| pre-miRNA Information | |
|---|---|
| pre-miRNA | hsa-mir-3616 |
| Genomic Coordinates | chr20: 47166967 - 47167058 |
| Description | Homo sapiens miR-3616 stem-loop |
| Comment | None |
| RNA Secondary Structure |  |
| Mature miRNA Information | ||||||||||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Mature miRNA | hsa-miR-3616-3p | |||||||||||||||||||||
| Sequence | 60| CGAGGGCAUUUCAUGAUGCAGGC |82 | |||||||||||||||||||||
| Evidence | Experimental | |||||||||||||||||||||
| Experiments | Illumina | |||||||||||||||||||||
| Editing Events in miRNAs |
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| SNPs in miRNA |
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| Putative Targets | ||||||||||||||||||||||
| miRNA Expression profile | |
|---|---|
| Human miRNA Tissue Atlas | |
| Circulating MicroRNA Expression Profiling | |
| Gene Information | |||||||||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Gene Symbol | EIF5AL1 | ||||||||||||||||||||
| Synonyms | EIF5AP1, bA342M3.3 | ||||||||||||||||||||
| Description | eukaryotic translation initiation factor 5A-like 1 | ||||||||||||||||||||
| Transcript | NM_001099692 | ||||||||||||||||||||
| Expression | |||||||||||||||||||||
| Putative miRNA Targets on EIF5AL1 | |||||||||||||||||||||
| 3'UTR of EIF5AL1 (miRNA target sites are highlighted) |
>EIF5AL1|NM_001099692|3'UTR 1 CTGGCTCCCAAGGTGGCAGTGGTGGCAGCAGTGATCCTCCGAACCTGCAGAGGCCCCCTCCCCCAGCCTGGCCTGGCTCT 81 GGCCTGGTCCTAGGTTGGACTCCTCCTACACAATTTATTTGACGTTTTATTTTGGTTTTCCCCACCCCCTCAATCTGTCA 161 GGGAGCCCCTGCCCTTCACCTAGCTCCCTTGGCCAGGAGCGAGCGAAGCCATGGCCTTGGTGAAGCTGCCCTCCTCTTCT 241 CCCCTCACACTACAGCCCTGGTGGGGGAGAAGGGGGTGGGTGCTGCTTGTGGTTTAGTCTTTTTTTTTTTTTTAAATTCA 321 ATCTGGAATCAGAAAGCGGTGGATTCTGGCAAATGGTCCTTGTGCCCTCCCCACTCATCCTTGGTCTGGTCCCCTGTTGC 401 CCATAGCCCTTTACCCTGAGCACCACCCAACAGACTGGGGACCAGCCCCCTCGCCTGCCTGTGTCTCTCCCCAAACCCCT 481 TTAGATGGGGAGGGAAGAAGAGGAGAGGGGAGGGGACCTGCCCCCTCCTCAGGCATCTGGGAAGGGCCTGCCCCCATGGG 561 CTTTACCCTTCCCTGCGGGCTCTCTCCCCGACACATTTGTTAAAATCAAACCTGAATAAAACTACAAGTTTAATATGAAA 641 AAAAAAAAAAAAGAAAGAAAGACGTGTAAAATGCCAAGAACTCTAGGAAACAGGGACAAAAACACTTCAAAGAGAAAGTT 721 CATGCACTTGTTTCTGACCACCCAGGGCACCCTTCAGCACACGCTGTCTGGAGTGGCCTGAAGCAAGGAGTGTCTTGTGA 801 GGTGCAGAGGATGCAATGGGAGCAGGGTCCTGTCCCCACCCTAAAGGAGTTCACAGTTTAACGCAAATGAGAAGCCAGTG 881 AGGACATCACTACTCCTGCTGTGAACTTGGGAACTAGAAACACAAAACCTGAGTCTGGAGGGAAGCTAAGGAAGCATTCT 961 GCTCTGGAGTAGACATGAGTGCGTGTGAAGCTTCTGATCTCCCATGAGAGCAATGGGGACATGGGGCAGAATCTAAAACC 1041 CATGACTGAAAGCACCAAATTGCTAAAATGGCAATAAAGAGACATGAGGCCAAGATGGAGAAGAAGGAACCCAGGACGAG 1121 GGTCAGCCTCACATTTGGGGCTCATTTCCCTCAGTTTCCTCACTGAATTTCAGAAGGGACTAACTGAGATGCAAAGAAGC 1201 AGAGCAGCTTTTGCACCATGTGGAGGACTAGATGGAAAACAAGTAGACTGAGGGTCTGCTAGTGAAGGTGACCCCTACTG 1281 AAGTCCACTGGCTTTGGTTGGGACCCAGAAGAGTCACACGCCAGGAATAGAGGTGGACAGGAAACACCCTGACTTTTGTA 1361 GGGACTGAACCTCACTGATAACCTCAATTGCGGATGGTATGGAGGGTGTCTAGGTGTGCTAGGACCCCTGCCCATTCCCC 1441 AGAAATAGACTCCCATCTTTTCTACAGCAAGATAACGTGCTAGTAGGCCTCAATTCATTGCTAAATATTTTTAACGAGTG 1521 TCTTACATTTAGCCAAAAAGACTAGTCATGTGGCAGGAAAAATACAATGTCATATGACCAAAAGCTAAAAGACTGTGAAA 1601 ATGAATCCAGAGGTGACCCAAGCATTGAATTTAACAATGCCAGTACCTGGACCTCCGCTTGCCCCTAAAACATTACAATC 1681 AAGAATGTAGGAAGGGAAAGGAAACACGAAGATTAATCAAGCAGGAAGGACAAGCTCAGTTTTGCACCCACTGAATTTGC 1761 CACAAATATTGTGGAAAATATTCTCGGGGACATTGCAGTTGTCTACTTTGGTTGGCACATGGTTCATACAACAGTGTTTG 1841 TGTCAGTGAACATCTTACTCTTCCTCGGCAGTCTTTCTTTGCCCAGAGATTTCGCAATGACTGTTGACCTTCATCATCAC 1921 CTTTTGGACTTTGGCTTGCACTTTAGCTTCTGTAGATCTCCATGATGTAAAGAAGTATTTTAGGTCCATTTTAATTCCTG 2001 CAAAGGATAAAATCCTTCTATTTGTGTGCATATAAGTGGACCTGAGCCCTTGGTTAGGGTGTAGAGAGGAGAAGGGGAGA 2081 AACCTGAGGGCCAGAAGCTGTTCTTTCCCTTAAAAGGGCAAACTCATTTCCACACTATGGGGACTCTGACAGATAGCATA 2161 CCTTCCTGTCTATGGCTATTGGACCTGCAGGCTTTCCCCTGTAAATCCGTGTTCTGTCATTGACATTTTGTGACTGTAAG 2241 ACAGACTTGAGATAAGACATCTAGAAAACAATAATTGAACAATGATGTGAATATATTTCACACAACTGAACTGTACATTT 2321 CAACAAGGTTAAGATGGTAATTATCACGTTATACATTTTTTACCGCAGGTTAAAATGTTTCACAGGTTGAAAGGAAAGCA 2401 ACTACCTTCAGTTCTCTGAGTTCAAGAATTTGTAACATTTCACCCCCTGCTCCTTCCTGATCTTCTGTGGAGCATCTTTT 2481 TTCCATCCATGCTCTACTCAGAGCCCACTTTCCCTTCCCTGACACCAGCTTCACTGAGGCTGGTTGGAACCTAACACAAA 2561 ACATTCTCAGTAATGACTGAATTCCCACAAAGAATTCCATATAGACTGCATATGAGTTGAATCTTCTAAGACATGAAATA 2641 TTTGTTCTCTTCTTGGCTAATATGCAATGCAAATCCTGTTGCAGATGTACGTCATATACCTCTGAAATTCCTGATGTATT 2721 CAATGAAATAACATCTTTAAAGTTCTGTGTAGAATGTTTTTTTTCTGATTTCTTCACATACGATAGAAAAAAAAACCCAA 2801 AAAAACATGTACTAGGATTTCAATAGAAGCAATGGGTGATCTAAAAAGATGAAAGAGCAACCGCATGCGCCCTACAGCTA 2881 CCGCTAGATTTTATGGGGAAAGCAGCTGGCCCAGTTTGCAGCTAGGAGAAATGTCAAACACATGAAGAAATGAGAAGCAA 2961 AGAAAAACCATGAGGCATGAACATTTCATGGCAATCACGATGTCCTGGTTTGTGAGATAATGGGATAGAGGAGTAGAAAA 3041 CAAGGAGAAAGATGAGAAGGTACAAAGTGGTTCAAGTCAAACAGCTCAACTGAACTTTTCTTAATGGAATATTTAAAAAG 3121 TGGTACATTAAAAAACTTCCCCCAGTTCACATCAAAAATTCTCTCTTCAGGACTAAGTTGGGTAGAGACTGTTCAATGTG 3201 CCTAGATATCTTCAGAACTTATATATTTTCTGTTTTCTACGTATGTTGAAGGGCAGTGCCAAATGATGTGTAATTATCTA 3281 GGTTGTAAAAATAAAACATACTCCCCCTTCCCTTGAGGATAAAAAAAAAAAAAAA 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 | ||||||||||
|---|---|---|---|---|---|---|---|---|---|---|
| miRNA:Target | ---- | |||||||||
| Validation Method |
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| 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. |
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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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| Experimental Support 2 for Functional miRNA-Target Interaction | |
|---|---|
| miRNA:Target | ---- |
| Validation Method |
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| Conditions | HCT116 |
| 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 ERX177616. RNA binding protein: AGO2. Condition:p53_V_AGO_CLIP_3_6
PAR-CLIP data was present in ERX177618. RNA binding protein: AGO2. Condition:KO_V_AGO_CLIP_3_8
PAR-CLIP data was present in ERX177630. RNA binding protein: AGO2. Condition:KO_V_AGO_CLIP_4_8
PAR-CLIP data was present in ERX177606. RNA binding protein: AGO2. Condition:KO_V_AGO_CLIP_2_8
PAR-CLIP data was present in ERX177629. RNA binding protein: AGO2. Condition:KO_D_AGO_CLIP_4_7
... - Krell J; Stebbing J; Carissimi C; Dabrowska et al., 2016, Genome research. |
| Article |
- Krell J; Stebbing J; Carissimi C; Dabrowska et al. - Genome research, 2016
DNA damage activates TP53-regulated surveillance mechanisms that are crucial in suppressing tumorigenesis. TP53 orchestrates these responses directly by transcriptionally modulating genes, including microRNAs (miRNAs), and by regulating miRNA biogenesis through interacting with the DROSHA complex. However, whether the association between miRNAs and AGO2 is regulated following DNA damage is not yet known. Here, we show that, following DNA damage, TP53 interacts with AGO2 to induce or reduce AGO2's association of a subset of miRNAs, including multiple let-7 family members. Furthermore, we show that specific mutations in TP53 decrease rather than increase the association of let-7 family miRNAs, reducing their activity without preventing TP53 from interacting with AGO2. This is consistent with the oncogenic properties of these mutants. Using AGO2 RIP-seq and PAR-CLIP-seq, we show that the DNA damage-induced increase in binding of let-7 family members to the RISC complex is functional. We unambiguously determine the global miRNA-mRNA interaction networks involved in the DNA damage response, validating them through the identification of miRNA-target chimeras formed by endogenous ligation reactions. We find that the target complementary region of the let-7 seed tends to have highly fixed positions and more variable ones. Additionally, we observe that miRNAs, whose cellular abundance or differential association with AGO2 is regulated by TP53, are involved in an intricate network of regulatory feedback and feedforward circuits. TP53-mediated regulation of AGO2-miRNA interaction represents a new mechanism of miRNA regulation in carcinogenesis.
LinkOut: [PMID: 26701625]
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| 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 | ENST00000520547.2 | 3UTR | CCUUGUGCCCUCCCCACUCAUCCUUGGUCUGGUCCCCUG |
| 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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65 hsa-miR-3616-3p Target Genes:
Functional analysis:
ID |
Target | Description | Validation methods |
 |
 |
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| Strong evidence | Less strong evidence | |||||||||||
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 |
 |
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| MIRT064769 | CCND2 | cyclin D2 |  |
|
2 | 2 | ||||||
| MIRT066953 | ATXN7L3B | ataxin 7 like 3B | |
|
2 | 8 | ||||||
| MIRT109451 | KLHL15 | kelch like family member 15 | |
|
2 | 4 | ||||||
| MIRT110074 | OGT | O-linked N-acetylglucosamine (GlcNAc) transferase | |
|
2 | 2 | ||||||
| MIRT253112 | BCL2L12 | BCL2 like 12 | |
|
2 | 2 | ||||||
| MIRT444698 | GATSL2 | cytosolic arginine sensor for mTORC1 subunit 2 | |
|
2 | 2 | ||||||
| MIRT445748 | AGO1 | argonaute 1, RISC catalytic component | |
|
2 | 2 | ||||||
| MIRT446453 | CHST15 | carbohydrate sulfotransferase 15 | |
|
2 | 2 | ||||||
| MIRT451956 | TMPRSS5 | transmembrane protease, serine 5 | |
|
2 | 2 | ||||||
| MIRT452332 | EIF5AL1 | eukaryotic translation initiation factor 5A-like 1 | |
|
2 | 2 | ||||||
| MIRT453115 | HOXC4 | homeobox C4 | |
|
2 | 2 | ||||||
| MIRT455167 | SUV39H1 | suppressor of variegation 3-9 homolog 1 | |
|
2 | 2 | ||||||
| MIRT457105 | DCX | doublecortin | |
|
2 | 2 | ||||||
| MIRT458349 | NOC2L | NOC2 like nucleolar associated transcriptional repressor | |
|
2 | 2 | ||||||
| MIRT461635 | ZSWIM4 | zinc finger SWIM-type containing 4 | |
|
2 | 2 | ||||||
| MIRT462354 | BCL7B | BCL tumor suppressor 7B | |
|
2 | 2 | ||||||
| MIRT462750 | EFNB1 | ephrin B1 | |
|
2 | 2 | ||||||
| MIRT465801 | TMEM91 | transmembrane protein 91 | |
|
2 | 2 | ||||||
| MIRT468741 | SDC2 | syndecan 2 | |
|
2 | 2 | ||||||
| MIRT468935 | RPS24 | ribosomal protein S24 | |
|
2 | 2 | ||||||
| MIRT469166 | RNF111 | ring finger protein 111 | |
|
2 | 2 | ||||||
| MIRT469466 | REEP5 | receptor accessory protein 5 | |
|
2 | 2 | ||||||
| MIRT469605 | RALGAPA2 | Ral GTPase activating protein catalytic alpha subunit 2 | |
|
2 | 2 | ||||||
| MIRT470600 | POTEM | POTE ankyrin domain family member M | |
|
2 | 2 | ||||||
| MIRT470630 | POTEG | POTE ankyrin domain family member G | |
|
2 | 2 | ||||||
| MIRT471061 | PIM2 | Pim-2 proto-oncogene, serine/threonine kinase | |
|
2 | 2 | ||||||
| MIRT473179 | MLEC | malectin | |
|
2 | 2 | ||||||
| MIRT474351 | KMT2D | lysine methyltransferase 2D | |
|
2 | 2 | ||||||
| MIRT477386 | ENTPD7 | ectonucleoside triphosphate diphosphohydrolase 7 | |
|
2 | 2 | ||||||
| MIRT477452 | ELOVL1 | ELOVL fatty acid elongase 1 | |
|
2 | 2 | ||||||
| MIRT479938 | CBX5 | chromobox 5 | |
|
2 | 2 | ||||||
| MIRT481633 | ARF1 | ADP ribosylation factor 1 | |
|
2 | 2 | ||||||
| MIRT485404 | MIDN | midnolin | |
|
2 | 2 | ||||||
| MIRT486996 | ZFAND2B | zinc finger AN1-type containing 2B | |
|
2 | 2 | ||||||
| MIRT488315 | LDOC1 | LDOC1, regulator of NFKB signaling | |
|
2 | 2 | ||||||
| MIRT490609 | SLC47A1 | solute carrier family 47 member 1 | |
|
2 | 4 | ||||||
| MIRT490686 | SSTR1 | somatostatin receptor 1 | |
|
2 | 2 | ||||||
| MIRT490864 | UPK2 | uroplakin 2 | |
|
2 | 2 | ||||||
| MIRT492572 | PPM1L | protein phosphatase, Mg2+/Mn2+ dependent 1L | |
|
2 | 2 | ||||||
| MIRT492687 | PHYHIP | phytanoyl-CoA 2-hydroxylase interacting protein | |
|
2 | 2 | ||||||
| MIRT492939 | NEUROD2 | neuronal differentiation 2 | |
|
2 | 2 | ||||||
| MIRT494944 | IFFO2 | intermediate filament family orphan 2 | |
|
2 | 2 | ||||||
| MIRT503137 | ATG9A | autophagy related 9A | |
|
2 | 6 | ||||||
| MIRT507792 | CDKN1B | cyclin dependent kinase inhibitor 1B | |
|
2 | 2 | ||||||
| MIRT512248 | ARPP19 | cAMP regulated phosphoprotein 19 | |
|
2 | 4 | ||||||
| MIRT512585 | ZNF223 | zinc finger protein 223 | |
|
2 | 2 | ||||||
| MIRT531029 | TDGF1P3 | teratocarcinoma-derived growth factor 1 pseudogene 3 | |
|
2 | 2 | ||||||
| MIRT532014 | NOX5 | NADPH oxidase 5 | |
|
2 | 2 | ||||||
| MIRT534906 | PUM2 | pumilio RNA binding family member 2 | |
|
2 | 2 | ||||||
| MIRT555370 | PPP1R12A | protein phosphatase 1 regulatory subunit 12A | |
|
2 | 2 | ||||||
| MIRT559524 | ARHGAP12 | Rho GTPase activating protein 12 | |
|
2 | 4 | ||||||
| MIRT560005 | ZNF282 | zinc finger protein 282 | |
|
2 | 2 | ||||||
| MIRT561566 | SLC6A9 | solute carrier family 6 member 9 | |
|
2 | 2 | ||||||
| MIRT565714 | SESN3 | sestrin 3 | |
|
2 | 2 | ||||||
| MIRT568365 | AURKA | aurora kinase A | |
|
2 | 2 | ||||||
| MIRT570343 | VAV3 | vav guanine nucleotide exchange factor 3 | |
|
2 | 4 | ||||||
| MIRT573036 | GREM2 | gremlin 2, DAN family BMP antagonist | |
|
2 | 2 | ||||||
| MIRT629706 | XKR4 | XK related 4 | |
|
2 | 2 | ||||||
| MIRT649162 | IQSEC1 | IQ motif and Sec7 domain 1 | |
|
2 | 2 | ||||||
| MIRT660691 | ANAPC1 | anaphase promoting complex subunit 1 | |
|
2 | 2 | ||||||
| MIRT666940 | PMEPA1 | prostate transmembrane protein, androgen induced 1 | |
|
2 | 2 | ||||||
| MIRT694390 | MTA1 | metastasis associated 1 | |
|
2 | 2 | ||||||
| MIRT704066 | SRCAP | Snf2 related CREBBP activator protein | |
|
2 | 2 | ||||||
| MIRT704316 | DCUN1D5 | defective in cullin neddylation 1 domain containing 5 | |
|
2 | 2 | ||||||
| MIRT709848 | SNX12 | sorting nexin 12 | |
|
2 | 2 | ||||||
| miRNA-Drug Resistance Associations | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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