ID	Duplex structure	Position	Score	MFE
1	miRNA 3' ucgugucUGAA-----CGACACUACAa 5' |||| :|||||||| Target 5' atctggcACTTTATAAATTGTGATGTa 3'	726 - 752	147.00	-14.26
2	miRNA 3' ucGUG-UCUGAACGACAC-UACAa 5' |:| || | |||||| |||| Target 5' ctCGCTAGTCAAGCTGTGAATGTa 3'	755 - 778	132.00	-13.70
3	miRNA 3' ucGUGUCUGAACGACAC-UACAa 5' :| || || || ||| |||| Target 5' gcTAAAG-CTGGCAGTGAATGTg 3'	311 - 332	127.00	-7.30

Mutant ID	Mutant Position	Mutant Source
COSM1660979	3	COSMIC
COSM5693351	8	COSMIC
COSM1361180	13	COSMIC
COSM938647	21	COSMIC
COSM3792517	36	COSMIC
COSM4777589	55	COSMIC
COSM7122598	60	COSMIC
COSM2205129	61	COSMIC
COSM6136828	62	COSMIC
COSM5346157	63	COSMIC
COSM6620007	63	COSMIC
COSM4926328	70	COSMIC
COSM3460085	73	COSMIC
COSM5580520	80	COSMIC
COSM7227440	96	COSMIC
COSM243477	97	COSMIC
COSM4849937	101	COSMIC
COSM4669197	102	COSMIC
COSM5949547	111	COSMIC
COSM5696414	113	COSMIC
COSM6620001	117	COSMIC
COSM9066392	122	COSMIC
COSM6619987	124	COSMIC
COSM5633827	138	COSMIC
COSM7598776	148	COSMIC
COSM2205128	150	COSMIC
COSM8412134	157	COSMIC
COSM4430152	168	COSMIC
COSM4041363	182	COSMIC
COSM1188461	183	COSMIC
COSM4622587	213	COSMIC
COSM8266468	228	COSMIC
COSM2205127	237	COSMIC
COSM2205126	238	COSMIC
COSM9466709	240	COSMIC
COSM9682514	255	COSMIC
COSM7464513	261	COSMIC
COSM4669196	268	COSMIC
COSM8550685	286	COSMIC
COSM8219450	294	COSMIC
COSM9014014	295	COSMIC
COSM5375014	299	COSMIC
COSM1676815	306	COSMIC
COSM3416782	316	COSMIC
COSM54384	317	COSMIC
COSM272458	365	COSMIC
COSM8342849	369	COSMIC
COSM5051540	382	COSMIC
COSM9617289	407	COSMIC
COSM938646	429	COSMIC
COSM1361179	440	COSMIC
COSM4669195	446	COSMIC
COSM9593529	457	COSMIC
COSM7789144	459	COSMIC
COSM3460084	461	COSMIC
COSM6619976	468	COSMIC
COSM938645	470	COSMIC
COSM4752045	475	COSMIC
COSM324919	480	COSMIC
COSM8617886	506	COSMIC
COSM938644	512	COSMIC
COSM4669194	513	COSMIC
COSM938643	518	COSMIC
COSM938642	519	COSMIC
COSM4895174	528	COSMIC
COSM3931617	541	COSMIC
COSN30743279	552	COSMIC
COSN31566830	556	COSMIC
COSN30155251	594	COSMIC
COSN30159637	617	COSMIC
COSN1147004	720	COSMIC
COSN30112699	758	COSMIC
COSN14492544	812	COSMIC
COSN14442204	843	COSMIC
COSN24609770	874	COSMIC

Mutant ID	Mutant Position	Mutant Source
rs767335762	11	dbSNP
rs761381989	12	dbSNP
rs1266097235	13	dbSNP
rs1291109213	14	dbSNP
rs371328465	20	dbSNP
rs763676110	21	dbSNP
rs201095477	32	dbSNP
rs775373364	33	dbSNP
rs927003563	35	dbSNP
rs1290081279	36	dbSNP
rs769605672	38	dbSNP
rs1203703629	39	dbSNP
rs1329347533	49	dbSNP
rs759274017	51	dbSNP
rs1387482218	54	dbSNP
rs367800608	60	dbSNP
rs772253137	61	dbSNP
rs1184415727	63	dbSNP
rs79552778	65	dbSNP
rs778912498	66	dbSNP
rs1160761901	67	dbSNP
rs1163985928	68	dbSNP
rs1321887575	81	dbSNP
rs375234262	83	dbSNP
rs878879989	87	dbSNP
rs976348698	97	dbSNP
rs535610393	98	dbSNP
rs1245791745	100	dbSNP
rs780659467	104	dbSNP
rs1407267158	105	dbSNP
rs1465146378	106	dbSNP
rs372208056	107	dbSNP
rs140741615	108	dbSNP
rs965803693	113	dbSNP
rs202247225	116	dbSNP
rs756917174	119	dbSNP
rs111761506	122	dbSNP
rs150951809	123	dbSNP
rs200055967	127	dbSNP
rs142547870	129	dbSNP
rs752649925	133	dbSNP
rs1389763799	135	dbSNP
rs570016104	136	dbSNP
rs765096929	137	dbSNP
rs759470076	140	dbSNP
rs957278438	147	dbSNP
rs1402077640	148	dbSNP
rs1455389279	155	dbSNP
rs1173720763	165	dbSNP
rs35671069	171	dbSNP
rs776471356	171	dbSNP
rs766177185	182	dbSNP
rs1187468293	185	dbSNP
rs951655638	186	dbSNP
rs368158820	190	dbSNP
rs774594835	192	dbSNP
rs768642984	198	dbSNP
rs375715809	202	dbSNP
rs776145639	212	dbSNP
rs1202129537	215	dbSNP
rs1207870603	225	dbSNP
rs770489821	233	dbSNP
rs1350095728	241	dbSNP
rs746362702	243	dbSNP
rs781457861	248	dbSNP
rs1366190046	249	dbSNP
rs774768463	252	dbSNP
rs900613675	270	dbSNP
rs1272219121	278	dbSNP
rs1446242687	290	dbSNP
rs7137533	293	dbSNP
rs746668837	294	dbSNP
rs777431817	296	dbSNP
rs995767047	309	dbSNP
rs1390514377	314	dbSNP
rs1431552996	316	dbSNP
rs1368096477	323	dbSNP
rs757913295	326	dbSNP
rs752132555	329	dbSNP
rs764717286	333	dbSNP
rs1421162128	338	dbSNP
rs1479836389	342	dbSNP
rs1179806087	365	dbSNP
rs754960381	366	dbSNP
rs1171614009	374	dbSNP
rs905471781	377	dbSNP
rs1237875538	378	dbSNP
rs1400936699	386	dbSNP
rs753786665	393	dbSNP
rs766120931	401	dbSNP
rs1251067671	407	dbSNP
rs1414537553	411	dbSNP
rs1204523298	413	dbSNP
rs181542791	425	dbSNP
rs774451227	429	dbSNP
rs1226851672	442	dbSNP
rs1324302170	443	dbSNP
rs1200599835	445	dbSNP
rs764345990	446	dbSNP
rs763263714	454	dbSNP
rs1297370920	455	dbSNP
rs1417071317	458	dbSNP
rs763274346	459	dbSNP
rs769971620	465	dbSNP
rs868684130	466	dbSNP
rs1273569334	473	dbSNP
rs1052436238	475	dbSNP
rs1355797209	487	dbSNP
rs746415665	488	dbSNP
rs371420705	491	dbSNP
rs925282811	496	dbSNP
rs886569319	506	dbSNP
rs766398707	511	dbSNP
rs552563059	512	dbSNP
rs777291280	523	dbSNP
rs1463736781	532	dbSNP
rs771471072	532	dbSNP
rs747779716	536	dbSNP
rs1480975218	541	dbSNP
rs1208271621	547	dbSNP
rs778437920	553	dbSNP
rs754447478	557	dbSNP
rs555054269	559	dbSNP
rs1043740457	560	dbSNP
rs779984888	562	dbSNP
rs1208500830	563	dbSNP
rs189968218	571	dbSNP
rs750299811	579	dbSNP
rs767407050	581	dbSNP
rs931902951	584	dbSNP
rs763315430	587	dbSNP
rs1173844666	595	dbSNP
rs1440990923	596	dbSNP
rs1385761857	597	dbSNP
rs563741832	601	dbSNP
rs1320742969	602	dbSNP
rs1314167580	603	dbSNP
rs1389913985	609	dbSNP
rs1413491435	610	dbSNP
rs899395230	629	dbSNP
rs762896446	638	dbSNP
rs140573371	640	dbSNP
rs770022713	669	dbSNP
rs748225054	671	dbSNP
rs1406212855	678	dbSNP
rs1158278811	683	dbSNP
rs1473240971	684	dbSNP
rs1420130415	687	dbSNP
rs1228072858	701	dbSNP
rs776477965	702	dbSNP
rs1268999418	704	dbSNP
rs927036348	719	dbSNP
rs7032	725	dbSNP
rs1266354119	730	dbSNP
rs1256654078	731	dbSNP
rs1216376636	745	dbSNP
rs559739172	754	dbSNP
rs983199926	757	dbSNP
rs1448556832	758	dbSNP
rs566062111	767	dbSNP
rs1281884601	775	dbSNP
rs1221739563	777	dbSNP
rs1222913652	789	dbSNP
rs1327827846	790	dbSNP
rs1292177073	801	dbSNP
rs988648503	811	dbSNP
rs1387874429	812	dbSNP
rs957308872	815	dbSNP
rs1294605120	816	dbSNP
rs1348776395	834	dbSNP
rs951811668	842	dbSNP
rs1027312391	845	dbSNP
rs1355410272	851	dbSNP
rs964649590	856	dbSNP
rs1433467809	861	dbSNP
rs1264648548	864	dbSNP
rs1356721292	866	dbSNP
rs1211627808	877	dbSNP
rs1249526074	881	dbSNP
rs1482466779	885	dbSNP
rs746846269	886	dbSNP
rs1343860850	887	dbSNP
rs1182294203	889	dbSNP

- 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.

- 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.