ID	Duplex structure	Position	Score	MFE
1	miRNA 3' ucgUGUAGGAACUC-UAGGUGUu 5' ||||| ||| |||||:| Target 5' tcaACATC--AGAGAATCCATAc 3'	363 - 383	143.00	-14.40
2	miRNA 3' ucguGUAGGA-ACUCUAGGUGuu 5' ::|| | ||||||||| Target 5' atttTGTCGTGAGAGATCCACtc 3'	594 - 616	138.00	-14.50
3	miRNA 3' ucgUGUAGGAACU-C-UAGGUGUu 5' || |::|||| | | |||:| Target 5' aaaACTTTTTTGATGAAACCATAc 3'	451 - 474	115.00	-8.20

Mutant ID	Mutant Position	Mutant Source
COSN20079425	30	COSMIC
COSN30530802	37	COSMIC
COSN31486894	41	COSMIC
COSN31570059	43	COSMIC
COSN4891648	46	COSMIC
COSN30534056	54	COSMIC
COSN18716512	125	COSMIC
COSN7448891	162	COSMIC
COSN8975507	320	COSMIC
COSN22620017	553	COSMIC

Mutant ID	Mutant Position	Mutant Source
rs765927489	2	dbSNP
rs1397031613	4	dbSNP
rs1169416430	7	dbSNP
rs200247745	10	dbSNP
rs1368049635	11	dbSNP
rs1318928500	17	dbSNP
rs772811659	22	dbSNP
rs927531991	30	dbSNP
rs1045985127	31	dbSNP
rs186220396	35	dbSNP
rs761459864	42	dbSNP
rs768769071	44	dbSNP
rs1188784429	45	dbSNP
rs768473445	46	dbSNP
rs1182170953	48	dbSNP
rs972726171	69	dbSNP
rs1026396662	70	dbSNP
rs994629893	71	dbSNP
rs1424815765	77	dbSNP
rs1468929921	82	dbSNP
rs963465291	83	dbSNP
rs1173820766	86	dbSNP
rs1407586073	88	dbSNP
rs183356999	96	dbSNP
rs1033388827	97	dbSNP
rs1391275612	102	dbSNP
rs1414603755	107	dbSNP
rs963078768	115	dbSNP
rs909975485	123	dbSNP
rs112408119	124	dbSNP
rs552094689	125	dbSNP
rs1223063356	128	dbSNP
rs1191892137	135	dbSNP
rs1281627343	138	dbSNP
rs1325741584	143	dbSNP
rs533924025	145	dbSNP
rs1231423440	160	dbSNP
rs1046707583	161	dbSNP
rs559722737	169	dbSNP
rs1218597037	173	dbSNP
rs1264264561	174	dbSNP
rs1204115061	179	dbSNP
rs372097471	182	dbSNP
rs1010218040	184	dbSNP
rs1196825526	189	dbSNP
rs190358999	200	dbSNP
rs1157532553	204	dbSNP
rs1046648	207	dbSNP
rs965970823	220	dbSNP
rs936654020	244	dbSNP
rs1298733739	259	dbSNP
rs377307964	260	dbSNP
rs1388051471	279	dbSNP
rs1301518929	282	dbSNP
rs1039740906	283	dbSNP
rs1234271976	284	dbSNP
rs1278994546	286	dbSNP
rs10383	289	dbSNP
rs772261150	292	dbSNP
rs1371566906	294	dbSNP
rs1287441316	306	dbSNP
rs1310313845	319	dbSNP
rs1433391600	320	dbSNP
rs1054252742	323	dbSNP
rs1451767157	323	dbSNP
rs1180681119	325	dbSNP
rs575518895	329	dbSNP
rs1470886426	330	dbSNP
rs556973863	332	dbSNP
rs1159166731	336	dbSNP
rs1176825409	337	dbSNP
rs1422479617	348	dbSNP
rs1435000123	348	dbSNP
rs1391229287	364	dbSNP
rs1387500563	369	dbSNP
rs929206228	373	dbSNP
rs1334048231	378	dbSNP
rs1449182091	390	dbSNP
rs1187560337	395	dbSNP
rs1310595107	396	dbSNP
rs906058952	402	dbSNP
rs371761063	404	dbSNP
rs571126369	404	dbSNP
rs1267562693	406	dbSNP
rs950277452	407	dbSNP
rs545314278	408	dbSNP
rs1248049453	413	dbSNP
rs1253687083	417	dbSNP
rs13103	424	dbSNP
rs1046679	425	dbSNP
rs879469146	426	dbSNP
rs909953240	426	dbSNP
rs1165401629	427	dbSNP
rs1368769721	428	dbSNP
rs1033439716	430	dbSNP
rs954284806	437	dbSNP
rs921739339	438	dbSNP
rs980501406	442	dbSNP
rs1234724516	446	dbSNP
rs1382162578	455	dbSNP
rs970911248	461	dbSNP
rs1315450680	462	dbSNP
rs1341433251	466	dbSNP
rs1025563826	470	dbSNP
rs1009858126	471	dbSNP
rs975916879	475	dbSNP
rs965920465	476	dbSNP
rs534340330	479	dbSNP
rs4664	482	dbSNP
rs1261897651	483	dbSNP
rs186042957	484	dbSNP
rs537240795	489	dbSNP
rs1228621452	490	dbSNP
rs376645460	491	dbSNP
rs1352015886	512	dbSNP
rs1427674157	514	dbSNP
rs1010316342	518	dbSNP
rs570274859	519	dbSNP
rs1033161355	523	dbSNP
rs1001260649	526	dbSNP
rs1171653729	528	dbSNP
rs1405361948	531	dbSNP
rs35120053	533	dbSNP
rs1468349151	539	dbSNP
rs905636652	542	dbSNP
rs1045836824	543	dbSNP
rs1381985967	546	dbSNP
rs1293818053	553	dbSNP
rs777402558	555	dbSNP
rs1218801211	558	dbSNP
rs1282305602	560	dbSNP
rs1320792804	564	dbSNP
rs551762850	567	dbSNP
rs1394681466	569	dbSNP
rs558457118	576	dbSNP
rs1014383804	582	dbSNP
rs899815763	583	dbSNP
rs1402056161	587	dbSNP
rs1303945158	590	dbSNP
rs897403976	590	dbSNP
rs755750209	593	dbSNP
rs944123699	599	dbSNP
rs1264974838	601	dbSNP
rs1037284496	602	dbSNP
rs1428936037	606	dbSNP
rs1431480091	606	dbSNP
rs941346297	608	dbSNP
rs890321687	615	dbSNP
rs1287646092	616	dbSNP
rs540159045	618	dbSNP
rs1401063093	634	dbSNP
rs1158595104	636	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.