ID	Duplex structure	Position	Score	MFE
1	miRNA 3' gugaaUGAAGA---AACGUCUACUc 5' || ||| || ||||||| Target 5' gatgcACCTCTGGATT-CAGATGAa 3'	295 - 318	152.00	-10.20
2	miRNA 3' guGAAUGAAGAA-AC---GUC-UACUc 5' :| | |||| || ||| |||: Target 5' atTTCAAGTCTTCTGAAACAGCATGGc 3'	378 - 404	104.00	-9.60
3	miRNA 3' gugaaUGAAGAAACGUCUAcuc 5' |:||||| ::||| Target 5' caaccATTTCTTCTTGGATacc 3'	227 - 248	93.00	-7.22

Mutant ID	Mutant Position	Mutant Source
COSM8189491	5	COSMIC
COSM3545877	27	COSMIC
COSM4485127	30	COSMIC
COSM5950749	50	COSMIC
COSM8286433	50	COSMIC
COSM5462954	56	COSMIC
COSM1411500	58	COSMIC
COSM1198595	72	COSMIC
COSM1142823	76	COSMIC
COSM3731658	82	COSMIC
COSM7903496	89	COSMIC
COSM7902656	90	COSMIC
COSM8522186	123	COSMIC
COSM1592592	126	COSMIC
COSM6004473	132	COSMIC
COSM7408965	160	COSMIC
COSN30674663	182	COSMIC
COSN30475625	192	COSMIC
COSN30125271	196	COSMIC
COSN30492975	207	COSMIC
COSN26968595	211	COSMIC
COSN13858921	222	COSMIC
COSN30186597	225	COSMIC
COSN1083011	237	COSMIC
COSN1083009	284	COSMIC
COSN30180977	305	COSMIC
COSN31563908	321	COSMIC
COSN1083007	373	COSMIC
COSN28647377	399	COSMIC
COSN17037889	414	COSMIC
COSN30540282	505	COSMIC

Mutant ID	Mutant Position	Mutant Source
rs775027581	4	dbSNP
rs746541430	5	dbSNP
rs145156759	6	dbSNP
rs776267934	8	dbSNP
rs1204102063	9	dbSNP
rs369227155	10	dbSNP
rs765136763	14	dbSNP
rs772993204	16	dbSNP
rs1323502135	22	dbSNP
rs1414225125	25	dbSNP
rs762996706	26	dbSNP
rs766251711	28	dbSNP
rs751651327	31	dbSNP
rs372092965	33	dbSNP
rs1438668337	38	dbSNP
rs138992970	40	dbSNP
rs753030412	44	dbSNP
rs1454763012	45	dbSNP
rs924073294	45	dbSNP
rs551295814	49	dbSNP
rs1392900963	50	dbSNP
rs143917410	53	dbSNP
rs935268879	55	dbSNP
rs1433522249	57	dbSNP
rs200804664	60	dbSNP
rs1304584283	65	dbSNP
rs542504187	66	dbSNP
rs763131205	66	dbSNP
rs1238182950	68	dbSNP
rs190742083	72	dbSNP
rs566354083	73	dbSNP
rs746447467	74	dbSNP
rs1010758693	83	dbSNP
rs1018418843	85	dbSNP
rs140513057	87	dbSNP
rs1178208135	88	dbSNP
rs1411322753	90	dbSNP
rs375889787	100	dbSNP
rs747875227	103	dbSNP
rs2232911	104	dbSNP
rs202088044	107	dbSNP
rs138333574	109	dbSNP
rs534176887	110	dbSNP
rs774446475	115	dbSNP
rs1212876657	118	dbSNP
rs367602721	122	dbSNP
rs200128148	123	dbSNP
rs1416386492	124	dbSNP
rs141883588	125	dbSNP
rs376043012	126	dbSNP
rs1376710676	130	dbSNP
rs1284681298	142	dbSNP
rs754188455	147	dbSNP
rs1440297079	149	dbSNP
rs555687131	155	dbSNP
rs1300055853	157	dbSNP
rs150570188	158	dbSNP
rs6028360	160	dbSNP
rs750986212	161	dbSNP
rs1332651315	162	dbSNP
rs1235015518	170	dbSNP
rs1382468449	175	dbSNP
rs764118873	176	dbSNP
rs1273580959	177	dbSNP
rs751801281	197	dbSNP
rs754480155	198	dbSNP
rs1202166025	199	dbSNP
rs1234320073	200	dbSNP
rs757409843	200	dbSNP
rs766162911	202	dbSNP
rs780730489	202	dbSNP
rs1180821895	208	dbSNP
rs1060320	211	dbSNP
rs747635237	217	dbSNP
rs753730822	221	dbSNP
rs769450047	221	dbSNP
rs777297390	222	dbSNP
rs1166200171	223	dbSNP
rs111270662	231	dbSNP
rs1017147781	232	dbSNP
rs1483885594	239	dbSNP
rs1240987464	248	dbSNP
rs527378761	250	dbSNP
rs1489065733	259	dbSNP
rs1286209228	260	dbSNP
rs1244812266	263	dbSNP
rs1319653518	270	dbSNP
rs1314648946	272	dbSNP
rs1228789064	274	dbSNP
rs1250846226	281	dbSNP
rs1024941049	282	dbSNP
rs1297646321	285	dbSNP
rs1186982298	286	dbSNP
rs1362552565	297	dbSNP
rs1298977043	298	dbSNP
rs549100811	302	dbSNP
rs1367051264	308	dbSNP
rs1167410277	317	dbSNP
rs1424888978	320	dbSNP
rs1423626690	322	dbSNP
rs752350101	324	dbSNP
rs1426855924	328	dbSNP
rs773302422	330	dbSNP
rs1488952605	333	dbSNP
rs566919258	338	dbSNP
rs915962519	339	dbSNP
rs1208829433	349	dbSNP
rs1463154826	350	dbSNP
rs924171336	352	dbSNP
rs1163227223	355	dbSNP
rs1491194247	355	dbSNP
rs1491398391	356	dbSNP
rs760961388	356	dbSNP
rs1436497708	363	dbSNP
rs1342402147	367	dbSNP
rs1278961966	369	dbSNP
rs142502467	369	dbSNP
rs1295646690	370	dbSNP
rs1360455670	374	dbSNP
rs1380094851	378	dbSNP
rs182263194	384	dbSNP
rs1169103824	385	dbSNP
rs990026520	386	dbSNP
rs1423690325	388	dbSNP
rs1197610374	393	dbSNP
rs1431086005	393	dbSNP
rs11540276	399	dbSNP
rs376471373	401	dbSNP
rs1191424299	403	dbSNP
rs1457113401	405	dbSNP
rs981840256	408	dbSNP
rs1200418547	409	dbSNP
rs766609435	414	dbSNP
rs1232710485	415	dbSNP
rs1329420125	426	dbSNP
rs1049500036	434	dbSNP
rs1387588782	435	dbSNP
rs1376575371	443	dbSNP
rs1234701473	448	dbSNP
rs11643	450	dbSNP
rs1467626861	451	dbSNP
rs1401739449	455	dbSNP
rs1333955697	457	dbSNP
rs1216201591	473	dbSNP
rs7870	475	dbSNP
rs1036681930	485	dbSNP
rs1199077764	488	dbSNP
rs893746487	490	dbSNP
rs1236111343	493	dbSNP
rs1484842991	493	dbSNP
rs1180337545	495	dbSNP
rs776941087	498	dbSNP
rs1186015092	501	dbSNP
rs1039570243	503	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.