ID	Duplex structure	Position	Score	MFE
1	miRNA 3' ggCCAGGCAUGUUUGAGACGUc 5' |||:| | : ||||||| Target 5' agGGTTCTT--TGTCTCTGCAt 3'	42 - 61	148.00	-13.90
2	miRNA 3' ggccagGCAUGUU--UGAGACGUc 5' | || :| :|||||| Target 5' aatgcaCTTAGGATGTTTCTGCAt 3'	254 - 277	126.00	-8.00
3	miRNA 3' ggccAGG--CA-UGU--UUGAGACGUc 5' ||| || ||| | || |||| Target 5' ttctTCCAGGTGACATCACCTATGCAc 3'	129 - 155	122.00	-8.50

Mutant ID	Mutant Position	Mutant Source
COSM1030267	1	COSMIC
COSN31598743	2	COSMIC
COSN15788881	45	COSMIC
COSN30178589	45	COSMIC
COSN19355224	127	COSMIC
COSN16542886	577	COSMIC
COSN15870920	611	COSMIC
COSN27266822	1027	COSMIC
COSN21432119	1742	COSMIC
COSN31779346	1985	COSMIC

Mutant ID	Mutant Position	Mutant Source
rs192198222	2	dbSNP
rs1358955065	4	dbSNP
rs765566959	5	dbSNP
rs1289033013	7	dbSNP
rs1215353744	10	dbSNP
rs1442501004	12	dbSNP
rs750603974	13	dbSNP
rs375471976	15	dbSNP
rs140249992	17	dbSNP
rs556052005	18	dbSNP
rs751495214	19	dbSNP
rs1236329590	23	dbSNP
rs955070761	25	dbSNP
rs983627248	32	dbSNP
rs754941271	37	dbSNP
rs369722524	41	dbSNP
rs200039707	45	dbSNP
rs781265873	46	dbSNP
rs574561112	53	dbSNP
rs535007432	54	dbSNP
rs973713001	56	dbSNP
rs1412764111	60	dbSNP
rs1397336206	61	dbSNP
rs919560712	66	dbSNP
rs948485851	68	dbSNP
rs1175269834	71	dbSNP
rs923263227	74	dbSNP
rs954737322	76	dbSNP
rs552928551	81	dbSNP
rs980236109	82	dbSNP
rs928391820	103	dbSNP
rs938546732	106	dbSNP
rs1052954297	107	dbSNP
rs1229111309	109	dbSNP
rs751746246	115	dbSNP
rs1481874505	116	dbSNP
rs767487515	117	dbSNP
rs1037857263	118	dbSNP
rs1347677563	119	dbSNP
rs8178430	129	dbSNP
rs535161691	136	dbSNP
rs1241851687	137	dbSNP
rs556665856	143	dbSNP
rs1336360526	151	dbSNP
rs1306403047	159	dbSNP
rs937583636	160	dbSNP
rs947252078	166	dbSNP
rs1305866593	167	dbSNP
rs1057379401	173	dbSNP
rs879854017	174	dbSNP
rs1305825640	176	dbSNP
rs575017442	178	dbSNP
rs1374647730	186	dbSNP
rs1009915537	193	dbSNP
rs1471122118	202	dbSNP
rs1363807878	207	dbSNP
rs1180445925	210	dbSNP
rs1041422601	213	dbSNP
rs1043090339	215	dbSNP
rs904261608	219	dbSNP
rs1211186807	225	dbSNP
rs184042271	235	dbSNP
rs200266441	238	dbSNP
rs557678234	239	dbSNP
rs573046709	245	dbSNP
rs1207351526	248	dbSNP
rs1276038519	253	dbSNP
rs1226619099	255	dbSNP
rs900478225	258	dbSNP
rs1357500327	262	dbSNP
rs999930279	265	dbSNP
rs1294079652	277	dbSNP
rs1414427468	280	dbSNP
rs1018054847	286	dbSNP
rs1331960659	290	dbSNP
rs1402286897	298	dbSNP
rs1385569662	304	dbSNP
rs142225927	308	dbSNP
rs1455144662	316	dbSNP
rs1419434395	318	dbSNP
rs1209268465	322	dbSNP
rs559691711	325	dbSNP
rs373335987	327	dbSNP
rs45549138	333	dbSNP
rs890538738	334	dbSNP
rs1195776131	337	dbSNP
rs1447979040	339	dbSNP
rs1284158138	342	dbSNP
rs1207412758	346	dbSNP
rs1005503462	351	dbSNP
rs150694208	351	dbSNP
rs1015007696	352	dbSNP
rs1273891197	353	dbSNP
rs1232836237	354	dbSNP
rs1354490868	355	dbSNP
rs1404318314	355	dbSNP
rs1411145631	355	dbSNP
rs58370026	355	dbSNP
rs759108613	355	dbSNP
rs76567948	355	dbSNP
rs777991215	355	dbSNP
rs796182073	355	dbSNP
rs77399922	357	dbSNP
rs1169339584	359	dbSNP
rs963607068	363	dbSNP
rs75889204	371	dbSNP
rs1416901041	373	dbSNP
rs1448401305	374	dbSNP
rs983470648	377	dbSNP
rs1168656204	378	dbSNP
rs1254242971	382	dbSNP
rs1213137216	386	dbSNP
rs1449977257	387	dbSNP
rs1275350844	390	dbSNP
rs1215415107	392	dbSNP
rs45529132	394	dbSNP
rs17860264	395	dbSNP
rs970157296	401	dbSNP
rs1326547171	406	dbSNP
rs771724772	407	dbSNP
rs979784717	408	dbSNP
rs928412298	409	dbSNP
rs1304847438	410	dbSNP
rs563735556	412	dbSNP
rs1434544379	414	dbSNP
rs927404048	421	dbSNP
rs1298423616	426	dbSNP
rs1167081746	428	dbSNP
rs1344330507	429	dbSNP
rs1396176359	432	dbSNP
rs1217993639	433	dbSNP
rs531034108	435	dbSNP
rs988649198	440	dbSNP
rs913039374	441	dbSNP
rs8178431	442	dbSNP
rs1234679402	465	dbSNP
rs1043016041	470	dbSNP
rs1313188351	474	dbSNP
rs771561488	482	dbSNP
rs8178432	482	dbSNP
rs56302063	483	dbSNP
rs528771197	484	dbSNP
rs1218606225	486	dbSNP
rs547012463	487	dbSNP
rs1280795385	504	dbSNP
rs890540667	505	dbSNP
rs1369553983	507	dbSNP
rs1305839843	508	dbSNP
rs1451976029	513	dbSNP
rs1376466091	516	dbSNP
rs1171954496	517	dbSNP
rs1175897432	520	dbSNP
rs1004935267	524	dbSNP
rs1431961566	525	dbSNP
rs1177849079	532	dbSNP
rs1472331028	539	dbSNP
rs946314449	542	dbSNP
rs1131673	543	dbSNP
rs376295633	547	dbSNP
rs1036503636	551	dbSNP
rs11549017	557	dbSNP
rs1041351668	558	dbSNP
rs568026095	564	dbSNP
rs150345738	569	dbSNP
rs1416005106	570	dbSNP
rs1156657008	594	dbSNP
rs1310350893	606	dbSNP
rs377668091	611	dbSNP
rs969663161	617	dbSNP
rs1001610322	618	dbSNP
rs1286017772	622	dbSNP
rs568571987	627	dbSNP
rs998042376	631	dbSNP
rs1367468513	638	dbSNP
rs111421383	641	dbSNP
rs1035327057	646	dbSNP
rs1302624072	647	dbSNP
rs1464917871	662	dbSNP
rs1347436997	664	dbSNP
rs1274818661	666	dbSNP
rs960071095	669	dbSNP
rs1456732615	672	dbSNP
rs887014062	674	dbSNP
rs1004163829	675	dbSNP
rs988534467	684	dbSNP
rs1255804439	689	dbSNP
rs571749531	692	dbSNP
rs539150604	693	dbSNP
rs746186363	698	dbSNP
rs973449117	700	dbSNP
rs1803787	707	dbSNP
rs1034450534	713	dbSNP
rs1265714139	717	dbSNP
rs959100246	721	dbSNP
rs557930309	722	dbSNP
rs572995992	727	dbSNP
rs534081117	728	dbSNP
rs921884565	732	dbSNP
rs1269578974	750	dbSNP
rs45602836	751	dbSNP
rs45455199	753	dbSNP
rs1386465416	757	dbSNP
rs911869316	761	dbSNP
rs1462090075	763	dbSNP
rs1247280841	765	dbSNP
rs1478967328	769	dbSNP
rs1175346880	777	dbSNP
rs977681577	779	dbSNP
rs940790303	787	dbSNP
rs1410979442	791	dbSNP
rs1189058595	792	dbSNP
rs780659310	793	dbSNP
rs558050478	797	dbSNP
rs899247456	799	dbSNP
rs1403726816	801	dbSNP
rs1322967906	805	dbSNP
rs1350472890	808	dbSNP
rs995005222	815	dbSNP
rs1039400999	817	dbSNP
rs899599647	818	dbSNP
rs1045169672	823	dbSNP
rs768216802	830	dbSNP
rs1286947313	831	dbSNP
rs542201606	834	dbSNP
rs1229356327	835	dbSNP
rs1441701311	836	dbSNP
rs1390136213	841	dbSNP
rs1050937685	847	dbSNP
rs1289884039	850	dbSNP
rs1463725036	853	dbSNP
rs1355395917	857	dbSNP
rs1003768124	860	dbSNP
rs1035780751	871	dbSNP
rs1388225550	874	dbSNP
rs1195449762	875	dbSNP
rs563674150	876	dbSNP
rs14861	877	dbSNP
rs1353802027	880	dbSNP
rs1433228122	883	dbSNP
rs1016866950	884	dbSNP
rs770728416	889	dbSNP
rs959754722	893	dbSNP
rs1289979881	895	dbSNP
rs575803427	906	dbSNP
rs370292682	908	dbSNP
rs776491145	911	dbSNP
rs1340540237	914	dbSNP
rs968457041	917	dbSNP
rs1250935127	918	dbSNP
rs1330524792	925	dbSNP
rs1299298033	931	dbSNP
rs1393284338	932	dbSNP
rs564686022	935	dbSNP
rs146476738	942	dbSNP
rs576292656	943	dbSNP
rs1471935308	949	dbSNP
rs1162830040	951	dbSNP
rs1414655172	957	dbSNP
rs1407110421	958	dbSNP
rs993355307	969	dbSNP
rs987383088	973	dbSNP
rs911780480	974	dbSNP
rs544076623	977	dbSNP
rs1410888242	988	dbSNP
rs1282915039	1000	dbSNP
rs977609576	1001	dbSNP
rs1310237296	1013	dbSNP
rs112806971	1014	dbSNP
rs1287924194	1014	dbSNP
rs1335926842	1014	dbSNP
rs1344920298	1014	dbSNP
rs1348335912	1014	dbSNP
rs1408242193	1014	dbSNP
rs559337682	1014	dbSNP
rs1396455143	1020	dbSNP
rs975088418	1023	dbSNP
rs1339009012	1025	dbSNP
rs79884167	1027	dbSNP
rs74462020	1028	dbSNP
rs1454844567	1029	dbSNP
rs1157870783	1031	dbSNP
rs1471412506	1034	dbSNP
rs1188643846	1035	dbSNP
rs920960083	1035	dbSNP
rs933750715	1047	dbSNP
rs920682002	1048	dbSNP
rs908338653	1055	dbSNP
rs939847181	1067	dbSNP
rs1038268995	1075	dbSNP
rs1357886719	1076	dbSNP
rs930693914	1090	dbSNP
rs1285044311	1092	dbSNP
rs1448448319	1102	dbSNP
rs1339675566	1103	dbSNP
rs1332064990	1105	dbSNP
rs374584214	1108	dbSNP
rs529552776	1110	dbSNP
rs1225505697	1112	dbSNP
rs1273894515	1114	dbSNP
rs1483335312	1116	dbSNP
rs1207126866	1124	dbSNP
rs905335008	1126	dbSNP
rs939494080	1127	dbSNP
rs1472651836	1129	dbSNP
rs1055791226	1131	dbSNP
rs140620666	1132	dbSNP
rs1187144251	1142	dbSNP
rs1465737351	1144	dbSNP
rs1248026297	1145	dbSNP
rs894506135	1153	dbSNP
rs1238232840	1164	dbSNP
rs1446569787	1166	dbSNP
rs892705775	1172	dbSNP
rs1166778799	1173	dbSNP
rs1014301036	1175	dbSNP
rs1230409945	1177	dbSNP
rs1296848623	1177	dbSNP
rs1365833510	1177	dbSNP
rs568559738	1178	dbSNP
rs368487878	1179	dbSNP
rs1199256131	1180	dbSNP
rs17860247	1181	dbSNP
rs17860265	1183	dbSNP
rs1395772944	1184	dbSNP
rs1334447957	1185	dbSNP
rs1187249734	1186	dbSNP
rs879548610	1187	dbSNP
rs998998886	1187	dbSNP
rs1033164973	1189	dbSNP
rs1275462968	1191	dbSNP
rs957605400	1191	dbSNP
rs976107068	1191	dbSNP
rs566639764	1192	dbSNP
rs955219811	1197	dbSNP
rs533722609	1199	dbSNP
rs1435220780	1200	dbSNP
rs1328971612	1205	dbSNP
rs760577971	1205	dbSNP
rs1309519000	1206	dbSNP
rs908309201	1209	dbSNP
rs1029261826	1213	dbSNP
rs1167184445	1215	dbSNP
rs1416666658	1222	dbSNP
rs1254131349	1225	dbSNP
rs1190680107	1227	dbSNP
rs1254188129	1228	dbSNP
rs1477104317	1228	dbSNP
rs370779855	1230	dbSNP
rs953262327	1231	dbSNP
rs1273668335	1236	dbSNP
rs1279673628	1238	dbSNP
rs1313880334	1244	dbSNP
rs919790886	1247	dbSNP
rs1218110778	1249	dbSNP
rs539294755	1250	dbSNP
rs1055454448	1255	dbSNP
rs555544338	1260	dbSNP
rs1410057529	1262	dbSNP
rs1350191586	1263	dbSNP
rs117234629	1264	dbSNP
rs987698224	1265	dbSNP
rs1412793875	1266	dbSNP
rs538187283	1268	dbSNP
rs1160109496	1269	dbSNP
rs1376397663	1277	dbSNP
rs1465898900	1283	dbSNP
rs11549753	1284	dbSNP
rs1175239606	1288	dbSNP
rs1484142537	1293	dbSNP
rs1014684804	1301	dbSNP
rs766330865	1306	dbSNP
rs1269489007	1307	dbSNP
rs1228530520	1312	dbSNP
rs1328041617	1322	dbSNP
rs1286114425	1325	dbSNP
rs998925287	1334	dbSNP
rs1380390796	1338	dbSNP
rs529485168	1353	dbSNP
rs1365333711	1356	dbSNP
rs575742409	1361	dbSNP
rs1436605939	1372	dbSNP
rs1321299007	1376	dbSNP
rs1299160996	1387	dbSNP
rs761938850	1389	dbSNP
rs995833456	1397	dbSNP
rs1410009513	1416	dbSNP
rs45582733	1418	dbSNP
rs1425289713	1423	dbSNP
rs45482393	1424	dbSNP
rs187498493	1429	dbSNP
rs1326747915	1436	dbSNP
rs1249891685	1448	dbSNP
rs980900016	1452	dbSNP
rs764291401	1454	dbSNP
rs3191758	1457	dbSNP
rs939568165	1483	dbSNP
rs1267703475	1484	dbSNP
rs1015296533	1496	dbSNP
rs1465436443	1499	dbSNP
rs138221859	1501	dbSNP
rs1322640020	1511	dbSNP
rs973857500	1524	dbSNP
rs1227033680	1529	dbSNP
rs1265953385	1556	dbSNP
rs919718564	1562	dbSNP
rs1434408553	1564	dbSNP
rs1200125938	1566	dbSNP
rs892727425	1568	dbSNP
rs2409482	1571	dbSNP
rs75450376	1587	dbSNP
rs1458613969	1604	dbSNP
rs1471791704	1605	dbSNP
rs945579665	1609	dbSNP
rs1041419534	1610	dbSNP
rs990722584	1611	dbSNP
rs1388882493	1612	dbSNP
rs1454944010	1648	dbSNP
rs1192485791	1649	dbSNP
rs1488601592	1653	dbSNP
rs1264535147	1655	dbSNP
rs1344789025	1659	dbSNP
rs1291280722	1661	dbSNP
rs904165888	1662	dbSNP
rs868533742	1667	dbSNP
rs865829986	1668	dbSNP
rs45482798	1671	dbSNP
rs1000251675	1673	dbSNP
rs1389300804	1676	dbSNP
rs1324697814	1677	dbSNP
rs1387296620	1689	dbSNP
rs1387489556	1692	dbSNP
rs917845606	1693	dbSNP
rs1303259207	1710	dbSNP
rs1028772062	1714	dbSNP
rs573301793	1719	dbSNP
rs1227525983	1721	dbSNP
rs540431148	1723	dbSNP
rs1330071185	1734	dbSNP
rs1241361734	1735	dbSNP
rs1371333648	1737	dbSNP
rs1200336996	1738	dbSNP
rs45447500	1740	dbSNP
rs1266173891	1751	dbSNP
rs934745374	1753	dbSNP
rs1253001463	1755	dbSNP
rs1204963840	1768	dbSNP
rs1488169087	1777	dbSNP
rs1258329123	1782	dbSNP
rs750631925	1783	dbSNP
rs1019159129	1784	dbSNP
rs1281568701	1789	dbSNP
rs1411912653	1790	dbSNP
rs1054473694	1792	dbSNP
rs893273519	1810	dbSNP
rs997438290	1811	dbSNP
rs1394224550	1822	dbSNP
rs961948831	1825	dbSNP
rs1174272684	1827	dbSNP
rs1466072780	1828	dbSNP
rs1376583962	1829	dbSNP
rs1181889678	1832	dbSNP
rs1473359096	1833	dbSNP
rs143418584	1834	dbSNP
rs1420504047	1837	dbSNP
rs17860266	1838	dbSNP
rs1258810839	1842	dbSNP
rs1201562266	1847	dbSNP
rs1027507539	1848	dbSNP
rs556517528	1849	dbSNP
rs148371628	1852	dbSNP
rs1457937379	1856	dbSNP
rs1238000879	1862	dbSNP
rs751061449	1862	dbSNP
rs1304923191	1864	dbSNP
rs182219109	1866	dbSNP
rs867116908	1868	dbSNP
rs1409051677	1874	dbSNP
rs1015265552	1880	dbSNP
rs961037558	1883	dbSNP
rs992349126	1884	dbSNP
rs914045270	1887	dbSNP
rs114293465	1903	dbSNP
rs1026747622	1904	dbSNP
rs1044025777	1912	dbSNP
rs1468886696	1919	dbSNP
rs925513793	1934	dbSNP
rs1375173680	1936	dbSNP
rs1225703854	1938	dbSNP
rs935715217	1940	dbSNP
rs1050475083	1941	dbSNP
rs991042303	1942	dbSNP
rs1423739969	1946	dbSNP
rs1222787595	1947	dbSNP
rs1210648413	1949	dbSNP
rs527380998	1956	dbSNP
rs1310794032	1959	dbSNP
rs888878124	1967	dbSNP
rs1267701711	1971	dbSNP
rs1321234316	1976	dbSNP
rs1245580166	1981	dbSNP
rs917788930	1985	dbSNP
rs45612538	1987	dbSNP
rs8178433	1989	dbSNP
rs1381905702	1990	dbSNP
rs1040201633	1994	dbSNP
rs1312895060	2007	dbSNP
rs533371084	2012	dbSNP
rs1388771113	2017	dbSNP
rs1317114848	2021	dbSNP
rs924576645	2024	dbSNP
rs1253003188	2029	dbSNP
rs934672295	2038	dbSNP
rs1457760760	2039	dbSNP
rs1481796241	2052	dbSNP
rs993275645	2055	dbSNP
rs1027561388	2056	dbSNP
rs1450087997	2062	dbSNP
rs567506565	2066	dbSNP
rs1423937970	2071	dbSNP
rs1453541030	2072	dbSNP
rs1230530667	2075	dbSNP
rs1289456640	2075	dbSNP
rs1358496143	2075	dbSNP
rs538120761	2075	dbSNP
rs932778492	2075	dbSNP
rs1034063848	2076	dbSNP
rs1164926225	2080	dbSNP
rs1428087184	2083	dbSNP
rs1332441034	2086	dbSNP
rs960837944	2089	dbSNP
rs1008444394	2090	dbSNP
rs8178434	2090	dbSNP
rs1429036489	2110	dbSNP
rs1430934657	2122	dbSNP
rs913970874	2147	dbSNP
rs966897253	2150	dbSNP
rs1166203556	2151	dbSNP
rs764055330	2151	dbSNP
rs979589800	2157	dbSNP
rs1445495685	2158	dbSNP
rs147515136	2159	dbSNP
rs1378697685	2160	dbSNP
rs1490106375	2163	dbSNP
rs932861826	2164	dbSNP
rs779331760	2165	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.

- 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.