>TRMT112|NM_016404|3'UTR
   1 TTGTGCCAGGCGCCAGTTTTTCTTGTTATGACTGTGTATTTTTGTTGATCTATACCCTGTTTCCGAATTCTGCCGTGTGT
  81 ATCCCCAACCCTTGACCCAATGACACCAAACACAGTGTTTTTGAGCTCGGTATTATATATTTTTTTCTCATTAAAGGTTT
 161 AAAACCAAAAGCGGTTTCTCTTTGCAGCAAATATACATTAAAATAGAGTCTCTGTACAGCCAAGGGCTCTGGGCCCTGGC
 241 TTGCCCCATGTCCCTGCGCCTCCCTGGCCAAACCCAAAAATAAATATAGTGTTATTGCTCTGCAGGGCATAGAGGCAGTG
 321 CTCTCCTACCCCCTGAGGAGGCTCGTTGGGAGCTGATGGGGAAGCCCTG

ID	Duplex structure	Position	Score	MFE
1	miRNA 3' aucucUUCCUGUC---GACACUCGAGa 5' || |||| :| ||||||| Target 5' acaccAAACACAGTGTTTTTGAGCTCg 3'	103 - 129	155.00	-12.70
2	miRNA 3' auCUCUUCCUGUCGACACUCGAga 5' |||:||| : |:|| ||||| Target 5' ctGAGGAGGCTCGTTGGGAGCTga 3'	333 - 356	130.00	-19.00
3	miRNA 3' aucucuuCCUGUCGACACUCGAGa 5' | ||||| |:|||| Target 5' agtctctGTACAGCCAAGGGCTCt 3'	207 - 230	113.00	-14.50

Mutant ID	Mutant Position	Mutant Source
COSN27000084	33	COSMIC
COSN31496670	47	COSMIC
COSN30502668	50	COSMIC
COSN2558076	51	COSMIC
COSN24396943	58	COSMIC
COSN30525184	128	COSMIC
COSN17076185	137	COSMIC
COSN31547245	178	COSMIC
COSN31960640	257	COSMIC

Mutant ID	Mutant Position	Mutant Source
rs1427270898	1	dbSNP
rs760170082	4	dbSNP
rs1375711364	6	dbSNP
rs776836709	11	dbSNP
rs751032853	15	dbSNP
rs539398953	16	dbSNP
rs893308432	21	dbSNP
rs760814525	22	dbSNP
rs1225071747	25	dbSNP
rs1244786681	25	dbSNP
rs1452397838	28	dbSNP
rs192294864	29	dbSNP
rs763739836	29	dbSNP
rs1203141967	30	dbSNP
rs1274146355	30	dbSNP
rs1486146826	32	dbSNP
rs747859882	35	dbSNP
rs758006261	38	dbSNP
rs774175841	38	dbSNP
rs922765396	38	dbSNP
rs1304754743	44	dbSNP
rs1193835289	47	dbSNP
rs1390374798	48	dbSNP
rs768562383	49	dbSNP
rs779967388	50	dbSNP
rs1193735211	52	dbSNP
rs752937694	53	dbSNP
rs1186145035	55	dbSNP
rs45463294	59	dbSNP
rs577934678	59	dbSNP
rs1395286609	64	dbSNP
rs1436263700	65	dbSNP
rs936440576	70	dbSNP
rs765448031	79	dbSNP
rs375161349	90	dbSNP
rs1314448637	95	dbSNP
rs1226241037	96	dbSNP
rs910207972	100	dbSNP
rs1348859239	101	dbSNP
rs1236684010	103	dbSNP
rs1218942361	106	dbSNP
rs1482776041	109	dbSNP
rs952669793	114	dbSNP
rs1362941317	115	dbSNP
rs1491547983	115	dbSNP
rs1491317731	116	dbSNP
rs760509012	121	dbSNP
rs1187374559	122	dbSNP
rs1253159020	130	dbSNP
rs1455196292	132	dbSNP
rs145155074	135	dbSNP
rs1364600564	136	dbSNP
rs1159552492	139	dbSNP
rs1391447686	140	dbSNP
rs149984080	141	dbSNP
rs1023266425	144	dbSNP
rs1012838753	147	dbSNP
rs1371741948	147	dbSNP
rs567342412	147	dbSNP
rs1239474197	148	dbSNP
rs1467580819	151	dbSNP
rs1327001716	157	dbSNP
rs1357289462	171	dbSNP
rs1253533713	172	dbSNP
rs959897966	178	dbSNP
rs1410274107	180	dbSNP
rs1266267807	182	dbSNP
rs1419248910	188	dbSNP
rs1182998472	208	dbSNP
rs1035509985	210	dbSNP
rs1455966422	214	dbSNP
rs572460127	219	dbSNP
rs679730	220	dbSNP
rs1448477431	222	dbSNP
rs1459540952	223	dbSNP
rs998629803	229	dbSNP
rs11541032	234	dbSNP
rs565583510	235	dbSNP
rs1392113548	240	dbSNP
rs373707219	245	dbSNP
rs1042743595	247	dbSNP
rs1236176902	253	dbSNP
rs1227530253	257	dbSNP
rs187444371	263	dbSNP
rs1308408132	265	dbSNP
rs369242666	268	dbSNP
rs1277175724	274	dbSNP
rs1264286551	290	dbSNP
rs866252902	300	dbSNP
rs1011618680	303	dbSNP
rs888783404	304	dbSNP
rs183554515	308	dbSNP
rs1315824478	312	dbSNP
rs3204919	312	dbSNP
rs544054283	314	dbSNP
rs1376912875	316	dbSNP
rs530174517	317	dbSNP
rs1162778561	319	dbSNP
rs561379177	320	dbSNP
rs879483780	323	dbSNP
rs1372228591	329	dbSNP
rs761700423	330	dbSNP
rs1428784565	331	dbSNP
rs1041170409	332	dbSNP
rs1226467391	333	dbSNP
rs1311910649	337	dbSNP
rs1307626489	343	dbSNP
rs1272082787	345	dbSNP
rs1482497750	350	dbSNP
rs1204911096	355	dbSNP
rs1166314308	358	dbSNP
rs1421495847	369	dbSNP
rs1180683934	377	dbSNP
rs1412303183	381	dbSNP
rs1413676307	383	dbSNP
rs1429237586	385	dbSNP
rs1181830488	387	dbSNP
rs1170520564	389	dbSNP
rs41294424	390	dbSNP
rs908585227	396	dbSNP
rs984142546	400	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.