ID	Duplex structure	Position	Score	MFE
1	miRNA 3' guCUGGACUCAUCGCGUUCCac 5' ||||| ||:| | |:|| Target 5' ctGACCT--GTGG-GGAGGGgg 3'	6 - 24	95.00	-15.20
2	miRNA 3' gucUGGACUCAUCGCGUUCCAc 5' :|:||| :||| || Target 5' gatGCTTGA----TGCACTGTt 3'	72 - 89	85.00	-6.30

Mutant ID	Mutant Position	Mutant Source
COSN30467059	22	COSMIC
COSN30475992	32	COSMIC
COSN31578230	33	COSMIC
COSN31559970	42	COSMIC
COSN28899462	45	COSMIC
COSN31533448	83	COSMIC
COSN28853551	85	COSMIC
COSN25485470	122	COSMIC
COSN20079996	123	COSMIC

Mutant ID	Mutant Position	Mutant Source
rs1266858194	7	dbSNP
rs1333080441	8	dbSNP
rs745324820	10	dbSNP
rs554702135	12	dbSNP
rs1317207999	13	dbSNP
rs1488901684	15	dbSNP
rs1228429653	16	dbSNP
rs1271792947	18	dbSNP
rs200214494	24	dbSNP
rs1220243932	28	dbSNP
rs746657706	29	dbSNP
rs1292029336	31	dbSNP
rs777457938	32	dbSNP
rs377688425	33	dbSNP
rs1327982983	34	dbSNP
rs749666787	35	dbSNP
rs1400216050	37	dbSNP
rs1006284372	41	dbSNP
rs886512314	42	dbSNP
rs759473871	44	dbSNP
rs1026285498	52	dbSNP
rs1034323602	53	dbSNP
rs1473788644	72	dbSNP
rs1163886589	75	dbSNP
rs1418943993	80	dbSNP
rs1464258502	80	dbSNP
rs1173165733	83	dbSNP
rs1001950654	94	dbSNP
rs1451654943	100	dbSNP
rs1332068217	104	dbSNP
rs1342220650	110	dbSNP
rs1448734150	117	dbSNP
rs1269051013	131	dbSNP
rs1337866237	132	dbSNP
rs1220076355	136	dbSNP

- Cell, 2013

MicroRNAs (miRNAs) play key roles in gene regulation, but reliable bioinformatic or experimental identification of their targets remains difficult. To provide an unbiased view of human miRNA targets, we developed a technique for ligation and sequencing of miRNA-target RNA duplexes associated with human AGO1. Here, we report data sets of more than 18,000 high-confidence miRNA-mRNA interactions. The binding of most miRNAs includes the 5' seed region, but around 60% of seed interactions are noncanonical, containing bulged or mismatched nucleotides. Moreover, seed interactions are generally accompanied by specific, nonseed base pairing. 18% of miRNA-mRNA interactions involve the miRNA 3' end, with little evidence for 5' contacts, and some of these were functionally validated. Analyses of miRNA:mRNA base pairing showed that miRNA species systematically differ in their target RNA interactions, and strongly overrepresented motifs were found in the interaction sites of several miRNAs. We speculate that these affect the response of RISC to miRNA-target binding.