>MRPS18B|NM_014046|3'UTR
   1 GAGCTGTAGACTGGGAAGAGAGGCCAGGCGTGGTGGCTCACTCCTGTAATCCCAGCACTTTGGGAAGCCAAGGTGGGCTG
  81 ATCACTTGATCCCAGGAGTTTGAGACCAGCCTGGGCACCATGGTGAAACCTCGTCTTTACCAAAAAATACAAAAATTAGC
 161 TGGGTGTGGTGGTGCACACCTGTAGTCTCAACTATTGGGGAGGCTAAGGTAGGATCACTTGATCCCAGGAGGCGGAGGTT
 241 GCAGTGAGTTGCAGTCACACCCCTGCACTCCAGCCTGGGTGACAGCTAGACCCTGTCTCAAAAAAAAAAAAAAAGACTGG
 321 GAAGAGAGCTAGAGGGACTAGGAGATAATGTGTATGTAGGTTTATGTGATGGGATATCACCCTGAAGAGTTGTGTCTTTT
 401 GTGGCCAGTGACAAATCCAGGAAATGAATGTTGCTGATAGGGATAAATCTTGAGGCTGAGGGCGGGTGGTACAGATGTGT
 481 ATGGGAAACCCCAACCCCTATATATTGTAAATAGATGGGCTGGGCTAAACATTGTTGCCGTTTCATACTTCTACCAACTC
 561 AGCTTTTACACAATAAAGCTCTACTGTCTCTGGTTTGCTTAA

ID	Duplex structure	Position	Score	MFE
1	miRNA 3' accuaacaaaGAAAACGGCAc 5' :| ||||||| Target 5' gggctaaacaTTGTTGCCGTt 3'	522 - 542	143.00	-10.35
2	miRNA 3' acCU-AACAAAGAAAACGGCac 5' || |||| |||||||: | Target 5' aaGAGTTGTGTCTTTTGTGGcc 3'	385 - 406	111.00	-11.70
3	miRNA 3' acCUAAC-AAAGAAAACGGCAc 5' |:||| | |||| || Target 5' gaGGTTGCAGTGAGTTGCAGTc 3'	235 - 256	111.00	-8.00

Mutant ID	Mutant Position	Mutant Source
COSN30146219	19	COSMIC
COSN31481223	42	COSMIC
COSN26985092	43	COSMIC
COSN30152272	89	COSMIC
COSN30474641	112	COSMIC
COSN9780199	427	COSMIC

Mutant ID	Mutant Position	Mutant Source
rs1392874952	10	dbSNP
rs756892909	12	dbSNP
rs767152122	13	dbSNP
rs758697434	18	dbSNP
rs750043003	23	dbSNP
rs1274737063	24	dbSNP
rs1331219682	25	dbSNP
rs756535909	26	dbSNP
rs780379042	28	dbSNP
rs749806087	29	dbSNP
rs755445924	30	dbSNP
rs748208549	31	dbSNP
rs377043280	33	dbSNP
rs907602867	35	dbSNP
rs747231378	37	dbSNP
rs1467733698	38	dbSNP
rs1181279985	39	dbSNP
rs769769516	40	dbSNP
rs1444641034	41	dbSNP
rs762806914	42	dbSNP
rs1371217307	43	dbSNP
rs1463374744	45	dbSNP
rs1045871717	55	dbSNP
rs913027140	57	dbSNP
rs928767818	67	dbSNP
rs1433997484	68	dbSNP
rs1310901759	69	dbSNP
rs551582747	73	dbSNP
rs937600204	74	dbSNP
rs1458082490	76	dbSNP
rs1238965548	77	dbSNP
rs1200792300	79	dbSNP
rs1440705911	83	dbSNP
rs142489658	84	dbSNP
rs1042893123	87	dbSNP
rs774164487	92	dbSNP
rs1278336806	93	dbSNP
rs183236532	95	dbSNP
rs1041841223	96	dbSNP
rs1294333886	97	dbSNP
rs1239852117	119	dbSNP
rs903267313	133	dbSNP
rs759210306	134	dbSNP
rs1235813166	141	dbSNP
rs1332911051	142	dbSNP
rs1450024746	142	dbSNP
rs1358018300	155	dbSNP
rs187747154	157	dbSNP
rs1334238166	165	dbSNP
rs1018799852	167	dbSNP
rs1041071383	178	dbSNP
rs965840376	182	dbSNP
rs1157993132	188	dbSNP
rs1440032697	191	dbSNP
rs900844887	195	dbSNP
rs201971528	196	dbSNP
rs1349265430	199	dbSNP
rs1471924938	201	dbSNP
rs1237188375	215	dbSNP
rs192259088	218	dbSNP
rs1444249560	226	dbSNP
rs951776033	228	dbSNP
rs371876825	234	dbSNP
rs556011045	235	dbSNP
rs1311941008	242	dbSNP
rs541339970	242	dbSNP
rs1227024802	244	dbSNP
rs1377946139	248	dbSNP
rs1487051178	251	dbSNP
rs1006382846	252	dbSNP
rs907655075	254	dbSNP
rs961772386	255	dbSNP
rs1358116421	260	dbSNP
rs1297431456	261	dbSNP
rs1420243517	264	dbSNP
rs1362441609	265	dbSNP
rs1161437928	266	dbSNP
rs564746909	267	dbSNP
rs1404593920	272	dbSNP
rs1413318500	278	dbSNP
rs1261267621	279	dbSNP
rs1182687579	281	dbSNP
rs374097554	292	dbSNP
rs1261135546	295	dbSNP
rs1195608087	299	dbSNP
rs1328868249	299	dbSNP
rs1204213149	300	dbSNP
rs1229680022	300	dbSNP
rs1290094124	300	dbSNP
rs1321518089	300	dbSNP
rs1337690105	300	dbSNP
rs35997671	300	dbSNP
rs368057496	300	dbSNP
rs1395711855	301	dbSNP
rs71552012	316	dbSNP
rs543517359	318	dbSNP
rs1400148894	324	dbSNP
rs1453733957	330	dbSNP
rs1173867800	342	dbSNP
rs1291765062	344	dbSNP
rs1435433892	350	dbSNP
rs146455019	356	dbSNP
rs1009857086	363	dbSNP
rs1454103739	369	dbSNP
rs937484268	372	dbSNP
rs1407309664	373	dbSNP
rs1001627477	375	dbSNP
rs1056073045	379	dbSNP
rs1036065937	387	dbSNP
rs1478215634	390	dbSNP
rs1190010512	393	dbSNP
rs1488320293	395	dbSNP
rs1247669799	398	dbSNP
rs914794371	404	dbSNP
rs1315678495	406	dbSNP
rs75407659	409	dbSNP
rs372073637	418	dbSNP
rs1299057965	433	dbSNP
rs559468285	441	dbSNP
rs1367976083	443	dbSNP
rs1326012399	453	dbSNP
rs1008331581	464	dbSNP
rs376685424	465	dbSNP
rs901701453	469	dbSNP
rs1444392335	470	dbSNP
rs996400748	474	dbSNP
rs978563947	479	dbSNP
rs1299804196	481	dbSNP
rs769188191	488	dbSNP
rs369731283	494	dbSNP
rs952051955	495	dbSNP
rs1260460763	497	dbSNP
rs1327365227	499	dbSNP
rs1215720846	501	dbSNP
rs1193253588	505	dbSNP
rs111850078	529	dbSNP
rs1237138256	531	dbSNP
rs1198919748	532	dbSNP
rs976544709	534	dbSNP
rs922239561	540	dbSNP
rs1312700568	545	dbSNP
rs536800195	546	dbSNP
rs961658373	548	dbSNP
rs1047198864	549	dbSNP
rs1189456778	552	dbSNP
rs112418429	554	dbSNP
rs928367917	556	dbSNP
rs1037832576	557	dbSNP
rs958892170	558	dbSNP
rs1301160973	559	dbSNP
rs1465642298	569	dbSNP
rs1360229250	571	dbSNP
rs1158134081	574	dbSNP
rs1409417835	576	dbSNP
rs1438179913	577	dbSNP
rs1462695722	583	dbSNP
rs1380082929	587	dbSNP
rs1178806569	589	dbSNP
rs992065651	589	dbSNP
rs914708726	591	dbSNP
rs1199362115	593	dbSNP
rs111609724	596	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.