>PABPC1|NM_002568|3'UTR
   1 AATTGATCAGGGACCATGAAAAGAAACTTGTGCTTCACCGAAGAAAAATATCTAAACATCGAAAAACTTAAATATTATGG
  81 AAAAAAAACATTGCAAAATATAAAATAAATAAAAAAAGGAAAGGAAACTTTGAACCTTATGTACCGAGCAAATGCCAGGT
 161 CTAGCAAACATAATGCTAGTCCTAGATTACTTATTGATTTAAAAACAAAAAAACACAAAAAAATAGTAAAATATAAAAAC
 241 AAATTAATGTTTTATAGACCCTGGGAAAAAGAATTTTCAGCAAAGTACAAAAATTTAAAGCATTCCTTTCTTTAATTTTG
 321 TAATTCTTTACTGTGGAATAGCTCAGAATGTCAGTTCTGTTTTAAGTAACAGAATTGATAACTGAGCAAGGAAACGTAAT
 401 TTGGATTATAAAATTCTTGCTTTAATAAAAATTCCTTAAACAGTGAAAAAAAAA

ID	Duplex structure	Position	Score	MFE
1	miRNA 3' uucaAUAUGGUU--UAUACGGUCc 5' |:||||:| | ||||||| Target 5' cttaTGTACCGAGCAAATGCCAGg 3'	136 - 159	164.00	-22.50
2	miRNA 3' uucaaUAU--GGUUUAUACGGUCc 5' ||| :||:| |||:||| Target 5' gtggaATAGCTCAGA-ATGTCAGt 3'	333 - 355	138.00	-9.10
3	miRNA 3' uuCAAUAUGGUU--UA-UACGGUCC- 5' | | || ||| || ||||:|| Target 5' caGGTCTAGCAAACATAATGCTAGTC 3'	156 - 181	134.00	-8.20

Mutant ID	Mutant Position	Mutant Source
805971	939	ClinVar
COSN32209168	42	COSMIC
COSN28881008	139	COSMIC
COSN16331634	249	COSMIC
COSN2247251	374	COSMIC
COSN1356573	692	COSMIC
COSN5105966	693	COSMIC
COSN21857189	791	COSMIC
COSN26508170	948	COSMIC
COSN15662286	991	COSMIC
COSN31545397	1029	COSMIC
COSN30534145	1048	COSMIC
COSN24358563	1082	COSMIC
COSN24356588	1086	COSMIC
COSN24357593	1122	COSMIC
COSN24367181	1131	COSMIC
COSN31563829	1143	COSMIC
COSN24366707	1149	COSMIC
COSN24355623	1150	COSMIC
COSN24359079	1152	COSMIC
COSN24360064	1153	COSMIC
COSN24357115	1154	COSMIC
COSN24357114	1172	COSMIC
COSN24360500	1177	COSMIC
COSN24367762	1180	COSMIC
COSN31548259	1189	COSMIC
COSN28249971	1203	COSMIC
COSN31535082	1208	COSMIC
COSN24357088	1221	COSMIC
COSN24358562	1240	COSMIC
COSN24360499	1249	COSMIC
COSN24355622	1250	COSMIC
COSN24356587	1250	COSMIC
COSN26576774	1261	COSMIC
COSN26581096	1281	COSMIC
COSN24358561	1283	COSMIC
COSN17132073	1291	COSMIC
COSN24359547	1296	COSMIC
COSN31482741	1314	COSMIC
COSN24368147	1321	COSMIC
COSN31540688	1333	COSMIC
COSN31573158	1373	COSMIC

Mutant ID	Mutant Position	Mutant Source
rs773256575	1	dbSNP
rs1277935093	4	dbSNP
rs1236679383	8	dbSNP
rs1371803931	11	dbSNP
rs1255158619	13	dbSNP
rs961234580	14	dbSNP
rs1421849492	15	dbSNP
rs1304136986	16	dbSNP
rs1440044073	17	dbSNP
rs35477078	18	dbSNP
rs1320066875	19	dbSNP
rs747197901	29	dbSNP
rs1466391095	32	dbSNP
rs372165707	33	dbSNP
rs761683036	38	dbSNP
rs1455237476	45	dbSNP
rs986932063	46	dbSNP
rs776704997	48	dbSNP
rs926621308	53	dbSNP
rs1028299361	54	dbSNP
rs1158630826	62	dbSNP
rs1001274738	65	dbSNP
rs1394645554	67	dbSNP
rs1480888004	69	dbSNP
rs982496123	71	dbSNP
rs1271401391	80	dbSNP
rs1197336895	85	dbSNP
rs564562113	89	dbSNP
rs753520422	101	dbSNP
rs1313462180	105	dbSNP
rs1242591601	117	dbSNP
rs1009691270	120	dbSNP
rs1217891203	121	dbSNP
rs552650073	123	dbSNP
rs527638468	135	dbSNP
rs1024636948	142	dbSNP
rs1267267911	150	dbSNP
rs28708714	152	dbSNP
rs1325230931	154	dbSNP
rs1281030922	156	dbSNP
rs1478254820	157	dbSNP
rs79077472	179	dbSNP
rs1032754127	180	dbSNP
rs938417802	187	dbSNP
rs999915501	188	dbSNP
rs1359079549	200	dbSNP
rs984241999	202	dbSNP
rs1465023914	203	dbSNP
rs900237421	206	dbSNP
rs1341553791	213	dbSNP
rs1398951394	214	dbSNP
rs905628714	215	dbSNP
rs1275927673	216	dbSNP
rs1289910339	218	dbSNP
rs929992837	218	dbSNP
rs1017274918	221	dbSNP
rs918589724	222	dbSNP
rs1044028703	223	dbSNP
rs1286420788	224	dbSNP
rs1320298711	225	dbSNP
rs930975145	227	dbSNP
rs919834746	229	dbSNP
rs1036973762	230	dbSNP
rs890746859	231	dbSNP
rs939822612	231	dbSNP
rs912368120	232	dbSNP
rs1191819022	233	dbSNP
rs1431679736	235	dbSNP
rs987055478	235	dbSNP
rs1174587237	236	dbSNP
rs1432618957	239	dbSNP
rs1420337550	242	dbSNP
rs1160995869	243	dbSNP
rs1222625052	244	dbSNP
rs1296808219	244	dbSNP
rs1346664618	244	dbSNP
rs1351245522	244	dbSNP
rs1361505028	244	dbSNP
rs1364920474	244	dbSNP
rs1419485052	244	dbSNP
rs34116624	244	dbSNP
rs564666321	244	dbSNP
rs58775495	244	dbSNP
rs755543450	244	dbSNP
rs1180979921	245	dbSNP
rs1188135878	245	dbSNP
rs1246149363	245	dbSNP
rs954114400	253	dbSNP
rs1439683842	255	dbSNP
rs1157171618	256	dbSNP
rs921354542	256	dbSNP
rs1405554113	257	dbSNP
rs1322503418	262	dbSNP
rs183750944	264	dbSNP
rs114161490	265	dbSNP
rs968058489	267	dbSNP
rs1376026539	269	dbSNP
rs1237917089	271	dbSNP
rs191273146	281	dbSNP
rs754805744	283	dbSNP
rs1356810487	285	dbSNP
rs111253254	286	dbSNP
rs960959722	287	dbSNP
rs1035173335	288	dbSNP
rs1002788580	289	dbSNP
rs538486207	291	dbSNP
rs905578857	291	dbSNP
rs558185411	294	dbSNP
rs995169408	295	dbSNP
rs1239536403	306	dbSNP
rs868189461	308	dbSNP
rs949413087	310	dbSNP
rs1036710104	311	dbSNP
rs1170752928	312	dbSNP
rs1398952489	313	dbSNP
rs1408789298	318	dbSNP
rs752080713	321	dbSNP
rs939894321	326	dbSNP
rs912470387	330	dbSNP
rs1282279987	338	dbSNP
rs751330547	342	dbSNP
rs112553497	343	dbSNP
rs572472895	350	dbSNP
rs1389442888	354	dbSNP
rs1184164920	357	dbSNP
rs1317406305	358	dbSNP
rs1194513058	360	dbSNP
rs978527927	361	dbSNP
rs921353297	370	dbSNP
rs964438782	371	dbSNP
rs186811496	374	dbSNP
rs1241052008	376	dbSNP
rs774266194	381	dbSNP
rs1008601714	385	dbSNP
rs968011337	386	dbSNP
rs890099040	397	dbSNP
rs913877022	403	dbSNP
rs12676042	415	dbSNP
rs1173880510	418	dbSNP
rs1402818330	423	dbSNP
rs34548518	424	dbSNP
rs1026595840	431	dbSNP
rs988121335	433	dbSNP
rs899388721	437	dbSNP
rs770597184	448	dbSNP
rs780108671	451	dbSNP
rs1035689667	454	dbSNP
rs763207116	457	dbSNP
rs905317139	460	dbSNP
rs1276752268	461	dbSNP
rs1346306040	463	dbSNP
rs1200412684	466	dbSNP
rs1278586943	470	dbSNP
rs1046900763	472	dbSNP
rs185437895	473	dbSNP
rs970000775	474	dbSNP
rs1426439029	475	dbSNP
rs1200333794	476	dbSNP
rs79842264	479	dbSNP
rs1477628057	480	dbSNP
rs193266897	482	dbSNP
rs898265788	483	dbSNP
rs1311025442	484	dbSNP
rs1297413195	496	dbSNP
rs1395873952	499	dbSNP
rs1036659581	506	dbSNP
rs1003887409	508	dbSNP
rs1331789144	509	dbSNP
rs891036618	510	dbSNP
rs1051490357	511	dbSNP
rs1374304639	520	dbSNP
rs748243846	521	dbSNP
rs1460490405	522	dbSNP
rs899695185	523	dbSNP
rs1164064523	525	dbSNP
rs1285807009	525	dbSNP
rs373240159	526	dbSNP
rs1211288219	532	dbSNP
rs1383377043	533	dbSNP
rs925840168	537	dbSNP
rs1382077736	539	dbSNP
rs1440308510	542	dbSNP
rs946781294	546	dbSNP
rs913992686	547	dbSNP
rs538431234	549	dbSNP
rs1295512628	551	dbSNP
rs1391470656	552	dbSNP
rs1440247492	554	dbSNP
rs543732659	557	dbSNP
rs552396728	557	dbSNP
rs1252181874	561	dbSNP
rs987613215	564	dbSNP
rs1315537479	570	dbSNP
rs1693550	570	dbSNP
rs1265675043	571	dbSNP
rs1355274916	583	dbSNP
rs1268984492	585	dbSNP
rs561095542	586	dbSNP
rs527700854	596	dbSNP
rs969679478	598	dbSNP
rs1264256011	604	dbSNP
rs1458137162	609	dbSNP
rs1244482747	615	dbSNP
rs1248076144	619	dbSNP
rs963629231	625	dbSNP
rs188305444	628	dbSNP
rs537864525	629	dbSNP
rs1461160709	631	dbSNP
rs1162851487	634	dbSNP
rs962417730	635	dbSNP
rs905348841	637	dbSNP
rs1046532449	642	dbSNP
rs1371554871	644	dbSNP
rs1014106430	647	dbSNP
rs1313966256	648	dbSNP
rs1354394023	655	dbSNP
rs143093453	660	dbSNP
rs1259388266	661	dbSNP
rs183769387	664	dbSNP
rs1249534542	665	dbSNP
rs1484234268	670	dbSNP
rs750777441	682	dbSNP
rs777571812	685	dbSNP
rs1029568566	692	dbSNP
rs997139782	696	dbSNP
rs1474975897	700	dbSNP
rs1186114128	707	dbSNP
rs1425784335	711	dbSNP
rs148980063	713	dbSNP
rs1454078170	723	dbSNP
rs79743746	729	dbSNP
rs573260490	732	dbSNP
rs892542758	737	dbSNP
rs1255210523	745	dbSNP
rs1412471788	746	dbSNP
rs1279717865	754	dbSNP
rs1340810163	762	dbSNP
rs1213475207	763	dbSNP
rs910389248	768	dbSNP
rs759555120	777	dbSNP
rs751425754	781	dbSNP
rs1200936304	783	dbSNP
rs1489663461	786	dbSNP
rs1208927767	788	dbSNP
rs1265590787	794	dbSNP
rs766251391	795	dbSNP
rs553166808	796	dbSNP
rs1209788255	798	dbSNP
rs73697500	800	dbSNP
rs190093549	814	dbSNP
rs1394801263	818	dbSNP
rs939349308	820	dbSNP
rs1300510026	825	dbSNP
rs1360733721	833	dbSNP
rs1429653586	833	dbSNP
rs73697492	834	dbSNP
rs971756195	842	dbSNP
rs963022502	843	dbSNP
rs1328737004	848	dbSNP
rs772635264	853	dbSNP
rs77390267	855	dbSNP
rs1242043799	857	dbSNP
rs948265317	858	dbSNP
rs762021165	865	dbSNP
rs1286521210	876	dbSNP
rs776813512	878	dbSNP
rs1225395286	888	dbSNP
rs969646187	889	dbSNP
rs1322747309	898	dbSNP
rs1025567168	904	dbSNP
rs1194417955	906	dbSNP
rs973558542	908	dbSNP
rs1387136037	920	dbSNP
rs1318284375	921	dbSNP
rs1013721335	923	dbSNP
rs1406320753	924	dbSNP
rs1178185695	926	dbSNP
rs1479140387	927	dbSNP
rs892580706	928	dbSNP
rs554178117	930	dbSNP
rs1198693037	931	dbSNP
rs1429622207	932	dbSNP
rs1000843658	933	dbSNP
rs1264549518	936	dbSNP
rs1313505600	937	dbSNP
rs1323625270	937	dbSNP
rs1207191260	938	dbSNP
rs1396022894	939	dbSNP
rs768598205	941	dbSNP
rs1351057692	942	dbSNP
rs1436556024	943	dbSNP
rs1324711058	945	dbSNP
rs796494714	948	dbSNP
rs1015332693	953	dbSNP
rs796815448	954	dbSNP
rs1349724335	960	dbSNP
rs1223361884	964	dbSNP
rs542599074	966	dbSNP
rs796562016	968	dbSNP
rs955165675	970	dbSNP
rs1029720784	976	dbSNP
rs113508923	977	dbSNP
rs78701194	991	dbSNP
rs1467490706	996	dbSNP
rs996530935	997	dbSNP
rs1469958509	998	dbSNP
rs899728412	1000	dbSNP
rs1328108762	1004	dbSNP
rs1295373556	1010	dbSNP
rs1461676197	1013	dbSNP
rs1163550639	1014	dbSNP
rs1022203245	1018	dbSNP
rs1383281924	1019	dbSNP
rs1338226115	1023	dbSNP
rs1331956992	1025	dbSNP
rs1335163278	1026	dbSNP
rs1439753261	1026	dbSNP
rs1381592617	1027	dbSNP
rs545824334	1027	dbSNP
rs1234157302	1028	dbSNP
rs1332775750	1028	dbSNP
rs140061105	1028	dbSNP
rs1401136224	1029	dbSNP
rs759902934	1031	dbSNP
rs1463111756	1036	dbSNP
rs1437825202	1038	dbSNP
rs1202828181	1039	dbSNP
rs1392535177	1041	dbSNP
rs113980929	1047	dbSNP
rs1475300714	1048	dbSNP
rs1187261319	1051	dbSNP
rs746942120	1051	dbSNP
rs1478522571	1054	dbSNP
rs1168062486	1056	dbSNP
rs72681438	1056	dbSNP
rs112175682	1057	dbSNP
rs79742698	1058	dbSNP
rs1335885494	1059	dbSNP
rs11558442	1060	dbSNP
rs1359559055	1061	dbSNP
rs1185884857	1062	dbSNP
rs892325485	1065	dbSNP
rs1440899214	1072	dbSNP
rs1278250779	1077	dbSNP
rs76395929	1082	dbSNP
rs1341604304	1083	dbSNP
rs199993304	1086	dbSNP
rs1486204438	1090	dbSNP
rs1052517099	1091	dbSNP
rs1227587209	1100	dbSNP
rs1254959501	1103	dbSNP
rs370019888	1107	dbSNP
rs1193252867	1116	dbSNP
rs1372027399	1117	dbSNP
rs1474362999	1119	dbSNP
rs1316882269	1120	dbSNP
rs187164034	1121	dbSNP
rs76094733	1122	dbSNP
rs1329172287	1129	dbSNP
rs77428365	1131	dbSNP
rs1368189196	1133	dbSNP
rs1167189361	1136	dbSNP
rs1429671836	1142	dbSNP
rs1225787166	1143	dbSNP
rs1489582325	1149	dbSNP
rs796428055	1149	dbSNP
rs13268309	1150	dbSNP
rs1165345168	1151	dbSNP
rs1205388570	1151	dbSNP
rs1278702705	1151	dbSNP
rs772800659	1151	dbSNP
rs1061107	1152	dbSNP
rs796893886	1153	dbSNP
rs1253543031	1154	dbSNP
rs76290134	1154	dbSNP
rs1171498756	1155	dbSNP
rs920842185	1155	dbSNP
rs1237083249	1156	dbSNP
rs1159366550	1161	dbSNP
rs1380588010	1161	dbSNP
rs1455501711	1161	dbSNP
rs903850042	1161	dbSNP
rs1332700037	1168	dbSNP
rs80148521	1172	dbSNP
rs1440856780	1173	dbSNP
rs1301657141	1175	dbSNP
rs77499026	1177	dbSNP
rs1249716058	1179	dbSNP
rs79779017	1180	dbSNP
rs141830861	1183	dbSNP
rs1293921213	1185	dbSNP
rs1211075818	1186	dbSNP
rs1273320725	1194	dbSNP
rs1226367087	1197	dbSNP
rs1467939427	1198	dbSNP
rs1191702292	1201	dbSNP
rs1419463649	1204	dbSNP
rs1355416228	1208	dbSNP
rs1180891739	1217	dbSNP
rs1037980347	1222	dbSNP
rs373574485	1222	dbSNP
rs556768806	1226	dbSNP
rs768628894	1229	dbSNP
rs908015627	1230	dbSNP
rs1429547922	1238	dbSNP
rs74668889	1240	dbSNP
rs1376240123	1241	dbSNP
rs77115628	1242	dbSNP
rs79270172	1243	dbSNP
rs75790239	1244	dbSNP
rs76975192	1245	dbSNP
rs79668849	1246	dbSNP
rs1157869099	1247	dbSNP
rs77856678	1247	dbSNP
rs79120533	1248	dbSNP
rs1333597286	1249	dbSNP
rs1472475655	1249	dbSNP
rs75237296	1250	dbSNP
rs1231482954	1251	dbSNP
rs80275021	1251	dbSNP
rs1293324472	1252	dbSNP
rs1184636888	1254	dbSNP
rs1211674434	1258	dbSNP
rs372610305	1263	dbSNP
rs1259896310	1266	dbSNP
rs1438863595	1268	dbSNP
rs571022332	1279	dbSNP
rs1248180560	1282	dbSNP
rs78517417	1283	dbSNP
rs772638888	1285	dbSNP
rs955263161	1286	dbSNP
rs1264007489	1289	dbSNP
rs1474914512	1290	dbSNP
rs1162963191	1291	dbSNP
rs1227966860	1293	dbSNP
rs3202310	1294	dbSNP
rs922387003	1299	dbSNP
rs1052039365	1301	dbSNP
rs1190747527	1301	dbSNP
rs1326856656	1302	dbSNP
rs1281043127	1306	dbSNP
rs1416172307	1309	dbSNP
rs975477699	1312	dbSNP
rs1354486606	1314	dbSNP
rs1239742467	1315	dbSNP
rs781264820	1317	dbSNP
rs75329335	1321	dbSNP
rs1268330110	1323	dbSNP
rs1331704418	1325	dbSNP
rs963720203	1329	dbSNP
rs76391000	1332	dbSNP
rs1406101423	1333	dbSNP
rs79370413	1337	dbSNP
rs1010808319	1339	dbSNP
rs78911026	1346	dbSNP
rs1406287689	1347	dbSNP
rs1216962513	1351	dbSNP
rs78571170	1355	dbSNP
rs1371637306	1371	dbSNP
rs1436952631	1377	dbSNP
rs3180369	1382	dbSNP
rs878921068	1383	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.

- Genome research, 2016

DNA damage activates TP53-regulated surveillance mechanisms that are crucial in suppressing tumorigenesis. TP53 orchestrates these responses directly by transcriptionally modulating genes, including microRNAs (miRNAs), and by regulating miRNA biogenesis through interacting with the DROSHA complex. However, whether the association between miRNAs and AGO2 is regulated following DNA damage is not yet known. Here, we show that, following DNA damage, TP53 interacts with AGO2 to induce or reduce AGO2's association of a subset of miRNAs, including multiple let-7 family members. Furthermore, we show that specific mutations in TP53 decrease rather than increase the association of let-7 family miRNAs, reducing their activity without preventing TP53 from interacting with AGO2. This is consistent with the oncogenic properties of these mutants. Using AGO2 RIP-seq and PAR-CLIP-seq, we show that the DNA damage-induced increase in binding of let-7 family members to the RISC complex is functional. We unambiguously determine the global miRNA-mRNA interaction networks involved in the DNA damage response, validating them through the identification of miRNA-target chimeras formed by endogenous ligation reactions. We find that the target complementary region of the let-7 seed tends to have highly fixed positions and more variable ones. Additionally, we observe that miRNAs, whose cellular abundance or differential association with AGO2 is regulated by TP53, are involved in an intricate network of regulatory feedback and feedforward circuits. TP53-mediated regulation of AGO2-miRNA interaction represents a new mechanism of miRNA regulation in carcinogenesis.