ID	Duplex structure	Position	Score	MFE
1	miRNA 3' ccuguaacaAAGUCA-CGGGUUCa 5' | || | |||:||| Target 5' aactaagacTGCACTAGCCTAAGc 3'	149 - 172	130.00	-8.70
2	miRNA 3' ccuguaacaaagucacGGGUUCa 5' |||||| Target 5' atcatcacataccctaCCCAAGa 3'	492 - 514	120.00	-9.20
3	miRNA 3' ccuguaacaAAGUCACGGGUUCa 5' | ||| |||| || Target 5' acttaagccTACAG-GCCCTAGc 3'	58 - 79	117.00	-11.50

Mutant ID	Mutant Position	Mutant Source
rs1220214422	2	dbSNP
rs1324419942	3	dbSNP
rs1294621693	8	dbSNP
rs753966712	9	dbSNP
rs764344566	11	dbSNP
rs186016507	12	dbSNP
rs748208942	18	dbSNP
rs1033235157	22	dbSNP
rs1329392845	33	dbSNP
rs1461049899	44	dbSNP
rs996035552	64	dbSNP
rs1243595605	65	dbSNP
rs747903287	71	dbSNP
rs1485213804	72	dbSNP
rs781329817	79	dbSNP
rs1268156071	87	dbSNP
rs1309962211	88	dbSNP
rs1481438039	90	dbSNP
rs1174577776	94	dbSNP
rs1428918037	99	dbSNP
rs1008856519	105	dbSNP
rs781144231	109	dbSNP
rs886100826	110	dbSNP
rs1047401446	111	dbSNP
rs1445361295	120	dbSNP
rs527992637	126	dbSNP
rs1370579733	131	dbSNP
rs1294869495	138	dbSNP
rs754936496	139	dbSNP
rs1349591063	151	dbSNP
rs1301668351	154	dbSNP
rs149160326	166	dbSNP
rs755125460	175	dbSNP
rs180767302	181	dbSNP
rs868459787	185	dbSNP
rs10521478	192	dbSNP
rs1315438091	193	dbSNP
rs1215748228	195	dbSNP
rs1266501480	198	dbSNP
rs1417358901	203	dbSNP
rs1197415050	204	dbSNP
rs373436446	207	dbSNP
rs938169664	208	dbSNP
rs1488282732	210	dbSNP
rs1440594144	211	dbSNP
rs928161205	221	dbSNP
rs764257563	231	dbSNP
rs1267121101	234	dbSNP
rs1418236441	235	dbSNP
rs562551311	240	dbSNP
rs1367414015	242	dbSNP
rs775806985	243	dbSNP
rs1411289874	245	dbSNP
rs1277371165	246	dbSNP
rs1371665103	251	dbSNP
rs75194172	275	dbSNP
rs111384380	276	dbSNP
rs77988349	277	dbSNP
rs1046623551	278	dbSNP
rs1239362010	281	dbSNP
rs1314552720	285	dbSNP
rs1362302487	292	dbSNP
rs574967656	313	dbSNP
rs1302767220	314	dbSNP
rs76243789	321	dbSNP
rs77862174	322	dbSNP
rs1483400139	323	dbSNP
rs945638069	328	dbSNP
rs1231440936	333	dbSNP
rs76449964	339	dbSNP
rs1480410713	343	dbSNP
rs1219370148	345	dbSNP
rs1366446719	346	dbSNP
rs1386840645	351	dbSNP
rs892342792	353	dbSNP
rs75459765	358	dbSNP
rs1281030647	369	dbSNP
rs76365251	371	dbSNP
rs768048981	372	dbSNP
rs913852788	379	dbSNP
rs5960403	385	dbSNP
rs773967357	386	dbSNP
rs989513921	394	dbSNP
rs373514350	397	dbSNP
rs191438385	399	dbSNP
rs1244460793	400	dbSNP
rs1314901645	403	dbSNP
rs921343219	404	dbSNP
rs1216442530	414	dbSNP
rs1270964077	415	dbSNP
rs1427436149	423	dbSNP
rs750817191	440	dbSNP
rs975517615	455	dbSNP
rs762456736	457	dbSNP
rs5960402	459	dbSNP
rs917554411	460	dbSNP
rs1182938700	482	dbSNP
rs1248623312	484	dbSNP
rs1476334647	491	dbSNP
rs1165720770	494	dbSNP
rs757722034	499	dbSNP
rs111749202	506	dbSNP

- 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.

- 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.