| pre-miRNA Information | |
|---|---|
| pre-miRNA | hsa-mir-125b-2 |
| Genomic Coordinates | chr21: 16590237 - 16590325 |
| Synonyms | MIRN125B2, MIR125B2 |
| Description | Homo sapiens miR-125b-2 stem-loop |
| Comment | This miRNA sequence is predicted based on homology to a verified miRNA from mouse . |
| RNA Secondary Structure |  |
| Associated Diseases |  |
| Mature miRNA Information | |||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Mature miRNA | hsa-miR-125b-2-3p | ||||||||||||||
| Sequence | 54| UCACAAGUCAGGCUCUUGGGAC |75 | ||||||||||||||
| Evidence | Experimental | ||||||||||||||
| Experiments | Cloned | ||||||||||||||
| Editing Events in miRNAs |
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| 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 | |||||||||||||||||||||
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| Gene Symbol | AMOTL1 | ||||||||||||||||||||
| Synonyms | JEAP | ||||||||||||||||||||
| Description | angiomotin like 1 | ||||||||||||||||||||
| Transcript | NM_130847 | ||||||||||||||||||||
| Expression | |||||||||||||||||||||
| Putative miRNA Targets on AMOTL1 | |||||||||||||||||||||
| 3'UTR of AMOTL1 (miRNA target sites are highlighted) |
>AMOTL1|NM_130847|3'UTR 1 CTGCCATCCCTGTGGAATTTCAGTACAGAACACTGACAAACAAGGAAAGCGGCAGAGAAAGAAGAAAGACCTAGAAGGTT 81 GTAGATGGGAAATCAGGAATGATTTGAACTGATAAAGATTTCAGACTCATAAGAACACATTTTATAAATGTTAAACACAA 161 AAACTACATGACTGAAGATAGAAGAGAATGCGATGGATTTTATTACACATGGTGGAAGAGAGAAGAGGCGTGTAGGTTTG 241 CAAACAAAGTTAAGAAATAGGAAACTGAATTTTTCATTGTACAGAAAATGTATCTCTTGGGGAGGGCCTGTGTACCCCCA 321 TTCTCTGATTATAAACAGATAAACCCAAATGTGGATCATCCTTGGAATACCCCCATTCTCCTTGCCTCTTAGCATGTTTG 401 ATTTAAGAAAAGCCTCCAGGAAATCTTGAGAGCCTGTCTTGGCATAATGCAGTGTCACCTGTGCCAACCATGGGGTGTCC 481 CGTGAGTGTGAGTGTGGCAGTGAGAAGAAGCATCGAGGGCGAGGGGAATATGAAAGTTGGTCTTCACCTAATTACCTGTT 561 TGGTTTGGATTTTCAAGAGATGATTGGGCTTCTTAGCTTTTCTGAATTCTGCAGTATTTTCTAAACAGGATAGATTATGA 641 TCTCGGTCCCCATCCATCCTAACTTCTGAGTTCATCTCTGTCTCTGCTTTACAGTCTTTAATTTTTTGTTGTTCCTTCAT 721 TTTTTTCTTTTTAATAAGACATAGCAGAATTCCTTAGGTATGGGATTTATGAGACCAGTACCTGAACTGTCATCATTCCT 801 ACTGTGTTTGATAGTGACCAGTAGGACAAAGCCACGTGCCGACTTCCTGGCTGCTTCACCTTTGCATAGCTGGGTTGCAG 881 CTGCGAACCTCATTCTGACTGTGAACTAAGCAAGCTTTGAGGAGGCAGGAGATTCCGTGGGTCCCTGTGACATATTGCAT 961 TAAGATCGTGGCACTTGCTTTTTTGTCTTTCACATCGGCTGTCTTGCAAGGAGCTTGACATTTCCAAATTCCATTGCTCT 1041 GTTTGGGGAAGACTTAGGACAGCACTCCAGGAAACAGATGACAATTTACAGACAGTTGTCTCAGTGGTTTCCAGAATCTC 1121 ACCAGCCTCCCGTATAGCTTCTTGTATTGAGGCTCATGAGCGTATTCACACTCTTTCCTCCCCCGCGCACGCCTCTGCTT 1201 GCTCTCGATCAGCATCCAGACCTCCGTGGCACCAGGTTGCCTCTGTTGTGAACTTCTTTTGTAACCTACCAGGCCAGTTG 1281 TATATACAGTGTTGTCAGGTTTTTCCGGGTTTCAGTTTTGAGGCAGTTTATTCAAAGTGAGACAGAAGTGCCACGGAAAA 1361 GAGGCAGGAGTGTGTTAGGTGGTGGGTCCATTAGACCTCTGCTGTGACATTGCATATTCAGCTCTGCAGACACTGGCTTC 1441 CTTTACAAATCTAAGAGATGCTGGATTAGAAAAGAGGAGAAGCTCATCGGGCCATCAGAGAGATGCTCCTACAGGGTCCT 1521 GATGTTTTTGTACCTCCAGGTCAGCTGGATCGCTGTTTTCCCAGTTCCCTTTGCTCATGCTTACTTAGAGGAAGAAAGAA 1601 AGGGGGGTACCTCTTCCAAGTACCTTCTAAATGAAACACTCAAGAGAGTGCTACTCAGGAAACTTTGCTTGGATCCTAAA 1681 ATGGACTGGTCTTGGGTGTGTAACCCCGGTGAAGTTATAGCCTCCCCAAATTGAGGTGACAGAAGGAAGACAAGAGGTGT 1761 AAGCTGGAGAGGGAAGGGAAGAAATCAGTGGCTTTGGCCAGCCTCTGTGCCACCCAGTACGACAGAGGAGTGGGAACTGG 1841 CCCTCTGGGGCTCTGCTTGGCCATAGGCACTGCACATTGTGCCACCTGCTCATCACCTCCTCTAGTCTCACACTGAGCAT 1921 CGGAGTACCTGTTGTGCAGACAGGAAAACTGAGGAGCTCTGAGAGGCTGAGCATGGAGCTCACCCCATGCCATAGGGTGT 2001 GGGAAGAGGGCACAGGAGGCCTCATCCATGGGGGAAAGGGTTGAGGATGGACATGGGTGGGGAGAGGGCATAGACATCCC 2081 TTCCTAATCTCTGTTCCCACCACATTTCATAGGAGATGAGTTAGGAGATGACAGCTAACTCTCTTAAGGACATTTTGACC 2161 CCAGTTTATGTTGGGGATGGACCAGAAAGGAAAATGTCTAGAGATAGGAAGGTAAATCAACTCTGCCAGCCCCTACCATC 2241 AGGTCTGGGCCACCCCAAACTTGGGCTGCCTCCCTTAGACATAGGTTAGAGTGAGAGACCCAGCTGTTTCTCCCGAAGCC 2321 TCGTCTTCATGCCCCAGACACCTGATTGCCCCAATCAGGTGTCAGACTTGCTTGCTCTTCGAGGTCCCCCTGAGCTGCCA 2401 AGTGTTTTCATTGTAAACAGACACATCGCCATGTTTCAGGGCTTCAACGGCATTGTATTTTGGACTTTGACCGTATTTTT 2481 TTTCTCTTAACCTACTGAGACTCTTCCTTAAGAACAGGATCTATAGCTTTAAAATGTCTTCTTCTATGGGAAATTTCCTG 2561 CCAAGCCAGGGCACTAAATTCTTTCATCATTAGAGCTTTCCTGAAGTCCGGCCATATACTGAGTACCTGCTCTGAGTTCT 2641 GGGCAGCTTACAATATCTTAAACAGATTTTCAGAAAAATAATGCAACTATATTTTCTAGTGTCAACTGTATGCAAACAGT 2721 GTGGTAAATACCTTTTAATTAGTCCTCCACCCACCTGGAGTACAGGGGGTGCGTTTATTATTCTGATTTCACTGATGAGG 2801 AAATGGGCTCAGAAAGGTTAAGTCCCTTCCTGAAATCTCACAGCCAGGAGAAGCTAGGATGATTTAAAACAAAGTTTGGA 2881 GAGGCACTGGGCATAGACCCTGGCTGTACAGCCTCTAACATGCGGCACTGCATCTTGGCAGTCTCTATGCCTGTCTGTGA 2961 TGTGTGTGTGCACGTGTAACTACACACACACACACACACACACACACACACACACACAGCTATCACACATCTCAGAGCCT 3041 AAGAAATAGGACTAAGCCCAGAACTCCTAGAATCACCTATAAATGCTAGGCATAGATGGAAATTATTGTGTTCCACCAGA 3121 AGCACAGCTCCAAACTATACCTAAAAAATATTTCTGCACTTCCCAGAGACCTGGACTTCAAACTTTCCCAGTGGAGCCTG 3201 ATTATAGAACTTGAGGGTCCTATCTCAGGATGAAGGGGAGAGGCCCTGGCTTCACGGGAAGGTATTCCAGCATTGTTCTG 3281 CTTCACCCTTGACTGCGTTGTCTGGCAGTTTCTGTGTGCTGCCAGGATATTATATGGAACTGGAGAAGTTGGAGTCAGGT 3361 CTCTGAAGCTAGAGTTTCACTAATTAGATGCCTCTGTACATGAGAACTATTACTGTCTGCAGGTCCATATAGCTAAGCTG 3441 CCAGGAAAAACACATTATCTTCCAAAACTTTCAGAGCATGTGCAGAACCCTTTCTTAGCGTTTTCTTCTCAGCATTTTCT 3521 CTGCCTCCCAGAGGCTGGCAGCCAGTGACACTGCAGAGTTCAGCATGTTCTAACCATGCACGCAGGGCAGGGGCTGCCTT 3601 GGCCCTCCTCAGGCTTTCGTTGGGAGAGCAGGCAGTGGTGGAGCCCTTCTGGGTGCAGTCCTCTGGGGTTGCTCTTTGGA 3681 ACTCATGTATGAGTTTGACTCCACAAGGCTTGGCATGGATACCAAAACAGTTGCAACAAATTAGTTCTGAACCTGGAACA 3761 GAGAATTCAGTGCTTCTGTTACTCAGGAAGGAGGTGTTCAGAATGCCCCGTGCAGAGCAGCCAGTCATTACTCTTGTTTG 3841 TTCTCACCTGGGTGCGCACCCTCATGATGCAGTGGCTGTAGCACCTTCATGCCAGGTGCTGAGAGAATGGGAAATTCTTC 3921 CTCCCCATTGACCTGAGTCCCAGAGACTTAGGGACACAGACTTCAGGTGAGGCTGCGGACCTCAGAAGCAGTGGATAATA 4001 GATTGGGGCATTAAAAGCTTTTGAGGCAGGGGGCTCATGTTTTGACTGCAGGGAGTTATGCTGAGCAAAGAGATGTGTTT 4081 TTCAAAACCAGGGTTCAAAACCAGTGTCCACGCTGGAGTAAGTGGAGCATGCTTCTCTGTGTTCTCTGAATGATCTTGCA 4161 CTCCTCTTAAGCAAAGGAGTACCATGACCATAGTCAGTGGGATCCCACAAATGTTCTTAAATGGGTAAGGCTTTAAGTAG 4241 CCAGAGAGTATCCAGCCTACCATTGGCTTCTCCACATCCTAAAACCTGAGACAGCCTTGGTATATGCTTTATAAATGTTT 4321 CTTTTCTTGTTGTTTAAGTAATTAAAGTGTTTAAAATGTCTTCATTAGATGTGACGATTGTTTAATGAGTTTGCCTCTGA 4401 CGTGTGGCTCCATGGGAGATAGGCAAAGTAATTAAGAAGTTACCAGAAATTGGTCGGCTGGGGAAATGCAAAAGTTAGCA 4481 TTTCAGTAGTGAATTTCTCCTGGAACAAATGAGCAATTTTTCCTCTTTCTCTTAAGTAGTATACCCTTTTCTCACTTAGT 4561 AATTTAATGGTATATAAAGACATGTGTATAAGTGAGTGCATACATATGAGGTATGACTATAGGGTTGTTTGTGGGAATTT 4641 CTTTTCCTAACATACAGAAGATCAAAGTGTTCATCTCACCCCGCCCTCCTTAAAAGGTGTCTTTTGGGAGACTATGTGCT 4721 CATTGACTATAGTGCTGCCAAGTAAAAATATCTTGGGAACTCTTCTACTAGAATGGCCTTCAGGGCTTGGCATGTTCCTT 4801 TGGTTTACCCTTAGAGATGAGAAATCCTCCTCCTTTGAGGATGGATTTAAGTTCTGGAAATAATCTCAAGTGCTTGATAG 4881 CACAGTTGGATGAAAAAAGATGGCAATTAAGGTAAGTTACACCATTTTTGTTTCTAAAAAAATCCCTAAGAAATTTCTTG 4961 GAATGAGTCTTTGGCCTCAGAGCCTCTCAAAGTGTCCACTTCAAGGGGGGATCATCCTCATTAGCACACAGATTTTTAAA 5041 AATCAATTCTCTTGCCATGCCTCCTATGTGTTCACATCTCTGCATACACTACAGATATAAGTGCATAATCATTCATATAA 5121 ACATCTGGTAGGTATTCTGTAAAACTGTGTTTACTTTAGTGCATGTTATTGTCATGTTATGATGTGACTGGGGTGTTTCT 5201 TTGTCATGAAACTTTGCTTCTTCACAGAATTAGAATACTGCTCTCTCTATATTGAACTACATATACAGCGTTTTCTTGTA 5281 TCAGCCCCCAAAGTCTGGATGCCCGGTGTTGTGTTTACATGTGATTGTGCCTAGGAGTCTGTTCACATAGAGACACCTGT 5361 AAGTATTTATTACAAAACGGAATGTAAGCAAATATATCCACATTGGTTTTATTTGAATCAAGGTGTTTTTTTGTTTTTTG 5441 TTTTTTTTCCTTTTGAGGAGGAACAGGGAGCCTCCTCCTCCATGAGCACTTACAGAATTGTGTAAAATTCTGTGAAACAG 5521 TGGTAAGCATGGGCACCCGATTTCAGCTGTCCTGCTGCCGCTGCCCTCCAACCTGCTCTGTGTGTGTGTGTCGCTGTGCT 5601 TGGTGGCAGTGTGCCGTGCTCGTGCCGGCTCTTCCCAGCAGACTGGTATCTGGCTGTAACGTTTGACGTCTTCATATTGC 5681 CAGTCTGTATTGAGGGGTGATGTACATGGCCATACAGCCAAATGGGTCTGTGTACCAGTGTGGGGATTCCAAGAACACTG 5761 CCTGTCCCCCACAGCAAATATTGATGCTGTTGGTCAGCCAAAGATTTTCCTCTCCTTTGCTGCTTAAACTTGTGCCTTAA 5841 TATTGTACATAATAAATGGATAAAATGGCAAAATGACTCTTTTCTCTCGCTTGCTCCTTTCTTCCTTAAAGAACTTATAA 5921 ACTGATGCTCAATAAATGTTTCATTTCATTGTACCCCA 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 GSM545212. RNA binding protein: AGO1. Condition:Control
PAR-CLIP data was present in GSM545213. RNA binding protein: AGO2. Condition:Control
PAR-CLIP data was present in GSM545214. RNA binding protein: AGO3. Condition:Control
PAR-CLIP data was present in GSM545215. RNA binding protein: AGO4. Condition:Control
PAR-CLIP data was present in GSM545216. RNA binding protein: AGO2. Condition:miR-124 transfection
... - 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 | |||||||
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| miRNA:Target | ---- | ||||||
| Validation Method |
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| Conditions | HEK293 | ||||||
| Disease | 154810.0 | ||||||
| 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 GSM714642. RNA binding protein: AGO2. Condition:completeT1
"PAR-CLIP data was present in GSM714645. RNA binding protein: AGO2. Condition:completeT1
... - Kishore S; Jaskiewicz L; Burger L; Hausser et al., 2011, Nature methods. |
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| miRNA-target interactions (Provided by authors) |
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| 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 | 154810.0 |
| 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 | 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. |
| 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 5 for Functional miRNA-Target Interaction | |
|---|---|
| miRNA:Target | ---- |
| Validation Method |
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| Conditions | MCF7 |
| 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 SRR1045082. RNA binding protein: AGO2. Condition:Untreated
... - Farazi TA; Ten Hoeve JJ; Brown M; et al., 2014, Genome biology. |
| Article |
- Farazi TA; Ten Hoeve JJ; Brown M; et al. - Genome biology, 2014
BACKGROUND: Various microRNAs (miRNAs) are up- or downregulated in tumors. However, the repression of cognate miRNA targets responsible for the phenotypic effects of this dysregulation in patients remains largely unexplored. To define miRNA targets and associated pathways, together with their relationship to outcome in breast cancer, we integrated patient-paired miRNA-mRNA expression data with a set of validated miRNA targets and pathway inference. RESULTS: To generate a biochemically-validated set of miRNA-binding sites, we performed argonaute-2 photoactivatable-ribonucleoside-enhanced crosslinking and immunoprecipitation (AGO2-PAR-CLIP) in MCF7 cells. We then defined putative miRNA-target interactions using a computational model, which ranked and selected additional TargetScan-predicted interactions based on features of our AGO2-PAR-CLIP binding-site data. We subselected modeled interactions according to the abundance of their constituent miRNA and mRNA transcripts in tumors, and we took advantage of the variability of miRNA expression within molecular subtypes to detect miRNA repression. Interestingly, our data suggest that miRNA families control subtype-specific pathways; for example, miR-17, miR-19a, miR-25, and miR-200b show high miRNA regulatory activity in the triple-negative, basal-like subtype, whereas miR-22 and miR-24 do so in the HER2 subtype. An independent dataset validated our findings for miR-17 and miR-25, and showed a correlation between the expression levels of miR-182 targets and overall patient survival. Pathway analysis associated miR-17, miR-19a, and miR-200b with leukocyte transendothelial migration. CONCLUSIONS: We combined PAR-CLIP data with patient expression data to predict regulatory miRNAs, revealing potential therapeutic targets and prognostic markers in breast cancer.
LinkOut: [PMID: 24398324]
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| CLIP-seq Support 1 for dataset GSM714642 | |
|---|---|
| Method / RBP | HITS-CLIP / AGO2 |
| Cell line / Condition | HEK293 / completeT1, repA |
| Location of target site | ENST00000317837.9 | 3UTR | AUUUUCCUCUCCUUUGCUGCUUAAACUUG |
| 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 GSM545212 | |
|---|---|
| Method / RBP | PAR-CLIP / AGO1 |
| Cell line / Condition | HEK293 / Control |
| Location of target site | ENST00000317837.9 | 3UTR | AUUUUCCUCUCCUUUGCUGCUUAAACUU |
| 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 GSM545213 | |
|---|---|
| Method / RBP | PAR-CLIP / AGO2 |
| Cell line / Condition | HEK293 / Control |
| Location of target site | ENST00000317837.9 | 3UTR | CCUCUCCUUUGCUGCUUAAACUU |
| Tools used in this analysis | TargetScan, miRTarCLIP, and Piranha |
| Article / Accession Series | PMID: 20371350 / GSE21578 |
| CLIP-seq Viewer | Link |
| CLIP-seq Support 4 for dataset GSM545214 | |
|---|---|
| Method / RBP | PAR-CLIP / AGO3 |
| Cell line / Condition | HEK293 / Control |
| Location of target site | ENST00000317837.9 | 3UTR | AUUUUCCUCUCCUUUGCUGCUUAAACU |
| Tools used in this analysis | TargetScan, miRTarCLIP, and Piranha |
| Article / Accession Series | PMID: 20371350 / GSE21578 |
| CLIP-seq Viewer | Link |
| CLIP-seq Support 5 for dataset GSM545215 | |
|---|---|
| Method / RBP | PAR-CLIP / AGO4 |
| Cell line / Condition | HEK293 / Control |
| Location of target site | ENST00000317837.9 | 3UTR | AUUUUCCUCUCCUUUGCUGCUUAAAC |
| Tools used in this analysis | TargetScan, miRTarCLIP, and Piranha |
| Article / Accession Series | PMID: 20371350 / GSE21578 |
| CLIP-seq Viewer | Link |
| CLIP-seq Support 6 for dataset GSM545216 | |
|---|---|
| Method / RBP | PAR-CLIP / AGO2 |
| Cell line / Condition | HEK293 / miR-124 transfection |
| Location of target site | ENST00000317837.9 | 3UTR | AUUUUCCUCUCCUUUGCUGCUUAAACUUGUGCCUUAAUAUUGUACAUAAUA |
| Tools used in this analysis | TargetScan, miRTarCLIP, and Piranha |
| Article / Accession Series | PMID: 20371350 / GSE21578 |
| CLIP-seq Viewer | Link |
| CLIP-seq Support 7 for dataset GSM714645 | |
|---|---|
| Method / RBP | PAR-CLIP / AGO2 |
| Cell line / Condition | HEK293 / completeT1, repB |
| Location of target site | ENST00000317837.9 | 3UTR | AUUUUCCUCUCCUUUGCUGCUUAAACUUG |
| Tools used in this analysis | TargetScan, miRTarCLIP, and Piranha |
| Article / Accession Series | PMID: 21572407 / GSE28865 |
| CLIP-seq Viewer | Link |
| CLIP-seq Support 8 for dataset SRR359787 | |
|---|---|
| Method / RBP | PAR-CLIP / AGO2 |
| Cell line / Condition | hESCs (WA-09) / 4-thiouridine, RNase T1 |
| Location of target site | ENST00000317837.9 | 3UTR | AUUUUCCUCUCCUUUGCUGCUUAAACUUGUGCCUUAAUAUUGUACAUAAUAAAU |
| Tools used in this analysis | TargetScan, miRTarCLIP, and Piranha |
| Article / Accession Series | PMID: 22012620 / SRX103431 |
| CLIP-seq Viewer | Link |
| CLIP-seq Support 9 for dataset SRR1045082 | |
|---|---|
| Method / RBP | PAR-CLIP / AGO2 |
| Cell line / Condition | MCF7 / Untreated |
| Location of target site | ENST00000317837.9 | 3UTR | AUUUUCCUCUCCUUUGCUGCUUAAACUU |
| Tools used in this analysis | TargetScan, miRTarCLIP, and Piranha |
| Article / Accession Series | PMID: 24398324 / SRX388831 |
| CLIP-seq Viewer | Link |
| CLIP-seq Support 10 for dataset GSM1462574 | |
|---|---|
| Method / RBP | PAR-CLIP / AGO2 |
| Cell line / Condition | TZM-bl / TZM-bl ami BaL |
| Location of target site | ENST00000317837.9 | 3UTR | AUUUUCCUCUCCUUUGCUGCUUAAACUUG |
| Tools used in this analysis | TargetScan, miRTarCLIP, and Piranha |
| Article / Accession Series | PMID: 23592263 / GSE59944 |
| CLIP-seq Viewer | Link |
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| MiRNA-Target Expression Profile (TCGA) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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91 hsa-miR-125b-2-3p 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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 |
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| MIRT038624 | HN1L | Jupiter microtubule associated homolog 2 |  |
1 | 1 | |||||||
| MIRT038625 | KDELC2 | KDEL motif containing 2 | |
1 | 1 | |||||||
| MIRT038626 | ABHD15 | abhydrolase domain containing 15 | |
1 | 1 | |||||||
| MIRT038627 | PPP1R12C | protein phosphatase 1 regulatory subunit 12C | |
1 | 1 | |||||||
| MIRT038628 | MSANTD4 | Myb/SANT DNA binding domain containing 4 with coiled-coils | |
1 | 1 | |||||||
| MIRT038629 | ASH2L | ASH2 like histone lysine methyltransferase complex subunit | |
1 | 1 | |||||||
| MIRT038630 | USP22 | ubiquitin specific peptidase 22 | |
1 | 1 | |||||||
| MIRT038631 | CSTB | cystatin B | |
1 | 1 | |||||||
| MIRT038632 | SYT2 | synaptotagmin 2 | |
1 | 1 | |||||||
| MIRT038633 | NDUFS7 | NADH:ubiquinone oxidoreductase core subunit S7 | |
1 | 1 | |||||||
| MIRT038634 | MTA2 | metastasis associated 1 family member 2 | |
1 | 1 | |||||||
| MIRT053086 | IGF1R | insulin like growth factor 1 receptor | |
|
|
3 | 1 | |||||
| MIRT055788 | PLEKHA1 | pleckstrin homology domain containing A1 | |
|
2 | 12 | ||||||
| MIRT061248 | AMOTL1 | angiomotin like 1 | |
|
2 | 10 | ||||||
| MIRT061649 | BTG2 | BTG anti-proliferation factor 2 | |
|
2 | 6 | ||||||
| MIRT079046 | TNRC6C | trinucleotide repeat containing 6C | |
|
2 | 4 | ||||||
| MIRT084583 | BCL2L11 | BCL2 like 11 | |
|
2 | 8 | ||||||
| MIRT093523 | GALNT7 | polypeptide N-acetylgalactosaminyltransferase 7 | |
|
2 | 2 | ||||||
| MIRT097383 | LHFPL2 | LHFPL tetraspan subfamily member 2 | |
|
2 | 4 | ||||||
| MIRT098030 | SOBP | sine oculis binding protein homolog | |
|
2 | 2 | ||||||
| MIRT186262 | TCEB3 | elongin A | |
|
2 | 2 | ||||||
| MIRT187284 | DAZAP2 | DAZ associated protein 2 | |
|
2 | 10 | ||||||
| MIRT361113 | LRRC1 | leucine rich repeat containing 1 | |
|
2 | 2 | ||||||
| MIRT443585 | FAM84B | family with sequence similarity 84 member B | |
|
2 | 2 | ||||||
| MIRT452249 | TRAM1 | translocation associated membrane protein 1 | |
|
2 | 2 | ||||||
| MIRT476289 | GMFB | glia maturation factor beta | |
|
2 | 8 | ||||||
| MIRT483871 | MRPL12 | mitochondrial ribosomal protein L12 | |
|
2 | 2 | ||||||
| MIRT484250 | ANK1 | ankyrin 1 | |
|
2 | 2 | ||||||
| MIRT499251 | VAV3 | vav guanine nucleotide exchange factor 3 | |
|
2 | 4 | ||||||
| MIRT502270 | HNRNPA1 | heterogeneous nuclear ribonucleoprotein A1 | |
|
2 | 4 | ||||||
| MIRT504652 | RPL9 | ribosomal protein L9 | |
|
2 | 6 | ||||||
| MIRT505210 | UBN2 | ubinuclein 2 | |
|
2 | 6 | ||||||
| MIRT512690 | POP1 | POP1 homolog, ribonuclease P/MRP subunit | |
|
2 | 2 | ||||||
| MIRT517341 | ZNF529 | zinc finger protein 529 | |
|
2 | 4 | ||||||
| MIRT518946 | LSG1 | large 60S subunit nuclear export GTPase 1 | |
|
2 | 2 | ||||||
| MIRT520866 | SUGT1 | SGT1 homolog, MIS12 kinetochore complex assembly cochaperone | |
|
2 | 2 | ||||||
| MIRT521236 | SAR1A | secretion associated Ras related GTPase 1A | |
|
2 | 2 | ||||||
| MIRT528324 | GIGYF2 | GRB10 interacting GYF protein 2 | |
|
2 | 2 | ||||||
| MIRT533297 | USP46 | ubiquitin specific peptidase 46 | |
|
2 | 2 | ||||||
| MIRT541024 | WEE1 | WEE1 G2 checkpoint kinase | |
|
2 | 4 | ||||||
| MIRT544034 | ERRFI1 | ERBB receptor feedback inhibitor 1 | |
|
2 | 2 | ||||||
| MIRT547037 | POGZ | pogo transposable element derived with ZNF domain | |
|
2 | 2 | ||||||
| MIRT556102 | MOAP1 | modulator of apoptosis 1 | |
|
2 | 2 | ||||||
| MIRT558320 | DR1 | down-regulator of transcription 1 | |
|
2 | 2 | ||||||
| MIRT558520 | CSRNP3 | cysteine and serine rich nuclear protein 3 | |
|
2 | 2 | ||||||
| MIRT566230 | PTMA | prothymosin, alpha | |
|
2 | 4 | ||||||
| MIRT568437 | ARPP19 | cAMP regulated phosphoprotein 19 | |
|
2 | 2 | ||||||
| MIRT570584 | OTUD7B | OTU deubiquitinase 7B | |
|
2 | 2 | ||||||
| MIRT571384 | JKAMP | JNK1/MAPK8-associated membrane protein | |
|
2 | 2 | ||||||
| MIRT572798 | SIGLEC14 | sialic acid binding Ig like lectin 14 | |
|
2 | 2 | ||||||
| MIRT573864 | C9orf78 | chromosome 9 open reading frame 78 | |
|
2 | 2 | ||||||
| MIRT609930 | SLC38A1 | solute carrier family 38 member 1 | |
|
2 | 4 | ||||||
| MIRT610437 | CSMD2 | CUB and Sushi multiple domains 2 | |
|
2 | 2 | ||||||
| MIRT614407 | MURC | caveolae associated protein 4 | |
|
2 | 2 | ||||||
| MIRT618625 | GREB1 | growth regulation by estrogen in breast cancer 1 | |
|
2 | 2 | ||||||
| MIRT620605 | SAP30 | Sin3A associated protein 30 | |
|
2 | 2 | ||||||
| MIRT635313 | FAM179A | TOG array regulator of axonemal microtubules 2 | |
|
2 | 2 | ||||||
| MIRT635918 | GLTSCR2 | NOP53 ribosome biogenesis factor | |
|
2 | 2 | ||||||
| MIRT638507 | MAP3K9 | mitogen-activated protein kinase kinase kinase 9 | |
|
2 | 2 | ||||||
| MIRT640597 | TM9SF4 | transmembrane 9 superfamily member 4 | |
|
2 | 2 | ||||||
| MIRT644066 | IQCE | IQ motif containing E | |
|
2 | 2 | ||||||
| MIRT648287 | TRAPPC2L | trafficking protein particle complex 2 like | |
|
2 | 2 | ||||||
| MIRT653089 | SSR3 | signal sequence receptor subunit 3 | |
|
2 | 2 | ||||||
| MIRT654651 | PTAFR | platelet activating factor receptor | |
|
2 | 2 | ||||||
| MIRT658084 | FOXR2 | forkhead box R2 | |
|
2 | 2 | ||||||
| MIRT665306 | ZBTB37 | zinc finger and BTB domain containing 37 | |
|
2 | 2 | ||||||
| MIRT665974 | SYTL4 | synaptotagmin like 4 | |
|
2 | 2 | ||||||
| MIRT674905 | RASSF9 | Ras association domain family member 9 | |
|
2 | 2 | ||||||
| MIRT680085 | THAP1 | THAP domain containing 1 | |
|
2 | 2 | ||||||
| MIRT681487 | DIP2A | disco interacting protein 2 homolog A | |
|
2 | 2 | ||||||
| MIRT691243 | DFNB59 | pejvakin | |
|
2 | 2 | ||||||
| MIRT692361 | AGTRAP | angiotensin II receptor associated protein | |
|
2 | 2 | ||||||
| MIRT693034 | MB21D1 | Mab-21 domain containing 1 | |
|
2 | 2 | ||||||
| MIRT694478 | LRTOMT | leucine rich transmembrane and O-methyltransferase domain containing | |
|
2 | 2 | ||||||
| MIRT696069 | ZNF264 | zinc finger protein 264 | |
|
2 | 2 | ||||||
| MIRT696579 | TTC21B | tetratricopeptide repeat domain 21B | |
|
2 | 2 | ||||||
| MIRT696759 | MTFMT | mitochondrial methionyl-tRNA formyltransferase | |
|
2 | 2 | ||||||
| MIRT697306 | ZNF652 | zinc finger protein 652 | |
|
2 | 2 | ||||||
| MIRT698736 | STX12 | syntaxin 12 | |
|
2 | 2 | ||||||
| MIRT701055 | PARP2 | poly(ADP-ribose) polymerase 2 | |
|
2 | 2 | ||||||
| MIRT701197 | OTUD3 | OTU deubiquitinase 3 | |
|
2 | 2 | ||||||
| MIRT701334 | NSD1 | nuclear receptor binding SET domain protein 1 | |
|
2 | 2 | ||||||
| MIRT703617 | FBXO45 | F-box protein 45 | |
|
2 | 2 | ||||||
| MIRT708893 | ZNF780A | zinc finger protein 780A | |
|
2 | 2 | ||||||
| MIRT711621 | DGKH | diacylglycerol kinase eta | |
|
2 | 2 | ||||||
| MIRT713744 | TMEM81 | transmembrane protein 81 | |
|
2 | 2 | ||||||
| MIRT715060 | TMTC1 | transmembrane and tetratricopeptide repeat containing 1 | |
|
2 | 2 | ||||||
| MIRT719711 | CD101 | CD101 molecule | |
|
2 | 2 | ||||||
| MIRT720293 | DLGAP3 | DLG associated protein 3 | |
|
2 | 2 | ||||||
| MIRT722605 | CCDC152 | coiled-coil domain containing 152 | |
|
2 | 2 | ||||||
| MIRT724565 | ACSBG1 | acyl-CoA synthetase bubblegum family member 1 | |
|
2 | 2 | ||||||
| miRNA-Drug Associations | ||||||||||||||||||
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| miRNA-Drug Resistance Associations | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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