pre-miRNA Information | |
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pre-miRNA | hsa-mir-6768 |
Genomic Coordinates | chr16: 2463967 - 2464038 |
Description | Homo sapiens miR-6768 stem-loop |
Comment | None |
RNA Secondary Structure | ![]() |
Mature miRNA Information | ||||||||||||||||||||||||||||||||||||||||||||||
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Mature miRNA | hsa-miR-6768-3p | |||||||||||||||||||||||||||||||||||||||||||||
Sequence | 45| CAAAGGCCACAUUCUCCUGUGCAC |68 | |||||||||||||||||||||||||||||||||||||||||||||
Evidence | Experimental | |||||||||||||||||||||||||||||||||||||||||||||
Experiments | Meta-analysis | DRVs in miRNA |
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SNPs in miRNA |
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Putative Targets |
Gene Information | |||||||||||||||||||||
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Gene Symbol | GBA2 | ||||||||||||||||||||
Synonyms | AD035, NLGase, SPG46 | ||||||||||||||||||||
Description | glucosylceramidase beta 2 | ||||||||||||||||||||
Transcript | NM_020944 | ||||||||||||||||||||
Expression | |||||||||||||||||||||
Putative miRNA Targets on GBA2 | |||||||||||||||||||||
3'UTR of GBA2 (miRNA target sites are highlighted) |
>GBA2|NM_020944|3'UTR 1 GCCGTCTGAACTGTGGGAGGGAAGTGCTAACAGCCCAGCCTCCAGCCTGGCCTTTCCTCCTTCCCCTCTGAACCTCCTGC 81 AACCCTGAGCCATCAGGACAATCATACCCCTTCCCTTCTCTCCACCCAATTGTGCCAGTAAATGGGGGTTGAGGGTGACC 161 TAGGCAGCATTAGAATCACTTATTTATTTCTTTCCTCACCTGTTCCCTGACTGCGTGAAATGTTCAGGGAGGTCAGTTGA 241 TTTCCCCAGGTACATTCATGGTGTGACAGACACATGGGTACAAATAAAAGACCCAGAAAGCCAAAAAAAAAAAAAAAAAA 321 AAAAAAAAAAA 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 | TZM-bl | ||||||
Location of target site | 3'UTR | ||||||
Tools used in this research | TargetScan , miRTarCLIP , Piranha | ||||||
Original Description (Extracted from the article) |
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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 | |
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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) |
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PAR-CLIP data was present in ERX177624. RNA binding protein: AGO2. Condition:p53_V_AGO_CLIP_4_2
PAR-CLIP data was present in ERX177604. RNA binding protein: AGO2. Condition:p53_V_AGO_CLIP_2_6
PAR-CLIP data was present in ERX177616. RNA binding protein: AGO2. Condition:p53_V_AGO_CLIP_3_6
... - 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 | |
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Method / RBP | PAR-CLIP / AGO2 |
Cell line / Condition | TZM-bl / TZM-bl ami BaL |
Location of target site | ENST00000378103.3 | 3UTR | CCUUUCCUCCUUCCCCUCUGAACCUCCUGCAACCCUGAGCCAUCAG |
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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95 hsa-miR-6768-3p Target Genes:
Functional analysis:
ID![]() |
Target | Description | Validation methods |
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Strong evidence | Less strong evidence | |||||||||||
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MIRT060980 | LAMC1 | laminin subunit gamma 1 | ![]() |
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2 | 2 | ||||||
MIRT145633 | LASP1 | LIM and SH3 protein 1 | ![]() |
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2 | 2 | ||||||
MIRT161065 | CDV3 | CDV3 homolog | ![]() |
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2 | 2 | ||||||
MIRT161171 | SLC25A36 | solute carrier family 25 member 36 | ![]() |
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2 | 2 | ||||||
MIRT177407 | ZMYND11 | zinc finger MYND-type containing 11 | ![]() |
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2 | 2 | ||||||
MIRT262237 | WAC | WW domain containing adaptor with coiled-coil | ![]() |
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2 | 2 | ||||||
MIRT300236 | INO80D | INO80 complex subunit D | ![]() |
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2 | 2 | ||||||
MIRT373993 | PEBP1 | phosphatidylethanolamine binding protein 1 | ![]() |
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2 | 4 | ||||||
MIRT379949 | CRY2 | cryptochrome circadian clock 2 | ![]() |
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2 | 2 | ||||||
MIRT405244 | ADIPOR2 | adiponectin receptor 2 | ![]() |
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2 | 2 | ||||||
MIRT441622 | ROCK1 | Rho associated coiled-coil containing protein kinase 1 | ![]() |
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2 | 6 | ||||||
MIRT441807 | NOC3L | NOC3 like DNA replication regulator | ![]() |
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2 | 2 | ||||||
MIRT442007 | NDUFV3 | NADH:ubiquinone oxidoreductase subunit V3 | ![]() |
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2 | 2 | ||||||
MIRT442254 | DCTN5 | dynactin subunit 5 | ![]() |
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2 | 2 | ||||||
MIRT442413 | LIMD1 | LIM domains containing 1 | ![]() |
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2 | 2 | ||||||
MIRT442741 | SERINC5 | serine incorporator 5 | ![]() |
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2 | 2 | ||||||
MIRT442796 | CEP170 | centrosomal protein 170 | ![]() |
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2 | 2 | ||||||
MIRT443332 | OCRL | OCRL, inositol polyphosphate-5-phosphatase | ![]() |
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2 | 2 | ||||||
MIRT443602 | ZNF91 | zinc finger protein 91 | ![]() |
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2 | 2 | ||||||
MIRT443695 | KCNN3 | potassium calcium-activated channel subfamily N member 3 | ![]() |
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2 | 2 | ||||||
MIRT443749 | ELL2 | elongation factor for RNA polymerase II 2 | ![]() |
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2 | 2 | ||||||
MIRT446376 | THSD4 | thrombospondin type 1 domain containing 4 | ![]() |
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2 | 2 | ||||||
MIRT452491 | BANK1 | B-cell scaffold protein with ankyrin repeats 1 | ![]() |
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2 | 16 | ||||||
MIRT456028 | PSMA7 | proteasome subunit alpha 7 | ![]() |
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2 | 2 | ||||||
MIRT461191 | TRIP4 | thyroid hormone receptor interactor 4 | ![]() |
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2 | 16 | ||||||
MIRT464498 | UCK2 | uridine-cytidine kinase 2 | ![]() |
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2 | 2 | ||||||
MIRT466640 | TAOK1 | TAO kinase 1 | ![]() |
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2 | 16 | ||||||
MIRT466703 | TAF13 | TATA-box binding protein associated factor 13 | ![]() |
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2 | 4 | ||||||
MIRT467765 | SLC30A7 | solute carrier family 30 member 7 | ![]() |
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2 | 2 | ||||||
MIRT469973 | PTPRF | protein tyrosine phosphatase, receptor type F | ![]() |
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2 | 2 | ||||||
MIRT470539 | COASY | Coenzyme A synthase | ![]() |
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2 | 2 | ||||||
MIRT474827 | KIAA0226 | RUN and cysteine rich domain containing beclin 1 interacting protein | ![]() |
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2 | 2 | ||||||
MIRT475961 | GXYLT1 | glucoside xylosyltransferase 1 | ![]() |
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2 | 4 | ||||||
MIRT476459 | GBA2 | glucosylceramidase beta 2 | ![]() |
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2 | 2 | ||||||
MIRT477658 | EFNA1 | ephrin A1 | ![]() |
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2 | 2 | ||||||
MIRT485320 | MZT1 | mitotic spindle organizing protein 1 | ![]() |
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2 | 4 | ||||||
MIRT485656 | CYP1B1 | cytochrome P450 family 1 subfamily B member 1 | ![]() |
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2 | 2 | ||||||
MIRT494145 | CTC1 | CST telomere replication complex component 1 | ![]() |
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2 | 10 | ||||||
MIRT495127 | CXorf67 | chromosome X open reading frame 67 | ![]() |
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2 | 2 | ||||||
MIRT498279 | POFUT1 | protein O-fucosyltransferase 1 | ![]() |
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2 | 2 | ||||||
MIRT498432 | DDX39A | DExD-box helicase 39A | ![]() |
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2 | 2 | ||||||
MIRT498853 | LITAF | lipopolysaccharide induced TNF factor | ![]() |
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2 | 4 | ||||||
MIRT499661 | SDR42E1 | short chain dehydrogenase/reductase family 42E, member 1 | ![]() |
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2 | 2 | ||||||
MIRT502927 | CDC42SE1 | CDC42 small effector 1 | ![]() |
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2 | 4 | ||||||
MIRT503758 | CEP19 | centrosomal protein 19 | ![]() |
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2 | 6 | ||||||
MIRT507753 | CERS2 | ceramide synthase 2 | ![]() |
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2 | 4 | ||||||
MIRT507893 | CAMSAP2 | calmodulin regulated spectrin associated protein family member 2 | ![]() |
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2 | 4 | ||||||
MIRT510091 | PPWD1 | peptidylprolyl isomerase domain and WD repeat containing 1 | ![]() |
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2 | 8 | ||||||
MIRT527065 | PPP6R1 | protein phosphatase 6 regulatory subunit 1 | ![]() |
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2 | 2 | ||||||
MIRT530314 | TNFRSF10D | TNF receptor superfamily member 10d | ![]() |
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2 | 2 | ||||||
MIRT530702 | P2RY1 | purinergic receptor P2Y1 | ![]() |
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2 | 2 | ||||||
MIRT532378 | LINC00598 | long intergenic non-protein coding RNA 598 | ![]() |
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2 | 2 | ||||||
MIRT532969 | ZNF148 | zinc finger protein 148 | ![]() |
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2 | 2 | ||||||
MIRT533958 | TAF1D | TATA-box binding protein associated factor, RNA polymerase I subunit D | ![]() |
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2 | 2 | ||||||
MIRT535186 | PLEKHA8 | pleckstrin homology domain containing A8 | ![]() |
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2 | 2 | ||||||
MIRT538751 | CADM1 | cell adhesion molecule 1 | ![]() |
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2 | 2 | ||||||
MIRT539473 | ADARB2 | adenosine deaminase, RNA specific B2 (inactive) | ![]() |
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2 | 2 | ||||||
MIRT543858 | APIP | APAF1 interacting protein | ![]() |
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2 | 2 | ||||||
MIRT558802 | CDON | cell adhesion associated, oncogene regulated | ![]() |
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2 | 2 | ||||||
MIRT560208 | AK4 | adenylate kinase 4 | ![]() |
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2 | 2 | ||||||
MIRT560318 | EFHD2 | EF-hand domain family member D2 | ![]() |
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2 | 2 | ||||||
MIRT560439 | GOLGA7B | golgin A7 family member B | ![]() |
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2 | 2 | ||||||
MIRT560846 | SUV39H2 | suppressor of variegation 3-9 homolog 2 | ![]() |
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2 | 2 | ||||||
MIRT562787 | LIMA1 | LIM domain and actin binding 1 | ![]() |
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2 | 2 | ||||||
MIRT563476 | POLE3 | DNA polymerase epsilon 3, accessory subunit | ![]() |
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2 | 2 | ||||||
MIRT563829 | RIPK4 | receptor interacting serine/threonine kinase 4 | ![]() |
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2 | 2 | ||||||
MIRT563996 | SLFN11 | schlafen family member 11 | ![]() |
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2 | 2 | ||||||
MIRT564596 | ZNF791 | zinc finger protein 791 | ![]() |
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2 | 2 | ||||||
MIRT565442 | SURF4 | surfeit 4 | ![]() |
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2 | 2 | ||||||
MIRT566020 | RHOA | ras homolog family member A | ![]() |
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2 | 2 | ||||||
MIRT566185 | PTPN14 | protein tyrosine phosphatase, non-receptor type 14 | ![]() |
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2 | 2 | ||||||
MIRT567643 | FAM160A1 | family with sequence similarity 160 member A1 | ![]() |
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2 | 2 | ||||||
MIRT568484 | ARL5B | ADP ribosylation factor like GTPase 5B | ![]() |
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2 | 2 | ||||||
MIRT568553 | AKT2 | AKT serine/threonine kinase 2 | ![]() |
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2 | 2 | ||||||
MIRT613420 | XRCC3 | X-ray repair cross complementing 3 | ![]() |
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2 | 2 | ||||||
MIRT613638 | ARHGAP35 | Rho GTPase activating protein 35 | ![]() |
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2 | 2 | ||||||
MIRT614841 | POU2F2 | POU class 2 homeobox 2 | ![]() |
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2 | 2 | ||||||
MIRT630143 | ZFYVE9 | zinc finger FYVE-type containing 9 | ![]() |
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2 | 2 | ||||||
MIRT634123 | ZMYM1 | zinc finger MYM-type containing 1 | ![]() |
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2 | 4 | ||||||
MIRT641841 | TCF7L2 | transcription factor 7 like 2 | ![]() |
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2 | 2 | ||||||
MIRT647123 | ZNF446 | zinc finger protein 446 | ![]() |
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2 | 2 | ||||||
MIRT647968 | FBXO31 | F-box protein 31 | ![]() |
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2 | 2 | ||||||
MIRT658186 | FBXO9 | F-box protein 9 | ![]() |
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2 | 2 | ||||||
MIRT659097 | DENR | density regulated re-initiation and release factor | ![]() |
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2 | 2 | ||||||
MIRT668980 | CLCN3 | chloride voltage-gated channel 3 | ![]() |
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2 | 2 | ||||||
MIRT670351 | C1orf106 | chromosome 1 open reading frame 106 | ![]() |
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2 | 4 | ||||||
MIRT671826 | TRPM6 | transient receptor potential cation channel subfamily M member 6 | ![]() |
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2 | 2 | ||||||
MIRT695610 | GATAD1 | GATA zinc finger domain containing 1 | ![]() |
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2 | 2 | ||||||
MIRT697722 | USP8 | ubiquitin specific peptidase 8 | ![]() |
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2 | 2 | ||||||
MIRT700069 | RPL14 | ribosomal protein L14 | ![]() |
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2 | 2 | ||||||
MIRT708474 | MAPKAPK5 | mitogen-activated protein kinase-activated protein kinase 5 | ![]() |
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2 | 2 | ||||||
MIRT717001 | ARL6IP4 | ADP ribosylation factor like GTPase 6 interacting protein 4 | ![]() |
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2 | 2 | ||||||
MIRT719591 | TFCP2L1 | transcription factor CP2 like 1 | ![]() |
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2 | 2 | ||||||
MIRT722026 | CBY3 | chibby family member 3 | ![]() |
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2 | 2 | ||||||
MIRT722901 | LRRC20 | leucine rich repeat containing 20 | ![]() |
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2 | 2 |
miRNA-Drug Resistance Associations | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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