesicular body protein 4B 2 2
MIRT332777 CAPRIN1 cell cycle associated protein 1 2 4
MIRT334112 PPP6R3 protein phosphatase 6 regulatory subunit 3 2 2
MIRT340971 IPO5 importin 5 2 2
MIRT354679 CDV3 CDV3 homolog 2 2
MIRT366662 PLP2 proteolipid protein 2 2 2
MIRT404272 PLEKHA8 pleckstrin homology domain containing A8 2 2
MIRT447536 RNF165 ring finger protein 165 2 2
MIRT449139 UQCRB ubiquinol-cytochrome c reductase binding protein 2 2
MIRT451301 LGALS3BP galectin 3 binding protein 2 2
MIRT451488 FOPNL FGFR1OP N-terminal like 2 2
MIRT455198 GNL1 G protein nucleolar 1 (putative) 2 2
MIRT459215 MRPS21 mitochondrial ribosomal protein S21 2 2
MIRT461764 MPDU1 mannose-P-dolichol utilization defect 1 2 2
MIRT463273 ZFX zinc finger protein, X-linked 2 2
MIRT464862 UBB ubiquitin B 2 8
MIRT464950 TWIST1 twist family bHLH transcription factor 1 2 2
MIRT467378 SON SON DNA binding protein 2 4
MIRT469282 RHOA ras homolog family member A 2 2
MIRT470293 PPTC7 PTC7 protein phosphatase homolog 2 2
MIRT470639 POM121C POM121 transmembrane nucleoporin C 2 2
MIRT477163 FABP3 fatty acid binding protein 3 2 2
MIRT477686 EFHD2 EF-hand domain family member D2 2 2
MIRT479725 CCNF cyclin F 2 2
MIRT481726 APH1A aph-1 homolog A, gamma-secretase subunit 2 2
MIRT485673 CCDC64 BICD family like cargo adaptor 1 2 2
MIRT498280 PADI2 peptidyl arginine deiminase 2 2 2
MIRT499921 GPX8 glutathione peroxidase 8 (putative) 2 2
MIRT503616 SLC25A36 solute carrier family 25 member 36 2 4
MIRT506927 IGDCC4 immunoglobulin superfamily DCC subclass member 4 2 6
MIRT507348 FAM129A family with sequence similarity 129 member A 2 6
MIRT508265 DYNLL2 dynein light chain LC8-type 2 2 4
MIRT508284 YES1 YES proto-oncogene 1, Src family tyrosine kinase 2 4
MIRT509353 COPS8 COP9 signalosome subunit 8 2 2
MIRT510892 RAB1A RAB1A, member RAS oncogene family 2 4
MIRT511882 GAS1 growth arrest specific 1 2 6
MIRT511990 E2F1 E2F transcription factor 1 2 4
MIRT512239 ARPP19 cAMP regulated phosphoprotein 19 2 4
MIRT512392 BUB1 BUB1 mitotic checkpoint serine/threonine kinase 2 4
MIRT514086 EPS15L1 epidermal growth factor receptor pathway substrate 15 like 1 2 6
MIRT514358 UBBP4 ubiquitin B pseudogene 4 2 6
MIRT523149 HNRNPU heterogeneous nuclear ribonucleoprotein U 2 2
MIRT525511 FSIP2 fibrous sheath interacting protein 2 2 2
MIRT526333 SH3TC2 SH3 domain and tetratricopeptide repeats 2 2 2
MIRT529962 ZNF71 zinc finger protein 71 2 2
MIRT530337 GABRB3 gamma-aminobutyric acid type A receptor beta3 subunit 2 2
MIRT530884 PHOX2A paired like homeobox 2a 2 2
MIRT533097 YOD1 YOD1 deubiquitinase 2 2
MIRT533250 VCAM1 vascular cell adhesion molecule 1 2 2
MIRT534786 RAB8B RAB8B, member RAS oncogene family 2 2
MIRT537917 DSTYK dual serine/threonine and tyrosine protein kinase 2 2
MIRT547799 JARID2 jumonji and AT-rich interaction domain containing 2 2 2
MIRT548714 CRK CRK proto-oncogene, adaptor protein 2 2
MIRT555509 PMEPA1 prostate transmembrane protein, androgen induced 1 2 2
MIRT555984 NFYB nuclear transcription factor Y subunit beta 2 2
MIRT557942 FAM222B family with sequence similarity 222 member B 2 2
MIRT560830 ZNF786 zinc finger protein 786 2 2
MIRT562720 ZNF714 zinc finger protein 714 2 2
MIRT565337 TMEM104 transmembrane protein 104 2 2
MIRT614453 REL REL proto-oncogene, NF-kB subunit 2 2
MIRT639474 SLC6A4 solute carrier family 6 member 4 2 2
MIRT644056 IQCE IQ motif containing E 2 2
MIRT651652 VWA1 von Willebrand factor A domain containing 1 2 2
MIRT651866 UNC119B unc-119 lipid binding chaperone B 2 2
MIRT653490 SLC43A2 solute carrier family 43 member 2 2 2
MIRT657039 KCNJ6 potassium voltage-gated channel subfamily J member 6 2 2
MIRT657985 GAN gigaxonin 2 2
MIRT672117 ATP6V0A2 ATPase H+ transporting V0 subunit a2 2 2
MIRT683583 GSTCD glutathione S-transferase C-terminal domain containing 2 2
MIRT688689 CPS1 carbamoyl-phosphate synthase 1 2 2
MIRT695375 NSA2 NSA2, ribosome biogenesis homolog 2 2
MIRT696351 EIF2S3 eukaryotic translation initiation factor 2 subunit gamma 2 2
MIRT700614 PRKAA2 protein kinase AMP-activated catalytic subunit alpha 2 2 2
MIRT703512 FKBP15 FK506 binding protein 15 2 2
MIRT705051 C5orf15 chromosome 5 open reading frame 15 2 2
MIRT705180 BTG1 BTG anti-proliferation factor 1 2 2
MIRT709409 FBXL20 F-box and leucine rich repeat protein 20 2 2
MIRT721053 DCC DCC netrin 1 receptor 2 2
miRNA-Drug Resistance Associations
miRNA Drug Name CID NSC FDA Effect/Pattern Detection Method Level Phenotype Condition
hsa-miR-3678-3p Platinum 23939 resistant tissue
hsa-miR-3678-3p Cisplatin 5460033 NSC119875 approved sensitive cell line (A549)
hsa-miR-3678-3p Gemcitabine 60750 NSC613327 approved resistant cell line (PANC-1) (1500 ng/ml)
hsa-miR-3678-3p Paclitaxel/Docetaxel/Vinorelbine/Doxorubicin/Etoposide resistant cell line (Bads-200)

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