| pre-miRNA Information | |
|---|---|
| pre-miRNA | hsa-mir-1246 |
| Genomic Coordinates | chr2: 176600980 - 176601052 |
| Synonyms | MIRN1246, hsa-mir-1246, MIR1246 |
| Description | Homo sapiens miR-1246 stem-loop |
| Comment | None |
| RNA Secondary Structure |  |
| Associated Diseases |  |
| Mature miRNA Information | ||||||||||
|---|---|---|---|---|---|---|---|---|---|---|
| Mature miRNA | hsa-miR-1246 | |||||||||
| Sequence | 11| AAUGGAUUUUUGGAGCAGG |29 | |||||||||
| Evidence | Experimental | |||||||||
| Experiments | Illumina | |||||||||
| SNPs in miRNA |
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| Putative Targets | ||||||||||
| miRNA Expression profile | |
|---|---|
| Human miRNA Tissue Atlas | |
| miRNAs in Extracellular Vesicles |
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| Circulating MicroRNA Expression Profiling | |
| Gene Information | |||||||||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Gene Symbol | TAOK1 | ||||||||||||||||||||
| Synonyms | KFC-B, MAP3K16, MARKK, PSK-2, PSK2, TAO1, hKFC-B, hTAOK1 | ||||||||||||||||||||
| Description | TAO kinase 1 | ||||||||||||||||||||
| Transcript | NM_020791 | ||||||||||||||||||||
| Expression | |||||||||||||||||||||
| Putative miRNA Targets on TAOK1 | |||||||||||||||||||||
| 3'UTR of TAOK1 (miRNA target sites are highlighted) |
>TAOK1|NM_020791|3'UTR 1 CTTAATAATTGAGAGTGGCAATTCCGCTGGAGCTGTCTGCCAAAAGAAACTGCCTACAGACATCATCACAGCAGCCTCCT 81 CACTTGGGTACTACAGTGTGGAAGCTGAGTGCATATGGTATATTTTATTCATTTTTGTAAAGCGTTCTGTTTTGTGTTTA 161 CTAATTGGGATGTCATAGTACTTGGCTGCCGGGTTTGTTTGTTTTTGGGGAAATTTTGAAAAGTGGAGTTGATATTAAAA 241 ATAAATGTGTATGTGTGTACATATATATACACACACATACACATATATTATGCATGTGGTGAAAAGAATTGGCTAGATAG 321 GGGATTTTTCTGAACACTGCAAAAATAGAACGTAGCAAAATGGCTTCAGTTATCACTTTTGGGTGTCTGTATCCTAAGAA 401 GTTTCTGAAAAGATCTAAAGCCTTTTTATCCCATATCCCAAATTCTTATGAGCCACTCACAGCAGGCAGCATATGTTGAA 481 ATAAGTTATTACTGGTACACACCTGCATTGCCTCACCAGTGTATTTATTTGTTATTAAATTGATCTGACTTCTCAGCCTC 561 ATTTGGACTAAAAAAAGAAAGCAGAAATCCATGAACACATTGCTTCTCGGCCTTTTGGCTAAGATCAAGTGTAGAAATCC 641 ATGAACACTAAAGGACTTCATTGATTTTTTCAGAGAGTAGAAAACAACTTAGTTTTTCTTTTTTCCTGAATGCGTCATAG 721 GCTTGTGAGTGATTTTTGTCCATTCAATTGTGCCTTCTTTGTATTATGATAAGATGGGGGTACTTAAGGAGATCACAAGT 801 TGTGTGAGGATTGCATTAACAAACCTATGAGCCTTCAATGGGGAAGACCAGAAGGGTGAGAGGGGCCCTGAAAGTTCATA 881 TGGTGGGTATGTCCCGCAGCAGAGTGAGGAGATGAAGCTTACGTGTCCTGACGTTTTGTTGCTTATACTGTGATATCTCA 961 TCCTAGCTAAGCTCTATAATGCCCAAGACCCCAAACAGTACTTTTACTTTGTTTGTACAAAAACAAAGACATATAGCCAA 1041 TACAAATCAAATGCCGGAGGTGTTTGATGCCATATTTGCAAATTGCCATCTATTGAAATTCTCGTCACACTACATAGACA 1121 TAATTGTTATCTCCTTTTGGCTTATGTGATTTTCTGTTTACAAGTAGAATAGCCAATTATTTAAATGTTTAGTTGCCACA 1201 GTGAACCAGGAGTCACTGAGCCAATGACTTTACCAGCTGCTGACTAATCTTCATCACCACTGTAGATTTTGCTGCATGTG 1281 CAGGTCCTCTATTTTTAATTGCTGTTTTCGTTGCTGCAGTACTTTACAAACTTCTAGTTCGTTGAGACTTAGTGACCATT 1361 TGGCATCAAGTTAACATCACACAATAGGAAACACCACTTCCACAAGTCTCAAGCCTCAGTGCTAAAGTACTACTGAAAAG 1441 GAACTAGGAAGTTTGGCCAATTAAAAAAAAAAAGTAAAATAAGTTATAGTGGTCAGGGAATCTCTTGACGAAAGCTAACT 1521 CTTATTTTTCAGGGGGCACATGTTTTGTTTTGTTATGTTTTGTTGTACAATGAAGGATGAACCCAATGCTAAAAAGTCAG 1601 TTATTTTCTTGGTTTTCCATTTCTTGTATATAAATTGTGTTGGAGGTGGGTAGGAAGCTGTGAGTATGACTTGAAGAAAA 1681 ATATCCTTTTCAGTGACAAATCAGAGTTTCTTACAAGTTATTGTCCTGCTCCCTTCCAAGTTGTCTTGAAGAATCCTTGC 1761 TGCTAACTCTGGATCCTGCTTTTCCTATAGTCAGAGGGCTCCAAGGTAGAACTCTCTAAGTCCCTCTCAATGGCACTCTT 1841 TGCCTAGACCAAACTAATGACCAAACAGTAATCAATCTATCACTGTTGAAGTCCTGGTTTTCTCAACCAAATTTTAAGTC 1921 TTTCCCAGGTATGTCAGTCGAGTTGCCATGAATCCTCACCTGTAGGAGTTTCTGGGATTCATTTTAAGGAAACTGGAAGA 2001 AAATTAATGTTTTAATGTAAATGTTTTTAAAACCAAGATCACCATAGAGTTCACACAAAATTTTAGGCAGTGTTTCAAGA 2081 AGCACTCTTATGTGTTGTTCTTTCAGCCCATGCTCCAGGTCACCGGTTTTTAGGTAAACATGACATGACATGTACTTGTA 2161 ATATCAGTGAAAGGGGCTTTTAGTCGTCTCAGTATCTTTTTTGCATTCAGGTATTATAGCGTTTCCAACAAATTGAGAAA 2241 TTACTTATTTGGTGTAAAATGACGAGAGAGCTTTAGAATTTAATAAAATGTCAAAAATACAATTTGATACCCTTAAAAAT 2321 TATTCATAGATCTGGCTGCTCTGTACTACTGGATGGGTGGAATAGGGAAGCAGATCACTTTTGCATACAAAAACTCTTTC 2401 AAACCCAAAATATTATTGGTGGTACATTTTAAAGTCCAATTGTGGACTTAAATTAGTCAAATTGAGAGTTACTGAGTCCA 2481 TTCAGATCTCCAGTAGGGTTTTGTATCTAATGTATTTGGCCACCAGTTTTACATGTAGGTCATGACTATACCTGGATTTT 2561 ATCATTAAGTTAACTTTAAAGTATATACAGTTTGCAAAAAATGATTCAAATTAATTGGTTTGTATATGTTTGTGAGATCT 2641 AGCTTCTGAGGAATCTCATACATAGTAGGAACCATCATAGAGTAAAGCTTGTAGCAGAAAAATTGGAAGGGTTTTGAGAT 2721 ATCCTAGAGAAAGAGCAAGCACTTTCTGAATCAGTGGGGAAATATCAATATTTGATCAAATTAACACTACCTCCTTCCCA 2801 GTGTTGGTGTTCACTCACTATATGTCTTTAAGAAAATTAAAACTATGGAAAATTTGTCTAGCATATCAGAAGTTGTAAAT 2881 GCTATATCTGGTATCCAGAGGCTGGCTGTAAAAAGTTCCTTGGGGTCACTCTATCTCACATTTTTTTTGGTTAGCATTTT 2961 AAAAATGCAAAGCCACATACTTTGAAATATATTATTCCAAATTGAGCTCCCTTCCCTTTGCACATATTTTTTCCTCCCCT 3041 TATTGAAGTCAGCTCTAACCCCAAATTCTAGTATCCAAAAGTATTTTTATTTGTATAATGCTATCTGAAAAATGTGTTTA 3121 TATTATATTTTCAGAGCTGCAATTCTTATTCGCCATTTCAATACCTAGAGATAGAGAGTCTTGTATTTGAAGCCACACAC 3201 ACTGGTGTAATATGCTTAGTACTCTAGGTCAAGGATTTGTTGGTAAATGGAACATTTTAGCATAGTCATGATTTTTGGTT 3281 GCCTAGACATCAGGTAAACATTCAGTACACTAAAGAAACTATCCTGGACACTCCCTCCTGCTTCCACCAATTTTTTTCTC 3361 ACCCCCTTTTCAAAAATTGAAAACTCTATGAGTGTCTTTTTGAGACCATAAAGCAGACTTTAGTAACTTTCTATTTCTGT 3441 AAGTACTAAATGTCTGGCATTTTAAACTTTTGTAGAATACATTATGTTGGACACTGGAATAATACTATTTATTTTCACCT 3521 GTGAAAAATGACTTCATTGTACTTGAAACACCTCCTTTGCATTTCTCCATTTGTGCCATTCACTAGTGGAAATAAATTGT 3601 ATTATACCATGATCTACTGGCTTTTTAAAACTGTATTAAATATGCACATTTTTGGTATAGCTATTATCATTTGTATGTAT 3681 ATATTGTATATACATATGAGTGTCTGTATGTGTGTATAGATGGATGGATGTAACTCATACTGTACATTTCCATCAGGGCA 3761 CTTAAAAGTTCTGTTATTTTTGTTTGGTTTTGTTATTTCAGTCCTCAGTTAAGGCAAGAATGCATGTGTTTCTTAAGAAT 3841 GAGTACTCTGCGTTGATGTTTATGAGAAGGTGGTCATTAGATGCAGTCTTTTCCTTTTTAATCCCCTCTTAGCACTTCTG 3921 TGAGTGGAGAGGACATTAAGTAAAATTTGGAATCATAAGTTGCAATGCAGTAAAATGGTGCTGGGGAAGGAGCCAGTTAG 4001 TGTTTCTGTGAGTTTGTGTTGTGATGCAATAAGAGATAAGTAATGCAGAGAGAAATGAACCATGGAAAGTAAGAACACTG 4081 ATGGTGATTCCTCTGCAAAGATGATAAGAAAAAGAACCAATAAATCACACAATCTTTATGTGCTTTCTATATGTATTTCT 4161 TAGTAGTGATACCATTGATCCTCTTACTTTTTTTACTCCATTAATACTAATAATTATATACTTTGCTGAGGATCAAAACA 4241 GCCAAGAAAGGAATTACTGCTAAAGCATCTAAGATTCTCCTGAACTGTAAAATCAACAGGAAATGGCCACTGGGAGAGAA 4321 GGATTTGGTATTGGGTGAGGGGCTTTCTCCCTTTACCTGCCTCTTCTTGCTTGCTAATAGTAAGTTCTTTGTGCACCTTC 4401 CACCACTTCTGAGCCACTACTATTCAAGTAGAGATTTGCCCCAACACATTAACTTTTTCCTTGGAGATTTATATGGTCCT 4481 GCATTTTGTCCTGTGCTCACAATGTGAAGTGTCTTCTGTATTCAAATCAAAAAATAATATATTTAAGGTATATAAGTGTG 4561 AATCTCCTATAATGATGGAAGAAGAGGTTCTCTTGTCTTAGATAGAAAAGAGCCTTCTCCAAGAGCAATGTCAAAACTTG 4641 GGCTGTCATCTTTGAGCTGTTTACCAAAATACAGACCATTATTGAAGAAAAACAAATTATCTATTTTGTTTTCCCCCATC 4721 TAACATGATAGTGCCCCCAACCAGGTTGTAGCATTGCCTTTTAAAAGAGACTCACTCACTCTTAGTTTTTAAGAACTGGA 4801 AATTTCCCATCCTCAGATCCCTTAAAGGATGAAGAGTTGGCTGTACACTTAGCGGACTTGCCTCTTGTATGCAAGGACTA 4881 CTGATTGAAGTCTGTTTTGCTGTGTCTGGTTATGTTGTCTGCACTTTTATGAAATCACTACAATAGGTCTGCATTGGAAA 4961 TGACTATTAATTTGTAAAGAAGTAAGTTTTATTAAACACTGTCTAGAAAAAGAAAGTGAAGCTGAGAACTCTTCCTTTAT 5041 TGTGCATTTATATTTTCTGCTGAATTCCGGTAGTTCCCTTTAAAGTCATGTTGACTAATGTTTTCCTCCTTGTTTGTATT 5121 CAGATTTCCAAAATTTCACTCATACAAGGGAAGAGACTCCATTTAGCTTAACGGTAGTCTTTAGATCATAAGAAATATAT 5201 AAATTAGTATGCACCTTATCTGCCTGTTGTGGGTTTCTTAAACTTGCACTTCCTACCCACCCAAAGATAGATATCCTTTA 5281 AAGAAAATAAAGGCAGAGAATTAAAACTGGGGAGCCATTTACTATGTCACCATCACTGTTAACTGTTTCCCAGCAATCTA 5361 AACTTTTTGAAGTTTCAGAGGTGTATTTTTTTTTTGTATATATGTCTGTGTGATTGTATTGTTTTGTTTCTAAATATACA 5441 AGGAATTCTTTAAATAGAGAAAAAGGTTAATCCTCACTGAAACACCAGGATGCCCACTGGATATACTAATCTGAACATCT 5521 GTAGGTAGTTTGTCATGAAAAAGTGGAGAGAAGATGAGACTTTTGAATGAATGAAAAAGGGTATCTTGATACCCAGAATT 5601 CCCCCCAAAGTACGGGTAATTCAACCTGCACAGTTTTCTTTCACTCAAAGTGTTCAGCACTTGTGAGTGAAAAATCATGT 5681 AATTATCTGTAAATATGTAGCTAACAAATTGACCTAGTTTCTGTATTTTTTTGTTTTTGTACTAAAGTTTATAGGTCTGT 5761 GCCAGCTAGAGAGAAGTTGCTGTCATTACCAGTTGTGGTCCTAGCATCTAACCCTGAAACCATCCTAGGTGACATTTTTA 5841 GAATTAATACTTAAATGTTAAACAGGGGGAAATGAAGCTTAATCATGGTCAGGTTTGAGATCTTTTGCAGTGAAATAATT 5921 TTATTTAATATAAATGATCACATGTCCTCAATCATGAATGAGGTAGGGAGCCTCTCTCCCCCAGTGGCCATGTTTACAAA 6001 AGTGTGTTTTGTCTATAAAGTGCAAGTGTTTTAATGTTTATGTAAATTATGCAGGTGATAACATGGTTTGGAACTGTTTA 6081 TTGGGCTCTTTAACTGAATTTTCAAATGAAATGAACTATGCTTATTGCTGGCACATTGATCCCATTTCTGGAACATTTTT 6161 CCTATTTCCAGAGTTACATATGTTCTTTTGTCATTACCCAATTTAACCTCCCTTTCTCTGATATGCCTTGTAGCCAAAGT 6241 ATTAAAGGCTGATGAACATAGACAAGGGAAATGCATTTCTTAGAAATCCGTGAACCCTCAGTTGTATGCTTTCAGTACTC 6321 GTGTTAATATGTTTCTATGGCAACTCTGAGGTCAGTGGTTTAGAAATGAGATACCAGTGTTAATGAAAAGTGTGTGCTCT 6401 TTGCTTTTGCATGGCTTGGCTTAGTATCCAAGGTATATTAGGGCCACTTGAAAGCATGAAGACCAGTTATATAGGGAACA 6481 GGTTTCTCTCAGTGGCACATTTTGCTTTTTCTGAGCCCCAAATACATTGCCTGGGCATGAACATTGTTACCGTAAATTGC 6561 ACATGGTCATGGACTGAATTATGTGACTTTAAAGGATGTAACTGCCCAACATTTGCAGATTCTGGGTGGTCTATGTGACC 6641 ATTTGTCTCGTATCCAAAAACCCCGGGGCTATTGGAACCCTTCCAACACTTTTTCCTTTGTCATAGACAAGTTTATATAT 6721 AACTTACCAAGATGTTGGCTGTCCTGGTGTATTGCCAGACAGCTCTCTTTTGGTTCCCATTCCAAATGTGCTGCTGTCCT 6801 TCTTTGCATTTCACAATATCAAAGAAACCACCACCCTTCTTCCTAACAGCATTTTATGCCTTTTATTCCACATTAAATGG 6881 GAATTGTGCCTACTTAGGAGTGCCCCTCCAATTAATTACATGTGTCCAAGAATAATCCAAGCTAGAGACACAAGGTGGGA 6961 AAACATTTCAAAAAAAAAAAGTCCTCTTAAGGCCAGTAATTTATCTGAAAAGGTATTTTATCACACCTTGACACCTTATA 7041 TATGAGCCTATTAGGAGCTGCAGGTGGTTTCATAGGGTAAAATCCAAGAAAAGAGAAGGATGTGTGGGGTTTCTATTAGA 7121 AGATAATTTTGTTCTCATTTTACCTTTTCTTTTATGATCCTTCTCTGCTAGAACAGGTTAATTCTCCAAATTTGTTTTGT 7201 TTTGTTTTGTTATTTTTTAGGGAACTCTTTTGCAAAAGCAATGGTCGGATGTAAATAACATTTAAAGTATAGTGCACATA 7281 ACTTCCCCGGACTGTTCCAATCTGATAATTTGTAAATGCTTTAGAGTTTTTTTAATTAACACTTGTGTTGCTAAATTCTA 7361 TTTATGTAAGTCTGCTAAAGTTTTTTAGCCCACTTAAAACTTAAGACAACCATTTAAAATAATGGATGGGTTACTATGAG 7441 CAATTTCGCTTTCAGAACCCCCTTGTTTTAGTATATGAAAAAGCCTAATGCGCATTAATGAGGTTGAAGAGACTATGAGA 7521 AATATGTATAGTGTATATTTTAAAACAGCTTTGCTTGTATTGTGAAGATTTAAAAACAAACTTGAGATTTTTAACGTAAC 7601 TATTAACACAGTTTTAACATAAGTTATCCCACTGGGTTTAAGAGCATCTTGAATGTATAATCCTTTTTGTAACCCAGGTT 7681 GGTTTCTACTTTTACCAGTCACCCAAACATATTTATGTTTTTAGTTTTATGTACTCATTTCCCTTTGTTTTCCTCAAACA 7761 GCATGATTTTTTTGCACATGTAGAAATTTTTTAAAAGAAAGAAATTAGTACATCATTTTCTCTGGATTTTCTTCACTTCC 7841 CTCTTCCTTTCTACTAACTCCTTCCTTAAAGGCCATATCACTCCATTTGCATTATTTGTGCAAATGCCAGGGTTGGTTTT 7921 TATTTTTATTTTTGCTATTTACCTAAAAAAAGAAAATGCTTCAGTCAATTGCTTTTTTATTTAAAAAAAAAAAGAAAAAA 8001 AGCTGTAACCTTATCATTTCTGAGTAGACCATTGAGCGATGAATGCACACCTGTAGTAGCCCAGGACCAGCTGTGGTGGC 8081 TAAAGGGAATATGTTAATTAAGCAAGAGGTTCTTTTCTAAAAGTGGTATCTGTTATCCACAATGTATTTTAGTTATTCCC 8161 ACAAGTCAGGGGTCCAGATAAAATGAGGGTTATCAGCTAACTGATATGCTATCATTGAGGTTCATCAATGAATTTGTACA 8241 TTTCTAGTTCCCTTTGGTGAAGGGAAAAATGATGATTTTGCAAGACCTAGATTTTGGCTTGGTTTCTTGCCTCCTTTTTT 8321 GGCAGCCTTCATCTTCTCATCTCCCAAACCCCCTGAGCCCGTAGGGTTTTCATAGTGGACAAAGAACTTGTGGTCTTTTA 8401 AAACTGGGACTGATACTTTTTTGAGAGAGTATCGTGTCGAAAGTGTGATGTTCTACCACTTTACCAATAACTAATTTTAA 8481 ATACACATTGTCCTCTCGATTTTTGGACCAAACAGACGCTCACAGTGGAGGCTTATCAAGGGTTGCATTGGGGAAGAAGC 8561 CTCTCCCTCTCTGTCAGCACCAGCTGGTAAAGGTGACTGTACAGATGTGCATTTTCCTTTTGGTATAAATGGTCCACAGC 8641 ACTAACTGGTAAGGCTTATTGTACAGTATATTGTCAGTATTCTTCTGGTTCAGCATACCTTATAGTTCATATATAACCTG 8721 TATTAATTGTATAGATTGTGCATTAAAAGCTGTTACCAAGTTGTCAGAACATAAGAGCGAAAACAAGGTCATATGTAATA 8801 TTTTGTTTGTAAGTATCCTTTGTATCATAGCAAAGGAAATGTTTAAAAAAATCAACTGTAATAAAGTAATTTTAGTACAC 8881 AAAAAAAAAAAAAAAA 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 | HEK293 |
| 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 GSM545215. RNA binding protein: AGO4. Condition:Control
... - Hafner M; Landthaler M; Burger L; Khorshid et al., 2010, Cell. |
| Article |
- Hafner M; Landthaler M; Burger L; Khorshid et al. - Cell, 2010
RNA transcripts are subject to posttranscriptional gene regulation involving hundreds of RNA-binding proteins (RBPs) and microRNA-containing ribonucleoprotein complexes (miRNPs) expressed in a cell-type dependent fashion. We developed a cell-based crosslinking approach to determine at high resolution and transcriptome-wide the binding sites of cellular RBPs and miRNPs. The crosslinked sites are revealed by thymidine to cytidine transitions in the cDNAs prepared from immunopurified RNPs of 4-thiouridine-treated cells. We determined the binding sites and regulatory consequences for several intensely studied RBPs and miRNPs, including PUM2, QKI, IGF2BP1-3, AGO/EIF2C1-4 and TNRC6A-C. Our study revealed that these factors bind thousands of sites containing defined sequence motifs and have distinct preferences for exonic versus intronic or coding versus untranslated transcript regions. The precise mapping of binding sites across the transcriptome will be critical to the interpretation of the rapidly emerging data on genetic variation between individuals and how these variations contribute to complex genetic diseases.
LinkOut: [PMID: 20371350]
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| Experimental Support 2 for Functional miRNA-Target Interaction | |
|---|---|
| miRNA:Target | ---- |
| Validation Method |
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| Conditions | HEK293 |
| Disease | 57551.0 |
| Location of target site | 3'UTR |
| Tools used in this research | TargetScan , miRTarCLIP , Piranha |
| Original Description (Extracted from the article) |
...
"HITS-CLIP data was present in GSM714643. RNA binding protein: AGO2. Condition:completeT1
"PAR-CLIP data was present in GSM714644. RNA binding protein: AGO2. Condition:completeT1
"PAR-CLIP data was present in GSM714647. RNA binding protein: AGO2. Condition:mildMNase
... - Kishore S; Jaskiewicz L; Burger L; Hausser et al., 2011, Nature methods. |
| Article |
- Kishore S; Jaskiewicz L; Burger L; Hausser et al. - Nature methods, 2011
Cross-linking and immunoprecipitation (CLIP) is increasingly used to map transcriptome-wide binding sites of RNA-binding proteins. We developed a method for CLIP data analysis, and applied it to compare CLIP with photoactivatable ribonucleoside-enhanced CLIP (PAR-CLIP) and to uncover how differences in cross-linking and ribonuclease digestion affect the identified sites. We found only small differences in accuracies of these methods in identifying binding sites of HuR, which binds low-complexity sequences, and Argonaute 2, which has a complex binding specificity. We found that cross-link-induced mutations led to single-nucleotide resolution for both PAR-CLIP and CLIP. Our results confirm the expectation from original CLIP publications that RNA-binding proteins do not protect their binding sites sufficiently under the denaturing conditions used during the CLIP procedure, and we show that extensive digestion with sequence-specific RNases strongly biases the recovered binding sites. This bias can be substantially reduced by milder nuclease digestion conditions.
LinkOut: [PMID: 21572407]
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| Experimental Support 3 for Functional miRNA-Target Interaction | |
|---|---|
| miRNA:Target | ---- |
| Validation Method |
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| Conditions | hESCs (WA-09) |
| Disease | 57551.0 |
| 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 SRR359787. RNA binding protein: AGO2. Condition:4-thiouridine
... - Lipchina I; Elkabetz Y; Hafner M; Sheridan et al., 2011, Genes & development. |
| Article |
- Lipchina I; Elkabetz Y; Hafner M; Sheridan et al. - Genes & development, 2011
MicroRNAs are important regulators in many cellular processes, including stem cell self-renewal. Recent studies demonstrated their function as pluripotency factors with the capacity for somatic cell reprogramming. However, their role in human embryonic stem (ES) cells (hESCs) remains poorly understood, partially due to the lack of genome-wide strategies to identify their targets. Here, we performed comprehensive microRNA profiling in hESCs and in purified neural and mesenchymal derivatives. Using a combination of AGO cross-linking and microRNA perturbation experiments, together with computational prediction, we identified the targets of the miR-302/367 cluster, the most abundant microRNAs in hESCs. Functional studies identified novel roles of miR-302/367 in maintaining pluripotency and regulating hESC differentiation. We show that in addition to its role in TGF-beta signaling, miR-302/367 promotes bone morphogenetic protein (BMP) signaling by targeting BMP inhibitors TOB2, DAZAP2, and SLAIN1. This study broadens our understanding of microRNA function in hESCs and is a valuable resource for future studies in this area.
LinkOut: [PMID: 22012620]
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| Experimental Support 4 for Functional miRNA-Target Interaction | |
|---|---|
| miRNA:Target | ---- |
| Validation Method |
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| Conditions | Prostate Tissue |
| 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 SRX1760616. RNA binding protein: AGO2. Condition:AGO-CLIP-PC3_A
PAR-CLIP data was present in SRX1760638. RNA binding protein: AGO2. Condition:AGO-CLIP-PC3-miR148
... - Hamilton MP; Rajapakshe KI; Bader DA; Cerne et al., 2016, Neoplasia (New York, N.Y.). |
| Article |
- Hamilton MP; Rajapakshe KI; Bader DA; Cerne et al. - Neoplasia (New York, N.Y.), 2016
MicroRNA (miRNA) deregulation in prostate cancer (PCa) contributes to PCa initiation and metastatic progression. To comprehensively define the cancer-associated changes in miRNA targeting and function in commonly studied models of PCa, we performed photoactivatable ribonucleoside-enhanced cross-linking immunoprecipitation of the Argonaute protein in a panel of PCa cell lines modeling different stages of PCa progression. Using this comprehensive catalogue of miRNA targets, we analyzed miRNA targeting on known drivers of PCa and examined tissue-specific and stage-specific pathway targeting by miRNAs. We found that androgen receptor is the most frequently targeted PCa oncogene and that miR-148a targets the largest number of known PCa drivers. Globally, tissue-specific and stage-specific changes in miRNA targeting are driven by homeostatic response to active oncogenic pathways. Our findings indicate that, even in advanced PCa, the miRNA pool adapts to regulate continuing alterations in the cancer genome to balance oncogenic molecular changes. These findings are important because they are the first to globally characterize miRNA changes in PCa and demonstrate how the miRNA target spectrum responds to staged tumorigenesis.
LinkOut: [PMID: 27292025]
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| Experimental Support 5 for Functional miRNA-Target Interaction | |
|---|---|
| miRNA:Target | ---- |
| Validation Method |
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| Conditions | Cardiac Tissues |
| Location of target site | 3'UTR |
| Tools used in this research | TargetScan , miRTarCLIP , Piranha |
| Original Description (Extracted from the article) |
...
HITS-CLIP data was present in GSM2202478. RNA binding protein: AGO2. Condition:S3_LV_36yo_Male_AGO2_bound_RNA
... - Spengler RM; Zhang X; Cheng C; McLendon JM; et al., 2016, Nucleic acids research. |
| Article |
Elucidation of transcriptome-wide microRNA binding sites in human cardiac tissues by Ago2 HITS-CLIP.
- Spengler RM; Zhang X; Cheng C; McLendon JM; et al.- Nucleic acids research, 2016
MicroRNAs (miRs) have emerged as key biological effectors in human health and disease. These small noncoding RNAs are incorporated into Argonaute (Ago) proteins, where they direct post-transcriptional gene silencing via base-pairing with target transcripts. Although miRs have become intriguing biological entities and attractive therapeutic targets, the translational impacts of miR research remain limited by a paucity of empirical miR targeting data, particularly in human primary tissues. Here, to improve our understanding of the diverse roles miRs play in cardiovascular function and disease, we applied high-throughput methods to globally profile miR:target interactions in human heart tissues. We deciphered Ago2:RNA interactions using crosslinking immunoprecipitation coupled with high-throughput sequencing (HITS-CLIP) to generate the first transcriptome-wide map of miR targeting events in human myocardium, detecting 4000 cardiac Ago2 binding sites across >2200 target transcripts. Our initial exploration of this interactome revealed an abundance of miR target sites in gene coding regions, including several sites pointing to new miR-29 functions in regulating cardiomyocyte calcium, growth and metabolism. Also, we uncovered several clinically-relevant interactions involving common genetic variants that alter miR targeting events in cardiomyopathy-associated genes. Overall, these data provide a critical resource for bolstering translational miR research in heart, and likely beyond.
LinkOut: [PMID: 27418678]
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| CLIP-seq Support 1 for dataset GSM714643 | |
|---|---|
| Method / RBP | HITS-CLIP / AGO2 |
| Cell line / Condition | HEK293 / completeT1, repB |
| Location of target site | ENST00000261716.3 | 3UTR | CUUCUCGGCCUUUUGGCUAAGAUCAAGUGUAGAA |
| Tools used in this analysis | TargetScan, miRTarCLIP, and Piranha |
| Article / Accession Series | PMID: 21572407 / GSE28865 |
| CLIP-seq Viewer | Link |
| CLIP-seq Support 2 for dataset GSM545215 | |
|---|---|
| Method / RBP | PAR-CLIP / AGO4 |
| Cell line / Condition | HEK293 / Control |
| Location of target site | ENST00000261716.3 | 3UTR | CAUUGCUUCUCGGCCUUUUGGCUAAGAUCAAGUGUAGAA |
| Tools used in this analysis | TargetScan, miRTarCLIP, and Piranha |
| Article / Accession Series | PMID: 20371350 / GSE21578 |
| CLIP-seq Viewer | Link |
| CLIP-seq Support 3 for dataset GSM714644 | |
|---|---|
| Method / RBP | PAR-CLIP / AGO2 |
| Cell line / Condition | HEK293 / completeT1, repA |
| Location of target site | ENST00000261716.3 | 3UTR | AUUGCUUCUCGGCCUUUUGGCUAAGAUCAAGUGUAGAA |
| Tools used in this analysis | TargetScan, miRTarCLIP, and Piranha |
| Article / Accession Series | PMID: 21572407 / GSE28865 |
| CLIP-seq Viewer | Link |
| CLIP-seq Support 4 for dataset GSM714647 | |
|---|---|
| Method / RBP | PAR-CLIP / AGO2 |
| Cell line / Condition | HEK293 / mildMNase, repB |
| Location of target site | ENST00000261716.3 | 3UTR | AUUGCUUCUCGGCCUUUUGGCUAAGAUCAAGUGUAGAA |
| Tools used in this analysis | TargetScan, miRTarCLIP, and Piranha |
| Article / Accession Series | PMID: 21572407 / GSE28865 |
| CLIP-seq Viewer | Link |
| CLIP-seq Support 5 for dataset SRR359787 | |
|---|---|
| Method / RBP | PAR-CLIP / AGO2 |
| Cell line / Condition | hESCs (WA-09) / 4-thiouridine, RNase T1 |
| Location of target site | ENST00000261716.3 | 3UTR | AUUGCUUCUCGGCCUUUUGGCUAAGAUCAAGUGUAGAAAU |
| Tools used in this analysis | TargetScan, miRTarCLIP, and Piranha |
| Article / Accession Series | PMID: 22012620 / SRX103431 |
| CLIP-seq Viewer | Link |
| MiRNA-Target Expression Profile | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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| MiRNA-Target Expression Profile (TCGA) | ||||||||||||||||||||||||||||
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52 hsa-miR-1246 Target Genes:
Functional analysis:
ID |
Target | Description | Validation methods |
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| Strong evidence | Less strong evidence | |||||||||||
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| MIRT053774 | DYRK1A | dual specificity tyrosine phosphorylation regulated kinase 1A |  |
|
|
|
4 | 1 | ||||
| MIRT196431 | TAOK1 | TAO kinase 1 | |
|
2 | 6 | ||||||
| MIRT444394 | ZNF480 | zinc finger protein 480 | |
|
2 | 2 | ||||||
| MIRT447596 | MSH3 | mutS homolog 3 | |
|
2 | 2 | ||||||
| MIRT454049 | TMBIM4 | transmembrane BAX inhibitor motif containing 4 | |
|
2 | 2 | ||||||
| MIRT458257 | ZNF85 | zinc finger protein 85 | |
|
2 | 2 | ||||||
| MIRT461493 | KIAA1009 | centrosomal protein 162 | |
1 | 1 | |||||||
| MIRT474057 | LMNB2 | lamin B2 | |
|
2 | 2 | ||||||
| MIRT479231 | CKS2 | CDC28 protein kinase regulatory subunit 2 | |
|
2 | 6 | ||||||
| MIRT485663 | CHD7 | chromodomain helicase DNA binding protein 7 | |
|
2 | 2 | ||||||
| MIRT485735 | CALM2 | calmodulin 2 | |
|
2 | 2 | ||||||
| MIRT498809 | SRRT | serrate, RNA effector molecule | |
|
2 | 8 | ||||||
| MIRT501190 | SKIL | SKI like proto-oncogene | |
|
2 | 2 | ||||||
| MIRT502619 | DGS2 | DiGeorge syndrome/velocardiofacial syndrome complex 2 | |
|
2 | 6 | ||||||
| MIRT502665 | CTC1 | CST telomere replication complex component 1 | |
|
2 | 13 | ||||||
| MIRT512313 | ADCY9 | adenylate cyclase 9 | |
|
2 | 6 | ||||||
| MIRT513756 | PIM1 | Pim-1 proto-oncogene, serine/threonine kinase | |
|
2 | 2 | ||||||
| MIRT514651 | CRADD | CASP2 and RIPK1 domain containing adaptor with death domain | |
|
2 | 2 | ||||||
| MIRT514865 | SHOX2 | short stature homeobox 2 | |
|
2 | 2 | ||||||
| MIRT527109 | ARHGAP15 | Rho GTPase activating protein 15 | |
|
2 | 2 | ||||||
| MIRT527145 | GPATCH11 | G-patch domain containing 11 | |
|
2 | 2 | ||||||
| MIRT528507 | HTR7 | 5-hydroxytryptamine receptor 7 | |
|
2 | 4 | ||||||
| MIRT532109 | RRP8 | ribosomal RNA processing 8 | |
|
2 | 2 | ||||||
| MIRT534601 | RORA | RAR related orphan receptor A | |
|
2 | 2 | ||||||
| MIRT538906 | BRI3BP | BRI3 binding protein | |
|
2 | 4 | ||||||
| MIRT544541 | GDE1 | glycerophosphodiester phosphodiesterase 1 | |
|
2 | 2 | ||||||
| MIRT547430 | MED4 | mediator complex subunit 4 | |
|
2 | 2 | ||||||
| MIRT553029 | USP48 | ubiquitin specific peptidase 48 | |
|
2 | 2 | ||||||
| MIRT555136 | PTPRD | protein tyrosine phosphatase, receptor type D | |
|
2 | 2 | ||||||
| MIRT562091 | KIAA0895 | KIAA0895 | |
|
2 | 2 | ||||||
| MIRT562584 | CBX3 | chromobox 3 | |
|
2 | 4 | ||||||
| MIRT563747 | ZNF763 | zinc finger protein 763 | |
|
2 | 2 | ||||||
| MIRT573310 | AKR7A2 | aldo-keto reductase family 7 member A2 | |
|
2 | 2 | ||||||
| MIRT687232 | PLAGL2 | PLAG1 like zinc finger 2 | |
|
2 | 2 | ||||||
| MIRT704465 | CREBRF | CREB3 regulatory factor | |
|
2 | 2 | ||||||
| MIRT718817 | PYGO1 | pygopus family PHD finger 1 | |
|
2 | 2 | ||||||
| MIRT731194 | NFIB | nuclear factor I B | |
|
2 | 1 | ||||||
| MIRT732503 | SPRED2 | sprouty related EVH1 domain containing 2 | |
|
|
3 | 0 | |||||
| MIRT733489 | MIF | macrophage migration inhibitory factor | |
|
2 | 0 | ||||||
| MIRT734071 | SRSF1 | serine and arginine rich splicing factor 1 | |
|
2 | 0 | ||||||
| MIRT734733 | AR | androgen receptor | |
|
|
3 | 0 | |||||
| MIRT734755 | GLS2 | glutaminase 2 | |
|
2 | 0 | ||||||
| MIRT735248 | CFTR | cystic fibrosis transmembrane conductance regulator | |
|
8 | 1 | ||||||
| MIRT736017 | ELAVL1 | ELAV like RNA binding protein 1 | |
|
2 | 0 | ||||||
| MIRT736329 | DNAH3 | dynein axonemal heavy chain 3 | |
|
2 | 0 | ||||||
| MIRT737381 | CCNG2 | cyclin G2 | |
|
2 | 0 | ||||||
| MIRT755524 | FOXA2 | forkhead box A2 | 3 | 1 | ||||||||
| MIRT755713 | DIXDC1 | DIX domain containing 1 | 2 | 1 | ||||||||
| MIRT755714 | WNT9A | Wnt family member 9A | 2 | 1 | ||||||||
| MIRT755715 | RAC2 | Rac family small GTPase 2 | 2 | 1 | ||||||||
| MIRT755716 | FRAT2 | FRAT2, WNT signaling pathway regulator | 2 | 1 | ||||||||
| MIRT756132 | ACE2 | angiotensin I converting enzyme 2 | 3 | 1 | ||||||||
| miRNA-Drug Associations | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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| miRNA-Drug Resistance Associations | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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