pre-miRNA Information
pre-miRNA hsa-mir-548t   
Genomic Coordinates chr4: 173268160 - 173268233
Description Homo sapiens miR-548t stem-loop
Comment None
RNA Secondary Structure

Mature miRNA Information
Mature miRNA hsa-miR-548t-3p
Sequence 46| AAAAACCACAAUUACUUUUGCACCA |70
Evidence Not_experimental
Experiments
Editing Events in miRNAs
Modification Type Position on miR Chromosome DNA Strand Genomic Position (hg38) List of PMIDs Variant details
A-to-I 2 4 + 173268206 29233923 MiREDiBase
A-to-I 3 4 + 173268207 29233923 MiREDiBase
A-to-I 4 4 + 173268208 29233923 MiREDiBase
A-to-I 10 4 + 173268214 29233923 MiREDiBase
SNPs in miRNA
Mutant ID Mutant Position Mutant Source
rs73872515 5 dbSNP
rs1426966747 6 dbSNP
rs1158401109 21 dbSNP
rs943938928 24 dbSNP
Putative Targets

Gene Information
Gene Symbol CCDC115   
Synonyms CDG2O, ccp1
Description coiled-coil domain containing 115
Transcript NM_032357   
Expression
Putative miRNA Targets on CCDC115
3'UTR of CCDC115
(miRNA target sites are highlighted)
>CCDC115|NM_032357|3'UTR
   1 CATGCGCGCAAAGAGGCAGGGCAGCGAGCACAGCTGTTCTCCGACATGGCTACGTGATCTCAGGCCTTCTTCCTTCACAA
  81 TTAGCTCTTGCCCCTACCCCACGCCAGCTAATGCCCCTTCTGTGTCCCTGCTCTGCATGTTTCCATTTTCCTTAGGTGTG
 161 AAGTTTGAAGAGGCAAACAGTAATTTTGAAAGCCACTACTTTGAAACCATTCTAAGGCCTGAGTTCCCATAGGACACACT
 241 CACATAGGCAGGTACACGTTAGTCAACAATTGGAACTGCCTCTTGGATCACTCAGCTGTGCTTTCATGGCTGGATGATGG
 321 AACACTGTGCGAAGAGAGATGGGGGCCAGGAAGTAGCGCTTCATGCTTAGTACATCCTCCAAATTGTCTTTGCTGGAGGA
 401 GAAAACCGTACTCAGCCAAAAGATCAGGACAATATGACTTGAGTCCACAAGGACACAAACACCTGAGTAGCTGGGCAGCC
 481 CTTGGCAGGGTCTAAGCCAGGAAGTAAAAATGATCTGGCCTAGATATTTAAGGGAACTCTAGGAAGAGGCCTAGGTTTTT
 561 AAAATCCTGTCTCTTTGTCTTACCATAAGAGGCTGAGCCTCTCTTCATTTTTTTGAAGGGCCACTTGTGTTTTCTGTTCT
 641 GGGAACTTCATTCATTTTTCTACTGGGTTGTTGATCTTTGCAGTAATTTCTAGGAGCTGTTTATGTTTGGAGGTAATTGG
 721 TCCTTTGTCCATATATATGAGATGTAAGTCTTATTTTCCAGTTTATCTTTTTGCTTATTTTTTTTGACTTTTTATTGTAA
 801 AATAAAACATCAAACTGCACAGAACAGTTGAATAGCTTAATGAATAACTACAGTAAAAGCTATGGTAACCACTACCCAAC
 881 TTTTGTGTTTTTTGATCATTATTTGTACGTACAGTTGAATGTATCCAGCTGTCACATGATTCTGAATTTGGGTTTGTAAC
 961 TGATAAGGCAATCAGGGAATTCTCCAGCATTTTCAAGAACCTCTGTGGTTTCAGTTGAAATGTCCAGTGAGTCATGTCCA
1041 GCTTTTCCACCATCCTCCCACGTGCTGTATGTCGGTTAATGCTGCCCTTTTGTTTTGCTAACTCCCAGTGTAAACCTAAT
1121 GTAATTTGGGGGTTTTCATTCTGTTTCGTGGACATTACTGTCAATACACCAGTACCACATTGTTTTAAAAAAAAAAAAA
Target sites Provided by authors   Predicted by miRanda    DRVs    SNPs    DRVs & SNPs
miRNA-target interactions
(Predicted by miRanda)
ID Duplex structure Position Score MFE
1
miRNA  3' acCACGUU----UU-CAUUAA--CACCAAAAa 5'
            |||:||    || ||||||  | |||||| 
Target 5' caGTGTAAACCTAATGTAATTTGGGGGTTTTc 3'
1106 - 1137 147.00 -12.10
2
miRNA  3' accACGUUUUCAUUAACACCAAAaa 5'
             | |||:|     ||||||||  
Target 5' attTTCAAGAACCTCTGTGGTTTca 3'
989 - 1013 138.00 -10.20
3
miRNA  3' acCACGUUUUCAUUAACACCA--AAAa 5'
            || :::|:|||||  ||||  ||| 
Target 5' atGTTTGGAGGTAAT--TGGTCCTTTg 3'
703 - 727 131.00 -8.53
DRVs in gene 3'UTRs
Mutant ID Mutant Position Mutant Source
COSN30535624 6 COSMIC
COSN26969394 7 COSMIC
COSN31501671 41 COSMIC
COSN31552815 102 COSMIC
COSN20632433 226 COSMIC
COSN17003521 270 COSMIC
COSN4909712 309 COSMIC
COSN15028229 722 COSMIC
COSN32064758 733 COSMIC
SNPs in gene 3'UTRs
Mutant ID Mutant Position Mutant Source
rs1175948466 1 dbSNP
rs754874231 2 dbSNP
rs1047757843 3 dbSNP
rs1281509581 5 dbSNP
rs534874133 5 dbSNP
rs370808973 6 dbSNP
rs377109686 7 dbSNP
rs749902681 8 dbSNP
rs1350095806 11 dbSNP
rs764659849 12 dbSNP
rs764476122 13 dbSNP
rs1013318072 16 dbSNP
rs1298528241 17 dbSNP
rs928740667 18 dbSNP
rs374101911 19 dbSNP
rs761524820 22 dbSNP
rs774004174 25 dbSNP
rs370285987 26 dbSNP
rs566881555 28 dbSNP
rs377453920 29 dbSNP
rs771381451 30 dbSNP
rs551865712 42 dbSNP
rs773272941 43 dbSNP
rs769829512 47 dbSNP
rs1187021393 52 dbSNP
rs539963275 53 dbSNP
rs914764182 54 dbSNP
rs569054826 60 dbSNP
rs1168432780 64 dbSNP
rs1250559290 66 dbSNP
rs1323050362 67 dbSNP
rs1395618955 69 dbSNP
rs999195214 72 dbSNP
rs990273476 73 dbSNP
rs1162887723 78 dbSNP
rs1338951578 80 dbSNP
rs369581343 92 dbSNP
rs370055012 93 dbSNP
rs1385872491 97 dbSNP
rs750189219 102 dbSNP
rs144254230 103 dbSNP
rs1447648767 107 dbSNP
rs767360850 111 dbSNP
rs546585243 112 dbSNP
rs761751668 114 dbSNP
rs934101090 127 dbSNP
rs1440378872 131 dbSNP
rs189452334 138 dbSNP
rs996627003 139 dbSNP
rs918667136 154 dbSNP
rs1258035111 155 dbSNP
rs962436688 157 dbSNP
rs973152422 167 dbSNP
rs941331811 170 dbSNP
rs1191161236 178 dbSNP
rs910142213 179 dbSNP
rs552036137 180 dbSNP
rs1169762054 181 dbSNP
rs1186925857 194 dbSNP
rs1434397060 199 dbSNP
rs970272233 201 dbSNP
rs149557747 207 dbSNP
rs1277908502 209 dbSNP
rs887038894 221 dbSNP
rs376832795 224 dbSNP
rs1230221364 229 dbSNP
rs1271497927 231 dbSNP
rs960480197 234 dbSNP
rs1209459497 235 dbSNP
rs1280608236 238 dbSNP
rs1486427119 240 dbSNP
rs759590980 244 dbSNP
rs1359541072 248 dbSNP
rs1260752266 252 dbSNP
rs138233990 254 dbSNP
rs1195216909 255 dbSNP
rs999602243 257 dbSNP
rs112838887 258 dbSNP
rs1022364200 265 dbSNP
rs1006833413 266 dbSNP
rs889702634 269 dbSNP
rs1050946053 286 dbSNP
rs1367297690 294 dbSNP
rs146339274 297 dbSNP
rs776861662 307 dbSNP
rs1438810586 308 dbSNP
rs1370826463 313 dbSNP
rs1232970634 317 dbSNP
rs1366417097 319 dbSNP
rs771145371 320 dbSNP
rs1349667457 322 dbSNP
rs142004417 324 dbSNP
rs1391999536 329 dbSNP
rs73960308 330 dbSNP
rs941370766 331 dbSNP
rs909915016 336 dbSNP
rs1422711485 342 dbSNP
rs1044774475 357 dbSNP
rs1490427960 358 dbSNP
rs1438139535 359 dbSNP
rs1158641926 384 dbSNP
rs1054557531 386 dbSNP
rs1202474442 387 dbSNP
rs555986727 391 dbSNP
rs879113396 395 dbSNP
rs373629899 407 dbSNP
rs867038107 408 dbSNP
rs1228711253 413 dbSNP
rs1442258752 414 dbSNP
rs1326047918 426 dbSNP
rs1372517754 426 dbSNP
rs924906241 427 dbSNP
rs1311990183 432 dbSNP
rs987429970 447 dbSNP
rs1305857342 448 dbSNP
rs1299719740 471 dbSNP
rs1317095194 480 dbSNP
rs1240942999 481 dbSNP
rs14187 486 dbSNP
rs770359596 488 dbSNP
rs1225734199 490 dbSNP
rs917492397 497 dbSNP
rs1346425204 499 dbSNP
rs934246452 509 dbSNP
rs1456512250 510 dbSNP
rs1176626619 513 dbSNP
rs920954563 515 dbSNP
rs956171534 523 dbSNP
rs1185935623 533 dbSNP
rs560547519 536 dbSNP
rs1417557184 539 dbSNP
rs975074086 542 dbSNP
rs1462478609 543 dbSNP
rs138967799 547 dbSNP
rs1372439104 551 dbSNP
rs977841385 555 dbSNP
rs185663941 557 dbSNP
rs1021998827 566 dbSNP
rs1006551851 568 dbSNP
rs370250324 569 dbSNP
rs1480628562 572 dbSNP
rs1354570164 573 dbSNP
rs982640957 576 dbSNP
rs1029546689 577 dbSNP
rs1305654625 583 dbSNP
rs998036833 585 dbSNP
rs1251946324 590 dbSNP
rs951268578 595 dbSNP
rs896957476 599 dbSNP
rs1198945827 601 dbSNP
rs1037260728 605 dbSNP
rs1475739917 622 dbSNP
rs386650480 623 dbSNP
rs1190462953 624 dbSNP
rs1422134448 634 dbSNP
rs1199379539 636 dbSNP
rs1428417640 638 dbSNP
rs558217140 640 dbSNP
rs1254733498 657 dbSNP
rs1206019360 662 dbSNP
rs1310710290 664 dbSNP
rs1374401806 666 dbSNP
rs778144866 676 dbSNP
rs1324650426 677 dbSNP
rs1359844958 686 dbSNP
rs1034959217 694 dbSNP
rs1003901446 705 dbSNP
rs1020444011 708 dbSNP
rs1232087095 712 dbSNP
rs540198075 714 dbSNP
rs1279914592 722 dbSNP
rs888527060 729 dbSNP
rs905104440 731 dbSNP
rs1022954716 735 dbSNP
rs1012833063 737 dbSNP
rs539929425 750 dbSNP
rs948691054 757 dbSNP
rs574611417 764 dbSNP
rs917504121 767 dbSNP
rs569420998 768 dbSNP
rs1395521586 773 dbSNP
rs1400042841 777 dbSNP
rs1057293027 778 dbSNP
rs893223203 780 dbSNP
rs1394127269 786 dbSNP
rs1434928363 786 dbSNP
rs924825906 786 dbSNP
rs979335078 787 dbSNP
rs1304467076 788 dbSNP
rs368632277 794 dbSNP
rs967855521 794 dbSNP
rs1289375909 807 dbSNP
rs914939403 810 dbSNP
rs1054445467 812 dbSNP
rs1438826392 818 dbSNP
rs1052900 819 dbSNP
rs192666646 821 dbSNP
rs903377285 823 dbSNP
rs145084521 828 dbSNP
rs1282667151 839 dbSNP
rs1364018599 862 dbSNP
rs3178182 871 dbSNP
rs568174762 876 dbSNP
rs1244366480 877 dbSNP
rs1191262474 885 dbSNP
rs546842716 894 dbSNP
rs1454497362 899 dbSNP
rs1219007595 905 dbSNP
rs1421515912 906 dbSNP
rs998130174 908 dbSNP
rs748789793 909 dbSNP
rs1051253760 912 dbSNP
rs1438582978 913 dbSNP
rs141123589 914 dbSNP
rs921508990 920 dbSNP
rs1005790004 923 dbSNP
rs888547871 937 dbSNP
rs772314097 938 dbSNP
rs1372823888 952 dbSNP
rs1286757792 956 dbSNP
rs563725727 968 dbSNP
rs1207200906 976 dbSNP
rs1353191262 982 dbSNP
rs1012892065 996 dbSNP
rs1468552254 997 dbSNP
rs748758748 1011 dbSNP
rs1230839652 1019 dbSNP
rs1457895176 1027 dbSNP
rs1057049400 1035 dbSNP
rs1261508117 1039 dbSNP
rs1459863275 1040 dbSNP
rs982912980 1045 dbSNP
rs951151616 1055 dbSNP
rs1035290062 1062 dbSNP
rs981957535 1071 dbSNP
rs969283405 1073 dbSNP
rs1463108433 1074 dbSNP
rs1338736731 1082 dbSNP
rs1354218343 1099 dbSNP
rs566584064 1118 dbSNP
rs1281709038 1120 dbSNP
rs551798695 1131 dbSNP
rs1233000537 1132 dbSNP
rs530520644 1133 dbSNP
rs1294470885 1147 dbSNP
rs1337516740 1147 dbSNP
rs563351623 1148 dbSNP
rs1364359451 1154 dbSNP
rs947501912 1175 dbSNP
rs1204758664 1178 dbSNP
rs753346744 1180 dbSNP
Experimental Support 1 for Functional miRNA-Target Interaction
miRNA:Target ----
Validation Method
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 PAR-CLIP data was present in GSM545217. RNA binding protein: AGO2. Condition:miR-7 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]
Experimental Support 2 for Functional miRNA-Target Interaction
miRNA:Target ----
Validation Method
     
Conditions HEK293
Disease 84317.0
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 "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 GSM714645. RNA binding protein: AGO2. Condition:completeT1 "PAR-CLIP data was present in GSM714646. RNA binding protein: AGO2. Condition:mildMNase "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]
Experimental Support 3 for Functional miRNA-Target Interaction
miRNA:Target ----
Validation Method
Conditions hESCs (WA-09)
Disease 84317.0
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]
Experimental Support 4 for Functional miRNA-Target Interaction
miRNA:Target ----
Validation Method
     
Conditions BCBL-1
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 GSM1015448. RNA binding protein: AGO2. Condition:BCBL-1 mRNA ...

- Haecker I; Gay LA; Yang Y; Hu J; Morse AM; et al., 2012, PLoS pathogens.

Article - Haecker I; Gay LA; Yang Y; Hu J; Morse AM; et al.
- PLoS pathogens, 2012
KSHV is the etiological agent of Kaposi's sarcoma (KS), primary effusion lymphoma (PEL), and a subset of multicentricCastleman's disease (MCD). The fact that KSHV-encoded miRNAs are readily detectable in all KSHV-associated tumors suggests a potential role in viral pathogenesis and tumorigenesis. MiRNA-mediated regulation of gene expression is a complex network with each miRNA having many potential targets, and to date only few KSHV miRNA targets have been experimentally determined. A detailed understanding of KSHV miRNA functions requires high-through putribonomics to globally analyze putative miRNA targets in a cell type-specific manner. We performed Ago HITS-CLIP to identify viral and cellular miRNAs and their cognate targets in two latently KSHV-infected PEL cell lines. Ago HITS-CLIP recovered 1170 and 950 cellular KSHV miRNA targets from BCBL-1 and BC-3, respectively. Importantly, enriched clusters contained KSHV miRNA seed matches in the 3'UTRs of numerous well characterized targets, among them THBS1, BACH1, and C/EBPbeta. KSHV miRNA targets were strongly enriched for genes involved in multiple pathways central for KSHV biology, such as apoptosis, cell cycle regulation, lymphocyte proliferation, and immune evasion, thus further supporting a role in KSHV pathogenesis and potentially tumorigenesis. A limited number of viral transcripts were also enriched by HITS-CLIP including vIL-6 expressed only in a subset of PEL cells during latency. Interestingly, Ago HITS-CLIP revealed extremely high levels of Ago-associated KSHV miRNAs especially in BC-3 cells where more than 70% of all miRNAs are of viral origin. This suggests that in addition to seed match-specific targeting of cellular genes, KSHV miRNAs may also function by hijacking RISCs, thereby contributing to a global de-repression of cellular gene expression due to the loss of regulation by human miRNAs. In summary, we provide an extensive list of cellular and viral miRNA targets representing an important resource to decipher KSHV miRNA function.
LinkOut: [PMID: 22927820]
Experimental Support 5 for Functional miRNA-Target Interaction
miRNA:Target ----
Validation Method
Conditions HEK293
Disease 84317.0
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 GSM1065667. RNA binding protein: AGO1. Condition:4-thiouridine "PAR-CLIP data was present in GSM1065668. RNA binding protein: AGO1. Condition:4-thiouridine "PAR-CLIP data was present in GSM1065669. RNA binding protein: AGO1. Condition:4-thiouridine "PAR-CLIP data was present in GSM1065670. RNA binding protein: AGO2. Condition:4-thiouridine ...

- Memczak S; Jens M; Elefsinioti A; Torti F; et al., 2013, Nature.

Article - Memczak S; Jens M; Elefsinioti A; Torti F; et al.
- Nature, 2013
Circular RNAs (circRNAs) in animals are an enigmatic class of RNA with unknown function. To explore circRNAs systematically, we sequenced and computationally analysed human, mouse and nematode RNA. We detected thousands of well-expressed, stable circRNAs, often showing tissue/developmental-stage-specific expression. Sequence analysis indicated important regulatory functions for circRNAs. We found that a human circRNA, antisense to the cerebellar degeneration-related protein 1 transcript (CDR1as), is densely bound by microRNA (miRNA) effector complexes and harbours 63 conserved binding sites for the ancient miRNA miR-7. Further analyses indicated that CDR1as functions to bind miR-7 in neuronal tissues. Human CDR1as expression in zebrafish impaired midbrain development, similar to knocking down miR-7, suggesting that CDR1as is a miRNA antagonist with a miRNA-binding capacity ten times higher than any other known transcript. Together, our data provide evidence that circRNAs form a large class of post-transcriptional regulators. Numerous circRNAs form by head-to-tail splicing of exons, suggesting previously unrecognized regulatory potential of coding sequences.
LinkOut: [PMID: 23446348]
Experimental Support 6 for Functional miRNA-Target Interaction
miRNA:Target ----
Validation Method
Conditions TZM-bl
Location of target site 3'UTR
Tools used in this research TargetScan , miRTarCLIP , Piranha
Original Description (Extracted from the article) ... PAR-CLIP data was present in 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]
Experimental Support 7 for Functional miRNA-Target Interaction
miRNA:Target ----
Validation Method
     
Conditions HEK293/HeLa
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 GSM1067869. RNA binding protein: AGO2. Condition:Ago2 IP-seq (asynchronous cells) ...

- Kishore S; Gruber AR; Jedlinski DJ; Syed et al., 2013, Genome biology.

Article - Kishore S; Gruber AR; Jedlinski DJ; Syed et al.
- Genome biology, 2013
BACKGROUND: In recent years, a variety of small RNAs derived from other RNAs with well-known functions such as tRNAs and snoRNAs, have been identified. The functional relevance of these RNAs is largely unknown. To gain insight into the complexity of snoRNA processing and the functional relevance of snoRNA-derived small RNAs, we sequence long and short RNAs, small RNAs that co-precipitate with the Argonaute 2 protein and RNA fragments obtained in photoreactive nucleotide-enhanced crosslinking and immunoprecipitation (PAR-CLIP) of core snoRNA-associated proteins. RESULTS: Analysis of these data sets reveals that many loci in the human genome reproducibly give rise to C/D box-like snoRNAs, whose expression and evolutionary conservation are typically less pronounced relative to the snoRNAs that are currently cataloged. We further find that virtually all C/D box snoRNAs are specifically processed inside the regions of terminal complementarity, retaining in the mature form only 4-5 nucleotides upstream of the C box and 2-5 nucleotides downstream of the D box. Sequencing of the total and Argonaute 2-associated populations of small RNAs reveals that despite their cellular abundance, C/D box-derived small RNAs are not efficiently incorporated into the Ago2 protein. CONCLUSIONS: We conclude that the human genome encodes a large number of snoRNAs that are processed along the canonical pathway and expressed at relatively low levels. Generation of snoRNA-derived processing products with alternative, particularly miRNA-like, functions appears to be uncommon.
LinkOut: [PMID: 23706177]
Experimental Support 8 for Functional miRNA-Target Interaction
miRNA:Target ----
Validation Method
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]
Experimental Support 9 for Functional miRNA-Target Interaction
miRNA:Target ----
Validation Method
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 ERX177603. RNA binding protein: AGO2. Condition:p53_D_AGO_CLIP_2_5 PAR-CLIP data was present in ERX177615. RNA binding protein: AGO2. Condition:p53_D_AGO_CLIP_3_5 PAR-CLIP data was present in ERX177619. RNA binding protein: AGO2. Condition:p53_D_AGO_CLIP_3_9 PAR-CLIP data was present in ERX177627. RNA binding protein: AGO2. Condition:p53_D_AGO_CLIP_4_5 ...

- 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]
Experimental Support 10 for Functional miRNA-Target Interaction
miRNA:Target ----
Validation Method
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 SRX1760618. RNA binding protein: AGO2. Condition:AGO-CLIP-PC3_B PAR-CLIP data was present in SRX1760583. RNA binding protein: AGO2. Condition:AGO-CLIP-LNCaP_A PAR-CLIP data was present in SRX1760638. RNA binding protein: AGO2. Condition:AGO-CLIP-PC3-miR148 PAR-CLIP data was present in SRX1760591. RNA binding protein: AGO2. Condition:AGO-CLIP-LNCaP_B PAR-CLIP data was present in SRX1760628. RNA binding protein: AGO2. Condition:AGO-CLIP-LAPC4_B PAR-CLIP data was present in SRX1760616. RNA binding protein: AGO2. Condition:AGO-CLIP-PC3_A PAR-CLIP data was present in SRX1760620. RNA binding protein: AGO2. Condition:AGO-CLIP-LAPC4_A PAR-CLIP data was present in SRX1760630. RNA binding protein: AGO2. Condition:AGO-CLIP-22RV1_A PAR-CLIP data was present in SRX1760631. RNA binding protein: AGO2. Condition:AGO-CLIP-22RV1_B PAR-CLIP data was present in SRX1760597. RNA binding protein: AGO2. Condition:AGO-CLIP-LNCaP_C PAR-CLIP data was present in SRX1760632. RNA binding protein: AGO2. Condition:AGO-CLIP-22RV1_C PAR-CLIP data was present in SRX1760637. RNA binding protein: AGO2. Condition:AGO-CLIP-DU145_A PAR-CLIP data was present in SRX1760639. RNA binding protein: AGO2. Condition:AGO-CLIP-LNCaP-MDV_A PAR-CLIP data was present in SRX1760641. RNA binding protein: AGO2. Condition:AGO-CLIP-LNCaP-MDV_B ...

- 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]
CLIP-seq Support 1 for dataset GSM714642
Method / RBP HITS-CLIP / AGO2
Cell line / Condition HEK293 / completeT1, repA
Location of target site ENST00000437688.2 | 3UTR | UCCCAUAUGGUCUAGCGGUUAGGAUUCCUGGUUUUCACCCAGGUGGCCCGGGUUCGACUCCCGGUAUGGGAACAAAAGUGG
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 GSM714643
Method / RBP HITS-CLIP / AGO2
Cell line / Condition HEK293 / completeT1, repB
Location of target site ENST00000437688.2 | 3UTR | CACGGUGGCGUCACCUUUCAGCAGUUCCCAUAUGGUCUAGCGGUUAGGAUUCCUGGUUUUCACCCAGGUGGCCCGGGUUCGACUCCCGGUAUGGGAACAAAAGUGGCUUU
Tools used in this analysis TargetScan, miRTarCLIP, and Piranha
Article / Accession Series PMID: 21572407 / GSE28865
CLIP-seq Viewer Link
CLIP-seq Support 3 for dataset GSM1015448
Method / RBP HITS-CLIP / AGO2
Cell line / Condition BCBL-1 / BCBL-1 mRNA
Location of target site ENST00000437688.2 | 3UTR | AGCAGUUCCCAUAUGGUCUAGCGGUUAGGAUUCCUGGUUUUCACCCAGGUGGCCCGGGUUCGACUCCCGGUAUGGGAACAA
Tools used in this analysis TargetScan, miRTarCLIP, and Piranha
Article / Accession Series PMID: 22927820 / GSE41357
CLIP-seq Viewer Link
CLIP-seq Support 4 for dataset GSM1067869
Method / RBP HITS-CLIP / AGO2
Cell line / Condition HEK293/HeLa / Ago2 IP-seq (asynchronous cells)
Location of target site ENST00000437688.2 | 3UTR | CACGGUGGCGUCACCUUUCAGCAGUUCCCAUAUGGUCUAGCGGUUAGGAUUCCUGGUUUUCACCCAGGUGGCCCGGGUUCGACUCCCGGUAUGGGAACAA
Tools used in this analysis TargetScan, miRTarCLIP, and Piranha
Article / Accession Series PMID: 23706177 / GSE43666
CLIP-seq Viewer Link
CLIP-seq Support 5 for dataset GSM1013106
Method / RBP HITS-CLIP  / AGO
Cell line / Condition HS27a / HS27a-replicate-2
Location of target site ENST00000437688.2 | 3UTR | GUCUAGCGGUUAGGAUUCCUGGUUUUCACCCAGGUGG
Tools used in this analysis TargetScan, miRTarCLIP, and Piranha
Article / Accession Series PMID: 24038734 / GSE41272
CLIP-seq Viewer Link
CLIP-seq Support 6 for dataset GSM545212
Method / RBP PAR-CLIP / AGO1
Cell line / Condition HEK293 / Control
Location of target site ENST00000437688.2 | 3UTR | CGGUGGCGUCACCUUUCAGCAGUUCCCAUAUGGUCUAGCGGUUAGGAUUCCUGGUUUUCACCCAGGUGGCCCGGGUUCGACUCCCGGUAUGGGAACAA
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 GSM545213
Method / RBP PAR-CLIP / AGO2
Cell line / Condition HEK293 / Control
Location of target site ENST00000437688.2 | 3UTR | AGCAGUUCCCAUAUGGUCUAGCGGUUAGGAUUCCUGGUUUUCACCCAGGUGGCCCGGGUUCGACUCCCGGUAUGGGAAC
Tools used in this analysis TargetScan, miRTarCLIP, and Piranha
Article / Accession Series PMID: 20371350 / GSE21578
CLIP-seq Viewer Link
CLIP-seq Support 8 for dataset GSM545214
Method / RBP PAR-CLIP / AGO3
Cell line / Condition HEK293 / Control
Location of target site ENST00000437688.2 | 3UTR | CGGUGGCGUCACCUUUCAGCAGUUCCCAUAUGGUCUAGCGGUUAGGAUUCCUGGUUUUCACCCAGGUGGCCCGGGUUCGACUCCCGGUAUGGGAACAA
Tools used in this analysis TargetScan, miRTarCLIP, and Piranha
Article / Accession Series PMID: 20371350 / GSE21578
CLIP-seq Viewer Link
CLIP-seq Support 9 for dataset GSM545215
Method / RBP PAR-CLIP / AGO4
Cell line / Condition HEK293 / Control
Location of target site ENST00000437688.2 | 3UTR | UUCCCAUAUGGUCUAGCGGUUAGGAUUCCUGGUUUUCACCCAGGUGGCCCGGGUUCGACUCCCGGUAUGGGAACAA
Tools used in this analysis TargetScan, miRTarCLIP, and Piranha
Article / Accession Series PMID: 20371350 / GSE21578
CLIP-seq Viewer Link
CLIP-seq Support 10 for dataset GSM545216
Method / RBP PAR-CLIP / AGO2
Cell line / Condition HEK293 / miR-124 transfection
Location of target site ENST00000437688.2 | 3UTR | AGCAGUUCCCAUAUGGUCUAGCGGUUAGGAUUCCUGGUUUUCACCCAGGUGGCCCGGGUUCGACUCCCGGUAUGGGAACAA
Tools used in this analysis TargetScan, miRTarCLIP, and Piranha
Article / Accession Series PMID: 20371350 / GSE21578
CLIP-seq Viewer Link
CLIP-seq Support 11 for dataset GSM545217
Method / RBP PAR-CLIP / AGO2
Cell line / Condition HEK293 / miR-7 transfection
Location of target site ENST00000437688.2 | 3UTR | AGCAGUUCCCAUAUGGUCUAGCGGUUAGGAUUCCUGGUUUUCACCCAGGUGGCCCGGGUUCGACUCCCGGUAUGGGAACAA
Tools used in this analysis TargetScan, miRTarCLIP, and Piranha
Article / Accession Series PMID: 20371350 / GSE21578
CLIP-seq Viewer Link
CLIP-seq Support 12 for dataset GSM714644
Method / RBP PAR-CLIP / AGO2
Cell line / Condition HEK293 / completeT1, repA
Location of target site ENST00000437688.2 | 3UTR | CACGGUGGCGUCACCUUUCAGCAGUUCCCAUAUGGUCUAGCGGUUAGGAUUCCUGGUUUUCACCCAGGUGGCCCGGGUUCGACUCCCGGUAUGGGAACAAAAGUGGCUUU
Tools used in this analysis TargetScan, miRTarCLIP, and Piranha
Article / Accession Series PMID: 21572407 / GSE28865
CLIP-seq Viewer Link
CLIP-seq Support 13 for dataset GSM714645
Method / RBP PAR-CLIP / AGO2
Cell line / Condition HEK293 / completeT1, repB
Location of target site ENST00000437688.2 | 3UTR | AGUUCCCAUAUGGUCUAGCGGUUAGGAUUCCUGGUUUUCACCCAGGUGGCCCGGGUUCGACUCCCGGUAUGGGAACAA
Tools used in this analysis TargetScan, miRTarCLIP, and Piranha
Article / Accession Series PMID: 21572407 / GSE28865
CLIP-seq Viewer Link
CLIP-seq Support 14 for dataset GSM714646
Method / RBP PAR-CLIP / AGO2
Cell line / Condition HEK293 / mildMNase, repA
Location of target site ENST00000437688.2 | 3UTR | ACGGUGGCGUCACCUUUCAGCAGUUCCCAUAUGGUCUAGCGGUUAGGAUUCCUGGUUUUCACCCAGGUGGCCCGGGUUCGACUCCCGGUAUGGGAACAAAAGUGGCUUU
Tools used in this analysis TargetScan, miRTarCLIP, and Piranha
Article / Accession Series PMID: 21572407 / GSE28865
CLIP-seq Viewer Link
CLIP-seq Support 15 for dataset GSM714647
Method / RBP PAR-CLIP / AGO2
Cell line / Condition HEK293 / mildMNase, repB
Location of target site ENST00000437688.2 | 3UTR | AGCAGUUCCCAUAUGGUCUAGCGGUUAGGAUUCCUGGUUUUCACCCAGGUGGCCCGGGUUCGACUCCCGGUAUGGGAACAAAAGUGG
Tools used in this analysis TargetScan, miRTarCLIP, and Piranha
Article / Accession Series PMID: 21572407 / GSE28865
CLIP-seq Viewer Link
CLIP-seq Support 16 for dataset SRR359787
Method / RBP PAR-CLIP / AGO2
Cell line / Condition hESCs (WA-09) / 4-thiouridine, RNase T1
Location of target site ENST00000437688.2 | 3UTR | AGCAGUUCCCAUAUGGUCUAGCGGUUAGGAUUCCUGGUUUUCACCCAGGUGGCCCGGGUUCGACUCCCGGUAUGGGAACAAAAGUGGCUUU
Tools used in this analysis TargetScan, miRTarCLIP, and Piranha
Article / Accession Series PMID: 22012620 / SRX103431
CLIP-seq Viewer Link
CLIP-seq Support 17 for dataset GSM1065667
Method / RBP PAR-CLIP / AGO1
Cell line / Condition HEK293 / 4-thiouridine, ML_MM_6
Location of target site ENST00000437688.2 | 3UTR | CACGGUGGCGUCACCUUUCAGCAGUUCCCAUAUGGUCUAGCGGUUAGGAUUCCUGGUUUUCACCCAGGUGGCCCGGGUUCGACUCCCGGUAUGGGAACAAAAG
Tools used in this analysis TargetScan, miRTarCLIP, and Piranha
Article / Accession Series PMID: 23446348 / GSE43573
CLIP-seq Viewer Link
CLIP-seq Support 18 for dataset GSM1065668
Method / RBP PAR-CLIP / AGO1
Cell line / Condition HEK293 / 4-thiouridine, ML_MM_7
Location of target site ENST00000437688.2 | 3UTR | AGCAGUUCCCAUAUGGUCUAGCGGUUAGGAUUCCUGGUUUUCACCCAGGUGGCCCGGGUUCGACUCCCGGUAUGGGAAC
Tools used in this analysis TargetScan, miRTarCLIP, and Piranha
Article / Accession Series PMID: 23446348 / GSE43573
CLIP-seq Viewer Link
CLIP-seq Support 19 for dataset GSM1065669
Method / RBP PAR-CLIP / AGO1
Cell line / Condition HEK293 / 4-thiouridine, ML_MM_8
Location of target site ENST00000437688.2 | 3UTR | CACGGUGGCGUCACCUUUCAGCAGUUCCCAUAUGGUCUAGCGGUUAGGAUUCCUGGUUUUCACCCAGGUGGCCCGGGUUCGACUCCCGGUAUGGGAACAA
Tools used in this analysis TargetScan, miRTarCLIP, and Piranha
Article / Accession Series PMID: 23446348 / GSE43573
CLIP-seq Viewer Link
CLIP-seq Support 20 for dataset GSM1065670
Method / RBP PAR-CLIP / AGO2
Cell line / Condition HEK293 / 4-thiouridine, 3_ML_LG
Location of target site ENST00000437688.2 | 3UTR | AGUUCCCAUAUGGUCUAGCGGUUAGGAUUCCUGGUUUUCACCCAGGUGGCCCGGGUUCGACUCCCGGUAUGGGAACAA
Tools used in this analysis TargetScan, miRTarCLIP, and Piranha
Article / Accession Series PMID: 23446348 / GSE43573
CLIP-seq Viewer Link
CLIP-seq Support 21 for dataset SRR1045082
Method / RBP PAR-CLIP / AGO2
Cell line / Condition MCF7 / Untreated
Location of target site ENST00000437688.2 | 3UTR | UUCCCAUAUGGUCUAGCGGUUAGGAUUCCUGGUUUUCACCCAGGUGGCCCGGGUUCGACUCCCGGUAUGGGAACAA
Tools used in this analysis TargetScan, miRTarCLIP, and Piranha
Article / Accession Series PMID: 24398324 / SRX388831
CLIP-seq Viewer Link
CLIP-seq Support 22 for dataset GSM1462574
Method / RBP PAR-CLIP / AGO2
Cell line / Condition TZM-bl / TZM-bl ami BaL
Location of target site ENST00000437688.2 | 3UTR | AGUUCCCAUAUGGUCUAGCGGUUAGGAUUCCUGGUUUUCACCCAGGUGGCCCGGGUUCGACUCCCGGUAUGGGAACA
Tools used in this analysis TargetScan, miRTarCLIP, and Piranha
Article / Accession Series PMID: 23592263 / GSE59944
CLIP-seq Viewer Link
MiRNA-Target Expression Profile
Dataset Pearson Correlation P-value for Pearson Correlation Spearman Correlation P-value for Spearman Correlation Samples Chart
MiRNA-Target Expression Profile (TCGA)
Tumor Pearson Correlation P-value for Pearson Correlation Spearman Correlation P-value for Spearman Correlation Samples Chart
168 hsa-miR-548t-3p Target Genes:
Functional analysis:
ID Target Description Validation methods
Strong evidence Less strong evidence
MIRT059365 ANP32E acidic nuclear phosphoprotein 32 family member E 2 2
MIRT072839 ARIH1 ariadne RBR E3 ubiquitin protein ligase 1 2 6
MIRT076945 PCGF2 polycomb group ring finger 2 2 6
MIRT083941 TFAP2C transcription factor AP-2 gamma 2 2
MIRT085401 ETS2 ETS proto-oncogene 2, transcription factor 2 2
MIRT109790 KLHL15 kelch like family member 15 2 2
MIRT114046 AKAP11 A-kinase anchoring protein 11 2 10
MIRT130165 TXNIP thioredoxin interacting protein 2 6
MIRT150013 MIDN midnolin 2 2
MIRT181258 ASH1L ASH1 like histone lysine methyltransferase 2 2
MIRT205594 NCL nucleolin 2 2
MIRT222253 ACTB actin beta 2 4
MIRT245653 EIF5AL1 eukaryotic translation initiation factor 5A-like 1 2 4
MIRT250947 CDK5R1 cyclin dependent kinase 5 regulatory subunit 1 2 4
MIRT252497 NWD1 NACHT and WD repeat domain containing 1 2 2
MIRT271990 ARF1 ADP ribosylation factor 1 2 4
MIRT280804 RNF11 ring finger protein 11 2 2
MIRT293803 FEM1A fem-1 homolog A 2 2
MIRT318231 RREB1 ras responsive element binding protein 1 2 2
MIRT341455 ATP6V0B ATPase H+ transporting V0 subunit b 2 2
MIRT347413 CEBPG CCAAT/enhancer binding protein gamma 2 4
MIRT351860 PLEKHA3 pleckstrin homology domain containing A3 2 2
MIRT357983 GRPEL2 GrpE like 2, mitochondrial 2 2
MIRT377094 PPP1CB protein phosphatase 1 catalytic subunit beta 2 2
MIRT407303 IGFBP5 insulin like growth factor binding protein 5 2 2
MIRT441564 LMOD3 leiomodin 3 2 2
MIRT442364 ZC3H12C zinc finger CCCH-type containing 12C 2 2
MIRT443228 ARL5B ADP ribosylation factor like GTPase 5B 2 2
MIRT443404 HMX3 H6 family homeobox 3 2 2
MIRT446055 NR5A2 nuclear receptor subfamily 5 group A member 2 2 2
MIRT448277 ZNF652 zinc finger protein 652 2 2
MIRT450822 KCNB1 potassium voltage-gated channel subfamily B member 1 2 2
MIRT453016 CCDC115 coiled-coil domain containing 115 2 17
MIRT454463 PPP2R2B protein phosphatase 2 regulatory subunit Bbeta 2 2
MIRT456360 CITED2 Cbp/p300 interacting transactivator with Glu/Asp rich carboxy-terminal domain 2 2 2
MIRT460007 DNALI1 dynein axonemal light intermediate chain 1 2 2
MIRT463154 ZNF385A zinc finger protein 385A 2 6
MIRT463766 YPEL2 yippee like 2 2 2
MIRT468310 SFT2D2 SFT2 domain containing 2 2 2
MIRT470668 POLR2D RNA polymerase II subunit D 2 4
MIRT478517 CTTN cortactin 2 2
MIRT480507 C11orf57 chromosome 11 open reading frame 57 2 2
MIRT484718 INHBA inhibin beta A subunit 2 12
MIRT485494 HMGN2 high mobility group nucleosomal binding domain 2 2 2
MIRT487302 SLC38A9 solute carrier family 38 member 9 2 2
MIRT487771 ANKEF1 ankyrin repeat and EF-hand domain containing 1 2 16
MIRT491876 YWHAZ tyrosine 3-monooxygenase/tryptophan 5-monooxygenase activation protein zeta 2 2
MIRT494304 CEP120 centrosomal protein 120 2 2
MIRT495396 TRIM24 tripartite motif containing 24 2 2
MIRT495646 CDK1 cyclin dependent kinase 1 2 2
MIRT496665 TMEM237 transmembrane protein 237 2 2
MIRT496837 ZNF460 zinc finger protein 460 2 2
MIRT498638 CHD4 chromodomain helicase DNA binding protein 4 2 10
MIRT503928 FBXL13 F-box and leucine rich repeat protein 13 2 4
MIRT506063 PPP2R2A protein phosphatase 2 regulatory subunit Balpha 2 2
MIRT506582 MIER3 MIER family member 3 2 4
MIRT506606 MAT2A methionine adenosyltransferase 2A 2 4
MIRT506844 KIF23 kinesin family member 23 2 6
MIRT508536 RPP14 ribonuclease P/MRP subunit p14 2 4
MIRT509669 ZNF354B zinc finger protein 354B 2 10
MIRT511170 MBNL3 muscleblind like splicing regulator 3 2 6
MIRT512147 COX6B1 cytochrome c oxidase subunit 6B1 2 2
MIRT512831 ID4 inhibitor of DNA binding 4, HLH protein 2 6
MIRT514558 XRCC3 X-ray repair cross complementing 3 2 4
MIRT515856 AJAP1 adherens junctions associated protein 1 2 4
MIRT521848 PNISR PNN interacting serine and arginine rich protein 2 4
MIRT525364 SYNM synemin 2 2
MIRT527120 ARHGAP15 Rho GTPase activating protein 15 2 2
MIRT527271 FBLN2 fibulin 2 2 2
MIRT527439 COL4A3 collagen type IV alpha 3 chain 2 2
MIRT527658 CD300E CD300e molecule 2 2
MIRT528334 TBC1D22B TBC1 domain family member 22B 2 2
MIRT529033 EXOC8 exocyst complex component 8 2 2
MIRT529321 PDE5A phosphodiesterase 5A 2 2
MIRT529677 TRPV2 transient receptor potential cation channel subfamily V member 2 2 2
MIRT529846 SMTN smoothelin 2 2
MIRT530385 ZNF431 zinc finger protein 431 2 2
MIRT530913 GPR85 G protein-coupled receptor 85 2 2
MIRT531794 KDR kinase insert domain receptor 2 2
MIRT532246 KLF2 Kruppel like factor 2 2 4
MIRT532658 CBX7 chromobox 7 2 2
MIRT533630 TMX3 thioredoxin related transmembrane protein 3 2 2
MIRT534811 RAB33B RAB33B, member RAS oncogene family 2 2
MIRT534975 PSD3 pleckstrin and Sec7 domain containing 3 2 2
MIRT536588 ITPKB inositol-trisphosphate 3-kinase B 2 2
MIRT536779 HNRNPD heterogeneous nuclear ribonucleoprotein D 2 2
MIRT538764 CABLES1 Cdk5 and Abl enzyme substrate 1 2 2
MIRT539294 ANGEL2 angel homolog 2 2 2
MIRT539621 SHISA9 shisa family member 9 2 2
MIRT539651 BUB1 BUB1 mitotic checkpoint serine/threonine kinase 2 2
MIRT540347 OPHN1 oligophrenin 1 2 2
MIRT540413 PITPNC1 phosphatidylinositol transfer protein, cytoplasmic 1 2 2
MIRT541396 CDC27 cell division cycle 27 2 2
MIRT542916 HSBP1 heat shock factor binding protein 1 2 2
MIRT544710 EIF5A eukaryotic translation initiation factor 5A 2 4
MIRT544998 MFF mitochondrial fission factor 2 4
MIRT553289 TSPAN3 tetraspanin 3 2 2
MIRT553455 TNRC6C trinucleotide repeat containing 6C 2 2
MIRT553782 TAF13 TATA-box binding protein associated factor 13 2 2
MIRT554656 ROBO1 roundabout guidance receptor 1 2 2
MIRT555104 PURB purine rich element binding protein B 2 2
MIRT557235 HNRNPA1 heterogeneous nuclear ribonucleoprotein A1 2 2
MIRT560861 GAL3ST3 galactose-3-O-sulfotransferase 3 2 2
MIRT561545 SON SON DNA binding protein 2 2
MIRT561554 SLMO2 PRELI domain containing 3B 2 2
MIRT563764 ZNF678 zinc finger protein 678 2 2
MIRT565653 SIX4 SIX homeobox 4 2 2
MIRT568080 CELF2 CUGBP Elav-like family member 2 2 2
MIRT568759 MYBL1 MYB proto-oncogene like 1 2 2
MIRT569078 CADM2 cell adhesion molecule 2 2 2
MIRT569509 THYN1 thymocyte nuclear protein 1 2 2
MIRT571268 CDKN2AIP CDKN2A interacting protein 2 2
MIRT571809 PHF19 PHD finger protein 19 2 2
MIRT572554 DKK3 dickkopf WNT signaling pathway inhibitor 3 2 2
MIRT573782 SLC24A4 solute carrier family 24 member 4 2 4
MIRT576441 Ccdc115 coiled-coil domain containing 115 2 10
MIRT576712 Slc30a3 solute carrier family 30 (zinc transporter), member 3 2 3
MIRT608377 PIWIL2 piwi like RNA-mediated gene silencing 2 2 2
MIRT608484 NKTR natural killer cell triggering receptor 2 6
MIRT610186 FAM49A family with sequence similarity 49 member A 2 2
MIRT611631 EDIL3 EGF like repeats and discoidin domains 3 2 2
MIRT613534 TRA2B transformer 2 beta homolog 2 2
MIRT616221 PTPN11 protein tyrosine phosphatase, non-receptor type 11 2 2
MIRT622370 SALL1 spalt like transcription factor 1 2 2
MIRT624371 CDK12 cyclin dependent kinase 12 2 2
MIRT624995 ZNF665 zinc finger protein 665 2 4
MIRT626875 AP3B1 adaptor related protein complex 3 beta 1 subunit 2 2
MIRT627737 RAP2B RAP2B, member of RAS oncogene family 2 4
MIRT628490 ADAT2 adenosine deaminase, tRNA specific 2 2 2
MIRT633647 PLEKHG7 pleckstrin homology and RhoGEF domain containing G7 2 4
MIRT634028 SLC30A3 solute carrier family 30 member 3 2 3
MIRT635923 GLTSCR2 NOP53 ribosome biogenesis factor 2 2
MIRT638287 SERBP1 SERPINE1 mRNA binding protein 1 2 2
MIRT641959 RNF115 ring finger protein 115 2 2
MIRT643573 CTNNA3 catenin alpha 3 2 2
MIRT645180 NOL9 nucleolar protein 9 2 4
MIRT647497 ZNF639 zinc finger protein 639 2 2
MIRT647682 PCK1 phosphoenolpyruvate carboxykinase 1 2 2
MIRT648422 MYOZ3 myozenin 3 2 2
MIRT650113 ZCCHC9 zinc finger CCHC-type containing 9 2 2
MIRT651076 ZNF518B zinc finger protein 518B 2 4
MIRT651415 ZADH2 zinc binding alcohol dehydrogenase domain containing 2 2 2
MIRT651456 XKR4 XK related 4 2 2
MIRT653619 SLC30A4 solute carrier family 30 member 4 2 2
MIRT653637 SLC30A1 solute carrier family 30 member 1 2 2
MIRT654896 POU2F1 POU class 2 homeobox 1 2 2
MIRT656483 MAP3K9 mitogen-activated protein kinase kinase kinase 9 2 2
MIRT658016 GABRA4 gamma-aminobutyric acid type A receptor alpha4 subunit 2 2
MIRT658041 FZD10 frizzled class receptor 10 2 2
MIRT660093 BTBD3 BTB domain containing 3 2 2
MIRT663923 MAGEF1 MAGE family member F1 2 2
MIRT665882 TGIF2 TGFB induced factor homeobox 2 2 2
MIRT669051 CEP128 centrosomal protein 128 2 2
MIRT669711 AAGAB alpha and gamma adaptin binding protein 2 2
MIRT686812 SNX2 sorting nexin 2 2 4
MIRT689883 SOD2 superoxide dismutase 2 2 2
MIRT693274 GLRX2 glutaredoxin 2 2 4
MIRT697056 BCAR1 BCAR1, Cas family scaffolding protein 2 2
MIRT703297 GID4 GID complex subunit 4 homolog 2 2
MIRT704087 DYRK2 dual specificity tyrosine phosphorylation regulated kinase 2 2 2
MIRT707719 CDC6 cell division cycle 6 2 2
MIRT708136 GK5 glycerol kinase 5 (putative) 2 2
MIRT709212 KLHL30 kelch like family member 30 2 2
MIRT710062 RWDD2A RWD domain containing 2A 2 2
MIRT712770 POU6F2 POU class 6 homeobox 2 2 2
MIRT715073 TMTC1 transmembrane and tetratricopeptide repeat containing 1 2 2
MIRT715387 TADA3 transcriptional adaptor 3 2 2
MIRT717712 NCKAP1 NCK associated protein 1 2 2
miRNA-Drug Resistance Associations
miRNA Drug Name CID NSC FDA Effect/Pattern Detection Method Level Phenotype Condition
hsa-mir-548t Paclitaxel 36314 NSC125973 approved sensitive cell line (W1)
hsa-mir-548t Cisplatin 5460033 NSC119875 approved sensitive cell line (W1)
hsa-mir-548t Doxorubicin 31703 NSC123127 approved sensitive cell line (W1)
hsa-mir-548t Topotecan 60699 NSC609699 approved sensitive cell line (W1)
hsa-mir-548t Vincristine 5978 approved sensitive cell line (W1)
hsa-miR-548t-3p Oxaliplatin 6857599 NSC266046 approved sensitive High Colorectal Cancer cell line (SW480, HCT-116)
hsa-miR-548t-3p Gefitinib 123631 NSC715055 approved sensitive cell line (PC9)
hsa-miR-548t-3p Osimertinib 71496458 NSC779217 approved sensitive cell line (HCC827)

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