MIRT581057 [miRNA, mmu-miR-486b-5p

miRTarBase - #MIRT581057

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pre-miRNA Information
pre-miRNA	mmu-mir-486b
Genomic Coordinates	chr8: 23142573 - 23142662
Description	Mus musculus miR-486b stem-loop
Comment	None
RNA Secondary Structure

Mature miRNA Information
Mature miRNA	mmu-miR-486b-5p
Sequence	15\| UCCUGUACUGAGCUGCCCCGAG \|36
Evidence	Experimental
Experiments	Illumina
Putative Targets

Gene Information

Gene Symbol

Shc4

Synonyms

6230417E10Rik, 9930029B02Rik, Gm685, RaLP

Description

SHC (Src homology 2 domain containing) family, member 4

Transcript

NM_199022

Expression

Putative miRNA Targets on Shc4

3'UTR of Shc4
(miRNA target sites are highlighted)

>Shc4|NM_199022|3'UTR
   1 TGACTCCCGGAACTGTGTCAGTGCTATGAGAAGCATATTCCTTTGGTGCCAGGAACAGTGGCCGCTCAACCCTTTTCTTC
  81 ACACAAAGTAGAACATAGACTGTGAAACATGTCTTTCTTAGACCGCCACAGACCAGGTCTTTTATAAAACATAGAAGTAA
 161 CAAACTATCTTCTGAGTATGAAAATCAGAGAATAATAATTTTGGTCCATTTGGAAATGCGATACTCATCTGCACGGAGGT
 241 CACTTTTTAAAGGTCACATTGCATTGGTGAAAAGCTAAAAGCACAACTTCAATTTCAGATGCTAAAGACAACTTGAACTG
 321 CTCAGGCAGTGGTACGTGCCTTTACCTTGATAATCCGGGGACATTTTCCTATGGGGGAGATTAGTTACACGTGTCTTCAC
 401 GTTCTATAGCTACAGAACCAGTTGCCAAAAAAGTTCTTCCTTGCTAAAAACAGCAAGAAGCAGCATTTTGACTAGTAGTG
 481 TTGACTTTATTACATTTTGTTTAGTAGCACTTTTTGCTGCCATGTTAACAATGACACTGACATCAAATTCAGACTGTGCC
 561 TGTGCTTGTGGAATGAAAGCAAACACCGCTGATGGTTTCCCAATTCTGTCTCATTTGCTGATTGAGAGGCTGGGGCTCAA
 641 ATTCACTGGCCAGCGTTCCTCAGTCTTTGCTACCTGAACTGTCCGTAGGCAGCATGGGACACATTCAGGAAGCCAAATCT
 721 CTTGGTTAGTTCTGATTTGGAGTATTTGGTTATAAAAGACAGCAAACAAAGCCATTGTTCTTCATGCTCAGCCCATACTG
 801 GTGCCATTGAAAATGCATTAAGGCAATCTAAAGTATATGAAAATCTCCTTGTGATTGGCTGCCACTGCGCCCTGGTGTCA
 881 CCTCGGTATGTGTCTTATCACCATCTGTACGTGTGATCAGACAAAATGCAGAAGGGCTGGGAAAGGTCTGCTACACACCG
 961 GACAATGGTTCAACCAGTGGTGAGATTAAGAATTCTCAGAGAAGCCCAAGGCTCAGACTATTCACCACTGTGAGTCTTGG
1041 CAGGTCGCTAAACCTGTCTGGATTCCAGTTTTCTTGTCCATAAGATGAGGGAGCTTGAGGTGCACTCAGAGGGCCGTTGC
1121 TATCCTAACATAGTAGTTTTTTTCTTTGTTAAAAGTTAACACTGATAAGCAGACTGTGCAGTTGAGGGCAAATATTTAGG
1201 ATTTTTCCCTTTATTCTGTGTCTATACTCTACAGGTAACAGGTTTAGCCAAATTACACTCTCATAGTCTGACCCCAAGTG
1281 TTTCAGCATAAATCAGGTAATGTTGGTTTAGTGGATCTGGTTGTCTTTAGTAATAGCAGAAATGCTTCAGTCAGTCCTTA
1361 CTTGCCTATGCATATAAAGATACAGTCACTACAGGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGA
1441 GAGAGAGAGAGAGAGAGAGGAGAGAGGAGAGAGGAGAGAGGAGAGAGGAGAGAGGAGAGAGATCCTAAGCTTTCTGGATA
1521 GTTATCTCAACACCACTTCATTTTGGCTAAGTAGAGACAACTTAACCTTTGTGATTATGATGTATTTGGTAAGTTTTAAG
1601 TATAGTATGGGATCGTTCCTATGGGTAGAAATCATCAGAAATCAAGTACATTGAAGCCTGGCATTTTTACATAACAACTC
1681 ACCATTTTATTTCTGTCGCCACTGGCTTCTTAGGTAAGTTTGTTTCCTTTCCACAGCTAGAAAGTCGTGCATATTCCATT
1761 GCTTTTCCTCCATCTATCTTAGGTCTTAATCATTTTTCTTCGTAAGAGGGATCAGCATAGTGATAGGGACTCATAGGTAA
1841 CCTGCAGCAGAGACAGGGCGGGCCTACTGCCTCCTTCCAGCTGGGGAACGCAGACTGGGTGGCCAGCGGAGTTCCAGATG
1921 CAGGGGGCACTGTGGTGTGAGCCGCACGCATGGGCAGTCAACACTGGACTGGTGCTGTTGTAGCCTGGGAGGCAGATGCT
2001 GCACTTTCAGATGCCATAGACACTGTTCACCAACCCTAAAAGATGTAAGAAATGTCTGCATGCGGTTTTAATCTCATAGT
2081 CTCAACCTCTATTTTAAAATGGTGGTTCATTTGCCTATAAATATCTGTAAATGAGTTTTCTTTAAAAAAATAAATGATTA
2161 TTGCTTTA

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' gagccccGUCGAGUCAUGUCCu 5' \|\|\| \|\|\| \|\|\|\|\|\| Target 5' aaagataCAG-TCACTACAGGa 3'	1376 - 1396	130.00	-15.50
2	miRNA 3' gagccccgUCGAGUCAUGUCCu 5' \|\|: :\|\|\|\|::\|\| Target 5' aagttttaAGTATAGTATGGGa 3'	1591 - 1612	122.00	-12.00
3	miRNA 3' gagccccgucgagucAUGUCCu 5' \|\|\|\|\|\| Target 5' tctgtgtctatactcTACAGGt 3'	1215 - 1236	120.00	-9.90

Experimental Support 1 for Functional miRNA-Target Interaction

miRNA:Target

----

Validation Method

Conditions

Brain (Mouse neocortex)

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 Chi_BrainB_130_50. RNA binding protein: AGO. Condition:Brain B 2A8 P13 130 KD HITS-CLIP data was present in Chi_BrainC_130_50. RNA binding protein: AGO. Condition:Brain C 2A8 P13 130 KD ...

- Chi SW; Zang JB; Mele A; Darnell RB, 2009, Nature.

miRNA-target interactions (Provided by authors)

ID	Duplex structure	Position
1	miRNA 3' gagccccgucgagucaUGUCCu 5' \|\|\|\|\| Target 5' ----------------ACAGGa 3'	1 - 6

Article

Argonaute HITS-CLIP decodes microRNA-mRNA interaction maps.

- Chi SW; Zang JB; Mele A; Darnell RB

- Nature, 2009

MicroRNAs (miRNAs) have critical roles in the regulation of gene expression; however, as miRNA activity requires base pairing with only 6-8 nucleotides of messenger RNA, predicting target mRNAs is a major challenge. Recently, high-throughput sequencing of RNAs isolated by crosslinking immunoprecipitation (HITS-CLIP) has identified functional protein-RNA interaction sites. Here we use HITS-CLIP to covalently crosslink native argonaute (Ago, also called Eif2c) protein-RNA complexes in mouse brain. This produced two simultaneous data sets-Ago-miRNA and Ago-mRNA binding sites-that were combined with bioinformatic analysis to identify interaction sites between miRNA and target mRNA. We validated genome-wide interaction maps for miR-124, and generated additional maps for the 20 most abundant miRNAs present in P13 mouse brain. Ago HITS-CLIP provides a general platform for exploring the specificity and range of miRNA action in vivo, and identifies precise sequences for targeting clinically relevant miRNA-mRNA interactions.

LinkOut: [PMID: 19536157]

Experimental Support 2 for Functional miRNA-Target Interaction
miRNA:Target	----
Validation Method
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 ERR266286. RNA binding protein: AGO2. Condition:A_Liver partial hapatectomy 1h HITS-CLIP data was present in ERR266293. RNA binding protein: AGO2. Condition:A_Liver partial hapatectomy 36h HITS-CLIP data was present in ERR266295. RNA binding protein: AGO2. Condition:B_Liver partial hapatectomy 1h ... - Schug J; McKenna LB; Walton G; Hand N; et al., 2013, BMC genomics.
Article	Dynamic recruitment of microRNAs to their mRNA targets in the regenerating liver. - 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]

Experimental Support 3 for Functional miRNA-Target Interaction
miRNA:Target	----
Validation Method
Conditions	C2C12
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 GSM1385342. RNA binding protein: 聽AGO2. Condition:C2C12_GM_Ago2_CLIP-Seq_myoblast HITS-CLIP data was present in GSM1385343. RNA binding protein: 聽AGO2. Condition:C2C12_DM_Ago2_CLIP-Seq_myotubes ... - Zhang X; Zuo X; Yang B; Li Z; Xue Y; Zhou et al., 2014, Cell.
Article	MicroRNA directly enhances mitochondrial translation during muscle differentiation. - Zhang X; Zuo X; Yang B; Li Z; Xue Y; Zhou et al. - Cell, 2014 MicroRNAs are well known to mediate translational repression and mRNA degradation in the cytoplasm. Various microRNAs have also been detected in membrane-compartmentalized organelles, but the functional significance has remained elusive. Here, we report that miR-1, a microRNA specifically induced during myogenesis, efficiently enters the mitochondria where it unexpectedly stimulates, rather than represses, the translation of specific mitochondrial genome-encoded transcripts. We show that this positive effect requires specific miR:mRNA base-pairing and Ago2, but not its functional partner GW182, which is excluded from the mitochondria. We provide evidence for the direct action of Ago2 in mitochondrial translation by crosslinking immunoprecipitation coupled with deep sequencing (CLIP-seq), functional rescue with mitochondria-targeted Ago2, and selective inhibition of the microRNA machinery in the cytoplasm. These findings unveil a positive function of microRNA in mitochondrial translation and suggest a highly coordinated myogenic program via miR-1-mediated translational stimulation in the mitochondria and repression in the cytoplasm. LinkOut: [PMID: 25083871]