>ZNF567|NM_152603|3'UTR
   1 ATGATGTGGTTTCTTATATGAATTCTTTACAAGCTGTTGTAAACATTTAGTTTTAAAAAGAAAAGCATGCTGAAACATGT
  81 TAATGTAATTTTAAATCACAAGTCTAATAATTATTAAAGTACCATACGGAATAACTGTCTACTGTTTACTAGCATATAAA
 161 ATAAGTATGATCATTATTATTGAACTCTATCAGCTATGAAGCTAAATTTTAAAGTCAACTGCTCTTCCTACTGACTCAAA
 241 TAGTTTATTTTTTAAAAATACTTATATAATACATGCAGAGACAAGATACACAATGATTATAAGTATTAATCTCCATAAGA
 321 GAAAATATTTATGAACTATATTTCTCATTGCACTCTGTAATAAAAAGCAGTTAGTTGTTACTTACCTAAGAGTTACCACT
 401 TCCGTAGCCTATAACATCAAAACGTAGTTTTTGCATGTTTTCAATTTTATAAATATATATTTTATCAGACATCATGAATT
 481 ATTTTGTGTCTTGCTTATTTCACTCAATTTTTTAAGATCTGTACATTATTGCATGTGGCAGTAGTGTATTTTCATTTTGC
 561 ATACTATTCCATTTTAAGAATATATTGCTGTTTATCCTATTGATGGATATTTGTATTTTTTATACTTTTGTGTAATAATA
 641 AAAATACTGCTGTAAATATTCTTGTTTAAAAAAAAAAAAAAAAAAAAAA

ID	Duplex structure	Position	Score	MFE
1	miRNA 3' ucGUCGUAAC-----AU-GUCCCGAUACu 5' :| :|||| || || |||||| Target 5' atTATTATTGAACTCTATCA--GCTATGa 3'	173 - 199	124.00	-9.20
2	miRNA 3' ucGUCGUAACAUGUCCCGAUAcu 5' || :|||| |:: ||| :| Target 5' taCATTATTGCATGTGGCAGTag 3'	522 - 544	101.00	-8.90
3	miRNA 3' ucgucGUAACAUGUCCCGAUAcu 5' :|||| | || ||| Target 5' tatccTATTG---ATGGATATtt 3'	593 - 612	99.00	-5.30

Mutant ID	Mutant Position	Mutant Source
COSN31543565	18	COSMIC
COSN31558021	33	COSMIC
COSN27006256	71	COSMIC
COSN7125767	320	COSMIC

Mutant ID	Mutant Position	Mutant Source
rs1475755001	7	dbSNP
rs1181847720	9	dbSNP
rs374004762	21	dbSNP
rs749314115	26	dbSNP
rs367886077	34	dbSNP
rs1444656453	45	dbSNP
rs774485884	46	dbSNP
rs762086545	47	dbSNP
rs933885690	60	dbSNP
rs1464952768	61	dbSNP
rs1428976674	72	dbSNP
rs1041564163	77	dbSNP
rs1388221739	79	dbSNP
rs902993869	85	dbSNP
rs1043044918	97	dbSNP
rs999955723	98	dbSNP
rs1179692541	100	dbSNP
rs1481413201	104	dbSNP
rs1032797802	107	dbSNP
rs534982408	128	dbSNP
rs8109548	129	dbSNP
rs1001035702	138	dbSNP
rs1012610332	141	dbSNP
rs1366289487	147	dbSNP
rs1470889741	148	dbSNP
rs1225646138	155	dbSNP
rs1351365319	157	dbSNP
rs553278721	169	dbSNP
rs1307716327	179	dbSNP
rs1408041801	180	dbSNP
rs1159204438	185	dbSNP
rs765495539	188	dbSNP
rs568544657	190	dbSNP
rs1410537290	198	dbSNP
rs1458355794	210	dbSNP
rs575658103	211	dbSNP
rs899616298	212	dbSNP
rs996984596	219	dbSNP
rs1412220557	221	dbSNP
rs1178488970	222	dbSNP
rs1029362135	223	dbSNP
rs1024378596	228	dbSNP
rs1402732980	228	dbSNP
rs971017808	232	dbSNP
rs982749329	234	dbSNP
rs982446460	236	dbSNP
rs1025815343	237	dbSNP
rs1218362342	238	dbSNP
rs1015468967	240	dbSNP
rs1287955927	247	dbSNP
rs1226852351	249	dbSNP
rs1347404777	252	dbSNP
rs1387237687	254	dbSNP
rs1395174498	254	dbSNP
rs1389950337	256	dbSNP
rs1333771462	264	dbSNP
rs1187985964	266	dbSNP
rs1455150195	267	dbSNP
rs1157883512	269	dbSNP
rs145705960	269	dbSNP
rs1338876834	271	dbSNP
rs554337072	274	dbSNP
rs1471408352	275	dbSNP
rs1430744955	281	dbSNP
rs1198986578	288	dbSNP
rs147666808	290	dbSNP
rs1289111933	316	dbSNP
rs1188868019	318	dbSNP
rs910009380	325	dbSNP
rs926455934	333	dbSNP
rs1267903338	346	dbSNP
rs543399736	361	dbSNP
rs1325963791	374	dbSNP
rs942769548	378	dbSNP
rs527469572	379	dbSNP
rs917978835	382	dbSNP
rs1346165928	384	dbSNP
rs945386922	387	dbSNP
rs200408786	389	dbSNP
rs1253677696	391	dbSNP
rs1483852703	392	dbSNP
rs1042350866	395	dbSNP
rs1182419916	395	dbSNP
rs1054520	396	dbSNP
rs1471323898	402	dbSNP
rs184852642	404	dbSNP
rs142319592	405	dbSNP
rs1039255746	412	dbSNP
rs903095871	424	dbSNP
rs549963525	425	dbSNP
rs1170555870	431	dbSNP
rs1247753646	435	dbSNP
rs997668713	439	dbSNP
rs1051309961	444	dbSNP
rs890842933	452	dbSNP
rs1431915419	454	dbSNP
rs1308858624	455	dbSNP
rs146382354	456	dbSNP
rs1230470314	472	dbSNP
rs1342817934	485	dbSNP
rs768284795	488	dbSNP
rs1432601619	491	dbSNP
rs1342114885	492	dbSNP
rs1013053697	494	dbSNP
rs1023993173	508	dbSNP
rs1395102621	508	dbSNP
rs906823988	514	dbSNP
rs1033501435	517	dbSNP
rs1430901040	521	dbSNP
rs1390077815	526	dbSNP
rs1167306216	534	dbSNP
rs1473975329	540	dbSNP
rs1003807551	542	dbSNP
rs773868452	547	dbSNP
rs959478923	549	dbSNP
rs371920597	553	dbSNP
rs542031274	563	dbSNP
rs1440941927	573	dbSNP
rs1252699453	600	dbSNP
rs991981636	601	dbSNP
rs917995873	609	dbSNP
rs1254673684	616	dbSNP
rs1273825451	626	dbSNP
rs1226170084	633	dbSNP
rs761582170	637	dbSNP
rs1344736763	648	dbSNP
rs1243556661	657	dbSNP
rs776472116	659	dbSNP
rs1273383836	661	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.