Experimental Support 1 for Functional miRNA-Target Interaction
miRNA:Target
mmu-miR-125a-5p
-- Functional MTI --
Lars2
Validation Method
miRNA and mRNA specific interaction
Conditions
mESCs
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 GSM622571. RNA binding protein: AGO2. Condition:WT1B
HITS-CLIP data was present in GSM622572. RNA binding protein: AGO2. Condition:WT2
HITS-CLIP data was present in GSM622573. RNA binding protein: AGO2. Condition:KO1
...
- Leung AK; Young AG; Bhutkar A; Zheng GX; et al., 2011,
Nature structural & molecular biology .
Article
- Leung AK; Young AG; Bhutkar A; Zheng GX; et al.
- Nature structural & molecular biology , 2011
MicroRNAs (miRNAs) are 19-22-nucleotide noncoding RNAs that post-transcriptionally regulate mRNA targets. We have identified endogenous miRNA binding sites in mouse embryonic stem cells (mESCs), by performing photo-cross-linking immunoprecipitation using antibodies to Argonaute (Ago2) followed by deep sequencing of RNAs (CLIP-seq). We also performed CLIP-seq in Dicer(-)/(-) mESCs that lack mature miRNAs, allowing us to define whether the association of Ago2 with the identified sites was miRNA dependent. A significantly enriched motif, GCACUU, was identified only in wild-type mESCs in 3' untranslated and coding regions. This motif matches the seed of a miRNA family that constitutes ~68% of the mESC miRNA population. Unexpectedly, a G-rich motif was enriched in sequences cross-linked to Ago2 in both the presence and absence of miRNAs. Expression analysis and reporter assays confirmed that the seed-related motif confers miRNA-directed regulation on host mRNAs and that the G-rich motif can modulate this regulation.
LinkOut: [ PMID: 21258322 ]
Experimental Support 2 for Functional miRNA-Target Interaction
miRNA:Target
mmu-miR-125a-5p
-- Functional MTI --
Lars2
Validation Method
miRNA and mRNA specific interaction
Conditions
Liver
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 ERR266298. RNA binding protein: AGO2. Condition:A_Untreated
HITS-CLIP data was present in ERR266300. RNA binding protein: AGO2. Condition:B_Untreated
...
- Schug J; McKenna LB; Walton G; Hand N; et al., 2013,
BMC genomics .
Article
- Schug J; McKenna LB; Walton G; Hand N; et al.
- BMC genomics , 2013
BACKGROUND: Validation of physiologic miRNA targets has been met with significant challenges. We employed HITS-CLIP to identify which miRNAs participate in liver regeneration, and to identify their target mRNAs. RESULTS: miRNA recruitment to the RISC is highly dynamic, changing more than five-fold for several miRNAs. miRNA recruitment to the RISC did not correlate with changes in overall miRNA expression for these dynamically recruited miRNAs, emphasizing the necessity to determine miRNA recruitment to the RISC in order to fully assess the impact of miRNA regulation. We incorporated RNA-seq quantification of total mRNA to identify expression-weighted Ago footprints, and developed a microRNA regulatory element (MRE) prediction algorithm that represents a greater than 20-fold refinement over computational methods alone. These high confidence MREs were used to generate candidate 'competing endogenous RNA' (ceRNA) networks. CONCLUSION: HITS-CLIP analysis provide novel insights into global miRNA:mRNA relationships in the regenerating liver.
LinkOut: [ PMID: 23597149 ]
CLIP-seq Support 1 for dataset GSM4656405
Method / RBP
HITS-CLIP / AGO
Cell line / Condition
mouse liver / e125
Location of target site
NM_153168 | 3UTR | GAGGACAGAAACCUCCCGUGGAGCAGAAGGGCAAAAGCUCGCUUGAUCU
Tools used in this analysis
TargetScan, miRTarCLIP, and Piranha
Accession Series
GSE153876
CLIP-seq Viewer
Link
CLIP-seq Support 2 for dataset GSM4751761
Method / RBP
HITS-CLIP / AGO
Cell line / Condition
adipose tissue / RNA sequencing of eWAT 2
Location of target site
NM_153168 | 3UTR | GGCAAACAUCAGGGA
Tools used in this analysis
TargetScan, miRTarCLIP, and Piranha
Accession Series
GSE142677
CLIP-seq Viewer
Link
CLIP-seq Support 3 for dataset GSM4751768
Method / RBP
HITS-CLIP / AGO
Cell line / Condition
adipose tissue / miRNA sequencing of aWAT 2
Location of target site
NM_153168 | 3UTR | UAAGGCGAGCUCAGGGAGGACAGAAACCUCCCGUGGAGCAGAAGGGCAAAAGCUCGCUUGAUCUUGA
Tools used in this analysis
TargetScan, miRTarCLIP, and Piranha
Accession Series
GSE142677
CLIP-seq Viewer
Link
CLIP-seq Support 4 for dataset GSM4751769
Method / RBP
HITS-CLIP / AGO
Cell line / Condition
adipose tissue / miRNA sequencing of aWAT 3
Location of target site
NM_153168 | 3UTR | AGGCGAGCUCAGGGAGGACAGAAACCUCCCGUGGAGCAGAAGGGCAAAAGCUCGCUUGAUCUUGAUUUUCAGUAGGAAUACAGACCGUGAAAGCGGGGCCUCACGAUCCUUCUGACCUUUUGGGUUUUAAGCAGGAU
Tools used in this analysis
TargetScan, miRTarCLIP, and Piranha
Accession Series
GSE142677
CLIP-seq Viewer
Link
CLIP-seq Support 5 for dataset GSM4751770
Method / RBP
HITS-CLIP / AGO
Cell line / Condition
adipose tissue / miRNA sequencing of mWAT 1
Location of target site
NM_153168 | 3UTR | CUAAGGCGAGCUCAGGGAGGACAGAAACCUCCCGUGGAGCAGAAGGGCAAAAGCUCGCUUGAUCUUGAUUUUCAGUAGGAAUACAGACCGUGAAAGCGGGGCCUCACGAUCCUUCUGACCUUUUGGGUUUUAAGCAGGAUGU
Tools used in this analysis
TargetScan, miRTarCLIP, and Piranha
Accession Series
GSE142677
CLIP-seq Viewer
Link
CLIP-seq Support 6 for dataset GSM4751771
Method / RBP
HITS-CLIP / AGO
Cell line / Condition
adipose tissue / miRNA sequencing of mWAT 2
Location of target site
NM_153168 | 3UTR | CUAAGGCGAGCUCAGGGAGGACAGAAACCUCCCGUGGAGCAGAAGGGCAAAAGCUCGCUUGAUCUUGAUUUUCAGUAGGAAUACAGACCGUGAAAGCGGGGCCUCACGAUCCUUCUGACCUUUUGGGUUUUAAGCAGGAU
Tools used in this analysis
TargetScan, miRTarCLIP, and Piranha
Accession Series
GSE142677
CLIP-seq Viewer
Link
CLIP-seq Support 7 for dataset GSM4751772
Method / RBP
HITS-CLIP / AGO
Cell line / Condition
adipose tissue / miRNA sequencing of mWAT 3
Location of target site
NM_153168 | 3UTR | CUAAGGCGAGCUCAG
Tools used in this analysis
TargetScan, miRTarCLIP, and Piranha
Accession Series
GSE142677
CLIP-seq Viewer
Link
CLIP-seq Support 8 for dataset GSM4751772
Method / RBP
HITS-CLIP / AGO
Cell line / Condition
adipose tissue / miRNA sequencing of mWAT 3
Location of target site
NM_153168 | 3UTR | AGGACAGAAACCUCCCGUGGAGCAGAAGGGCAAAAGCUCGCUUGAUCUUGA
Tools used in this analysis
TargetScan, miRTarCLIP, and Piranha
Accession Series
GSE142677
CLIP-seq Viewer
Link
CLIP-seq Support 9 for dataset GSM4751777
Method / RBP
HITS-CLIP / AGO
Cell line / Condition
adipose tissue / miRNA sequencing of cWAT 2
Location of target site
NM_153168 | 3UTR | GAGGACAGAAACCUCCCGUGGAGCAGAAGGGCAAAAGCUCGCUUGAUCUUGA
Tools used in this analysis
TargetScan, miRTarCLIP, and Piranha
Accession Series
GSE142677
CLIP-seq Viewer
Link
CLIP-seq Support 10 for dataset GSM4751778
Method / RBP
HITS-CLIP / AGO
Cell line / Condition
adipose tissue / miRNA sequencing of cWAT 3
Location of target site
NM_153168 | 3UTR | CUCAGGGAGGACAGAAACCUCCCGUGGAGCAGAAGGGCAAAAGCUCGCUUGAUCUUGAUUUUCAGUAGGAAUACAGACCGUGAAAGCGGGGCCUCACGAUCCUUCUGACCUUUUGGGUUUUAAGCAGGAU
Tools used in this analysis
TargetScan, miRTarCLIP, and Piranha
Accession Series
GSE142677
CLIP-seq Viewer
Link
CLIP-seq Support 11 for dataset GSM4751779
Method / RBP
HITS-CLIP / AGO
Cell line / Condition
adipose tissue / miRNA sequencing of iBAT 1
Location of target site
NM_153168 | 3UTR | GAGCUCAGGGAGGACAGAAACCUCCCGUGGAGCAGAAGGGCAAAAGCUCGCUUGAUCUUGAUUUUCAGUAGGAAUACAGACC
Tools used in this analysis
TargetScan, miRTarCLIP, and Piranha
Accession Series
GSE142677
CLIP-seq Viewer
Link
CLIP-seq Support 12 for dataset GSM4751780
Method / RBP
HITS-CLIP / AGO
Cell line / Condition
adipose tissue / miRNA sequencing of iBAT 2
Location of target site
NM_153168 | 3UTR | CGAGCUCAGGGAGGACAGAAACCUCCCGUGGAGCAGAAGGGCAAAAGCUCGCUUGAUCUUGAUUUUCAGUAGGAAUACAGACCGUGAAAGCGGGGCCUCACGAUCCUUCUGACCUUUUGGGUUUUAAGCAGGAU
Tools used in this analysis
TargetScan, miRTarCLIP, and Piranha
Accession Series
GSE142677
CLIP-seq Viewer
Link
CLIP-seq Support 13 for dataset GSM4751781
Method / RBP
HITS-CLIP / AGO
Cell line / Condition
adipose tissue / miRNA sequencing of iBAT 3
Location of target site
NM_153168 | 3UTR | AGCUCAGGGAGGACAGAAACCUCCCGUGGAGCAGAAGGGCAAAAGCUCGCUUGAUCUUGAUUUUCAGUAGGAAUACAGACCGUGAAAGCGGGGCCUCACGAUCCUUCUGACCUUUUGGGUUUUAAGCAGGAU
Tools used in this analysis
TargetScan, miRTarCLIP, and Piranha
Accession Series
GSE142677
CLIP-seq Viewer
Link
CLIP-seq Support 14 for dataset GSM622571
Method / RBP
HITS-CLIP / AGO2
Cell line / Condition
mESCs / WT1B
Location of target site
NM_153168 | 3UTR | GGCCUAAGGCGAGCUCAGGGAGGACAGAAACCUCCCGUGGAGCAGAAGGGCAAAAGCUCGCUUGAUCUUGAUUUUCAGUA
Tools used in this analysis
TargetScan, miRTarCLIP, and Piranha
Article / Accession Series
PMID: 21258322 / GSE25310
CLIP-seq Viewer
Link
CLIP-seq Support 15 for dataset GSM622572
Method / RBP
HITS-CLIP / AGO2
Cell line / Condition
mESCs / WT2
Location of target site
NM_153168 | 3UTR | GGCCUAAGGCGAGCUCAGGGAGGACAGAAACCUCCCGUGGAGCAGAAGGGCAAAAGCUCGCUUGAUCUUGAUUUUCAGUAGGAAUACAGACCGUGAAAGCGGGGCCUCACGAUCCUUCUGACCUUUUGGGUUUUAAGCAGGAUGUGUCAGAAAAGUUACCACAGGGAUAACUGGCUUGUGGCGGCCAAGCGUUCAUAGCGACGUCGCUUUUUGAUCCUUCGAUGUCGGCUCUUCCUAUCAUUGUGAAGCAGAAUUCACCAAGCGUUGGAUUGUUCACCCACUAAUAGGGAACGUGAGCUGGGAUUAGACCGUCGUGAGACAGGUUAGUUUUACCCUACUGAUGAUGUGUUGUUGCCAUGGUAAUCCUGCUCAGUACGAGAGGAACCGCAG
Tools used in this analysis
TargetScan, miRTarCLIP, and Piranha
Article / Accession Series
PMID: 21258322 / GSE25310
CLIP-seq Viewer
Link
CLIP-seq Support 16 for dataset GSM622573
Method / RBP
HITS-CLIP / AGO2
Cell line / Condition
mESCs / KO1
Location of target site
NM_153168 | 3UTR | CCUAAGGCGAGCUCAGGGAGGACAGAAACCUCCCGUGGAGCAGAAGGGCAAAAGCUCGCUUGAUCUUGAUUUUCAGUAGGAAUACAGACCGUGAAAGCGGGGCCUCACGAUCCUUCUGACCUUUUGGGUUUUAAGCAGGAUGUGUCAGAAAAGUUACCACAGGGAUAACUGGCUUGUGGCGGCCAAGCGUUCAUAGCGACGUCGCUUUUUGAUCCUUCGAUGUCGGCUCUUCCUAUCAUUGUGAAGCAGAAUUCACCAAGCGUUGGAUUGUUCACCCACUAAUAGGGAACGUGAGCUGGGAUUAGACCGUCGUGAGACAGGUUAGUUUUACCCUACUGAUGAUGUGUUGUUGCCAUGGUAAUCCUGCUCAGUACGAGAGGAACCGCA
Tools used in this analysis
TargetScan, miRTarCLIP, and Piranha
Article / Accession Series
PMID: 21258322 / GSE25310
CLIP-seq Viewer
Link
CLIP-seq Support 17 for dataset ERR266298
Method / RBP
HITS-CLIP / AGO2
Cell line / Condition
Liver / A_Untreated
Location of target site
NM_153168 | 3UTR | GGAGGCCUAAGGCGAGCUCAGGGAGGACAGAAACCUCCCGUGGAGCAGAAGGGCAAAAGCUCGCUUGAUCUUGAUUUUCAGUAGGAAUACAGACCGUGAAAGCGGGGCCUCACGAUCCUUCUGACCUUUUGGGUUUUAAGCAGGAUGUGUCAGAAAAGUUACCACAGGGAUAACUGGCUUGUGGCGGCCAAGCGUUCAUAGCGACGUCGCUUUUUGAUCCUUCGAUGUCGGCUCUUCCUAUCAUUGUGAAGCAGAAUUCACCAAGCGUUGGAUUGUUCACCCACUAAUAGGGAACGUGAGCUGGGAUUAGACCGUCGUGAGACAGGUUAGUUUUACCCUACUGAUGAUGUGUUGUUGCCAUGGUAAUCCUGCUCAGUACGAGAGGAACCGCAGCUA
Tools used in this analysis
TargetScan, miRTarCLIP, and Piranha
Article / Accession Series
PMID: 23597149 / E-MTAB-1612
CLIP-seq Viewer
Link
CLIP-seq Support 18 for dataset ERR266300
Method / RBP
HITS-CLIP / AGO2
Cell line / Condition
Liver / B_Untreated
Location of target site
NM_153168 | 3UTR | CAGGAGGCCUAAGGCGAGCUCAGGGAGGACAGAAACCUCCCGUGGAGCAGAAGGGCAAAAGCUCGCUUGAUCUUGAUUUUCAGUAGGAAUACAGACCGUGAAAGCGGGGCCUCACGAUCCUUCUGACCUUUUGGGUUUUAAGCAGGAUGUGUCAGAAAAGUUACCACAGGGAUAACUGGCUUGUGGCGGCCAAGCGUUCAUAGCGACGUCGCUUUUUGAUCCUUCGAUGUCGGCUCUUCCUAUCAUUGUGAAGCAGAAUUCACCAAGCGUUGGAUUGUUCACCCACUAAUAGGGAACGUGAGCUGGGAUUAGACCGUCGUGAGACAGGUUAGUUUUACCCUACUGAUGAUGUGUUGUUGCCAUGGUAAUCCUGCUCAGUACGAGAGGAACCGCAGCU
Tools used in this analysis
TargetScan, miRTarCLIP, and Piranha
Article / Accession Series
PMID: 23597149 / E-MTAB-1612
CLIP-seq Viewer
Link
28 mmu-miR-125a-5p Target Genes:
Functional analysis:
ID
Target
Description
Validation methods
Strong evidence
Less strong evidence
MIRT001716
Lin28a
lin-28 homolog A (C. elegans)
1
1
MIRT005597
Trim71
tripartite motif-containing 71
4
3
MIRT006310
Cbx7
chromobox 7
2
1
MIRT006967
4632428N05Rik
V-set immunoregulatory receptor
2
1
MIRT054177
Ptpn18
protein tyrosine phosphatase, non-receptor type 18
2
1
MIRT054178
Ptpn7
protein tyrosine phosphatase, non-receptor type 7
2
1
MIRT054179
Ppp1ca
protein phosphatase 1, catalytic subunit, alpha isoform
2
1
MIRT054180
Ppp2ca
protein phosphatase 2 (formerly 2A), catalytic subunit, alpha isoform
2
1
MIRT054570
Traf6
TNF receptor-associated factor 6
3
1
MIRT580227
Tspan12
tetraspanin 12
2
2
MIRT582368
Mtf1
metal response element binding transcription factor 1
2
2
MIRT582450
Mgat4a
mannoside acetylglucosaminyltransferase 4, isoenzyme A
2
2
MIRT584884
Antxr2
anthrax toxin receptor 2
2
2
MIRT587193
Foxk1
forkhead box K1
2
2
MIRT588848
Snrnp40
small nuclear ribonucleoprotein 40 (U5)
2
2
MIRT591275
Lars2
leucyl-tRNA synthetase, mitochondrial
2
4
MIRT592914
Madd
MAP-kinase activating death domain
2
2
MIRT594893
Il1rn
interleukin 1 receptor antagonist
2
4
MIRT596427
Hif1an
hypoxia-inducible factor 1, alpha subunit inhibitor
3
3
MIRT599142
Dqx1
DEAQ RNA-dependent ATPase
2
2
MIRT599717
Aph1c
aph1 homolog C, gamma secretase subunit
2
2
MIRT600832
Gm14137
predicted gene 14137
2
2
MIRT604902
Jmy
junction-mediating and regulatory protein
2
2
MIRT605441
Stat1
signal transducer and activator of transcription 1
2
2
MIRT606092
Wdr25
WD repeat domain 25
2
2
MIRT732537
Tnfrsf1b
tumor necrosis factor receptor superfamily, member 1b
4
0
MIRT734700
VDR
vitamin D receptor
2
0
MIRT734824
Sox11
SRY (sex determining region Y)-box 11
2
0
miRNA-Drug Associations
miRNA
Small Melocule
FDA
CID
Detection Method
Condition
PMID
Year
Expression Pattern of miRNA
miR-125a
Budesonide
approved
5281004
Microarray
neonatal mice liver
20145010
2010
down-regulated
miR-125a
Phenethyl isothiocyanate(PEITC)
NULL
16741
Microarray
neonatal mice lung
20145010
2010
down-regulated
miR-125a
Chaihu Shugan San
NULL
NULL
Microarray
hippocampus
23947143
2013
down-regualted
miR-125a
Perfluorooctane sulfonate
NULL
74483
Microarray
zebrafish embryos
20878907
2011
down-regulated
miR-125a
Hydroxamic acid HDACi LAQ824
NULL
NULL
Microarray
breast cancer cell line SKBr3
16452179
2006
up-regulated
miR-125a
Enoxacin
approved
3229
Quantitative real-time PCR
HEK293 cells
18641635
2008
up-regulated
miR-125a
4-hydroxynonenal
NULL
5283344
Microarray
human leukemic HL-60 cell
19022373
2009
up-regulated
miR-125a
Valproate
approved
3121
Quantitative real-time PCR
CD4+, CD25- T cells
20427269
2010
down-regulated
miR-125a
Formaldehyde
NULL
712
Microarray
Human lung epithelial cells (A549)
21147603
2011
down-regulated
miR-125a
Enoxacin
approved
3229
Northern blot
HCT-116 and RKO colon cancer cell lines
21368194
2011
up-regulated
miR-125a
Enoxacin
approved
3229
Quantitative real-time PCR
HCT-116 and RKO colon cancer cell lines
21368194
2011
up-regulated
miR-125a
5-aza-2'-deoxycytidine (5-Aza-CdR)
approved
451668
Microarray
breast cancer MDA-MB231
22076154
2011
down-regulated
miR-125a-5p
Hexahydro-1,3,5-trinitro-1,3,5-triazine (RDX)
NULL
8490
Microarray
mouse brain
19270793
2009
up-regulated
miR-125a-5p
Hexahydro-1,3,5-trinitro-1,3,5-triazine (RDX)
NULL
8490
Microarray
mouse liver
19270793
2009
down-regulated
miR-125a-5p
Curcumin
NULL
969516
Microarray
HONE1 cells
24896104
2014
down-regulated
miR-125a-5p
5-Fluorouracil
approved
3385
Microarray
MCF-7 breast cancer cells
21506117
2011
down-regulated
miR-125a-5p
Arsenic trioxide
approved
14888
Quantitative real-time PCR
acute promyelocytic leukemia
22072212
2012
up-regulated
miR-125a-5p
Trastuzumab
approved
NULL
Microarray
SKBR3 cells.
22384020
2012
up-regulated
miR-125a-5p
Glucocorticoid
NULL
NULL
TaqMan low-density array
Eosinophilic esophagitis
22815788
2012
up-regulated
miR-125a-5p
Marine fungal metabolite 1386A
NULL
NULL
Microarray
MCF-7 breast cancer cells.
22159329
2012
down-regulated
miRNA-Drug Resistance Associations
miRNA
Drug Name
CID
NSC
FDA
Effect/Pattern
Detection Method
Level
Phenotype
Condition
mmu-miR-125a-5p
Paclitaxel
36314
NSC125973
approved
sensitive
Low
Colon Cancer
tissue and cell line (HT-29)