ID	Duplex structure	Position	Score	MFE
1	miRNA 3' uuggUGGUC----GGGUGAGg 5' ||||| ||||||| Target 5' tcggACCAGTCCCCCCACTCc 3'	786 - 806	151.00	-21.70
2	miRNA 3' uugGUGGUC-GGGUGAGg 5' :| ||| ||||||| Target 5' ttaTAACAGTCCCACTCa 3'	559 - 576	150.00	-16.30
3	miRNA 3' uugGUGGUCGGGUGAGg 5' | | | |||:||| Target 5' gtgCTCAAACCCGCTCc 3'	746 - 762	130.00	-15.80

Mutant ID	Mutant Position	Mutant Source
COSN22624883	45	COSMIC
COSN26537747	61	COSMIC
COSN20113478	176	COSMIC
COSN26586750	214	COSMIC
COSN26578266	296	COSMIC
COSN31491167	394	COSMIC
COSN31531924	441	COSMIC
COSN25753379	617	COSMIC
COSN7456583	634	COSMIC
COSN31564345	724	COSMIC
COSN31538934	758	COSMIC
COSN26565104	847	COSMIC
COSN24306189	850	COSMIC
COSN20113482	895	COSMIC
COSN25422598	1088	COSMIC
COSN31518559	1120	COSMIC
rs112843870	888	GWAS

Mutant ID	Mutant Position	Mutant Source
rs1296947477	6	dbSNP
rs1364513855	8	dbSNP
rs1383059350	9	dbSNP
rs1017323151	14	dbSNP
rs1462539293	15	dbSNP
rs890310537	16	dbSNP
rs753721931	18	dbSNP
rs757314591	18	dbSNP
rs1292548641	19	dbSNP
rs1009134139	22	dbSNP
rs1214344661	24	dbSNP
rs374683893	30	dbSNP
rs967506082	32	dbSNP
rs767093904	33	dbSNP
rs1338120330	36	dbSNP
rs1249147671	37	dbSNP
rs1253848655	39	dbSNP
rs1425148622	42	dbSNP
rs1183867205	43	dbSNP
rs1379136185	44	dbSNP
rs1437348572	47	dbSNP
rs1359690522	49	dbSNP
rs754774343	53	dbSNP
rs544770538	57	dbSNP
rs1314008049	58	dbSNP
rs1337361103	60	dbSNP
rs1450145974	60	dbSNP
rs1329396466	82	dbSNP
rs1032643940	83	dbSNP
rs1166241535	85	dbSNP
rs1426691710	92	dbSNP
rs59129736	95	dbSNP
rs1386093454	98	dbSNP
rs1443144090	100	dbSNP
rs1232933013	104	dbSNP
rs958359360	105	dbSNP
rs1437764616	106	dbSNP
rs1249106069	107	dbSNP
rs1490382016	110	dbSNP
rs1290554337	115	dbSNP
rs991095804	119	dbSNP
rs1039953391	120	dbSNP
rs1279925464	123	dbSNP
rs563197638	124	dbSNP
rs533633614	126	dbSNP
rs1333897103	127	dbSNP
rs1304954657	128	dbSNP
rs1406817027	129	dbSNP
rs1366330170	134	dbSNP
rs778832032	136	dbSNP
rs1346309322	137	dbSNP
rs1221496831	138	dbSNP
rs1470005901	140	dbSNP
rs970936149	140	dbSNP
rs552080857	142	dbSNP
rs921068631	155	dbSNP
rs1464768742	160	dbSNP
rs1284587373	161	dbSNP
rs35202212	161	dbSNP
rs907957524	161	dbSNP
rs397822445	176	dbSNP
rs1209543054	177	dbSNP
rs1224075722	178	dbSNP
rs539430814	179	dbSNP
rs551546588	184	dbSNP
rs1346187604	185	dbSNP
rs940739533	186	dbSNP
rs569710071	187	dbSNP
rs1467144294	191	dbSNP
rs1198272952	194	dbSNP
rs28562210	196	dbSNP
rs1247426729	197	dbSNP
rs1347176132	197	dbSNP
rs28738673	198	dbSNP
rs1400468081	205	dbSNP
rs538087222	206	dbSNP
rs1037741428	207	dbSNP
rs528079939	210	dbSNP
rs1196627190	211	dbSNP
rs1476148349	213	dbSNP
rs1242310675	215	dbSNP
rs1192094110	218	dbSNP
rs1478967568	227	dbSNP
rs920634331	229	dbSNP
rs931964059	237	dbSNP
rs1261244395	241	dbSNP
rs1156790603	245	dbSNP
rs964367876	248	dbSNP
rs1410887497	252	dbSNP
rs1457597479	254	dbSNP
rs1270941271	260	dbSNP
rs1050329708	261	dbSNP
rs890341021	262	dbSNP
rs1339115322	277	dbSNP
rs1008749154	278	dbSNP
rs1405984460	279	dbSNP
rs1174627342	282	dbSNP
rs1411134973	285	dbSNP
rs1041901872	291	dbSNP
rs1166922550	292	dbSNP
rs1391854911	293	dbSNP
rs755846264	300	dbSNP
rs1183957263	306	dbSNP
rs11553166	308	dbSNP
rs1241172167	310	dbSNP
rs920491549	311	dbSNP
rs1309291909	312	dbSNP
rs568098740	313	dbSNP
rs1032745320	318	dbSNP
rs1340281759	319	dbSNP
rs1332360712	322	dbSNP
rs1453800210	324	dbSNP
rs1439196951	329	dbSNP
rs1053574343	334	dbSNP
rs958388971	336	dbSNP
rs1445035804	341	dbSNP
rs950600074	342	dbSNP
rs1012559584	343	dbSNP
rs1023913676	343	dbSNP
rs971350263	347	dbSNP
rs1443729088	353	dbSNP
rs1411395792	355	dbSNP
rs982312444	357	dbSNP
rs1232287267	358	dbSNP
rs983653993	360	dbSNP
rs535309931	361	dbSNP
rs1294195166	368	dbSNP
rs1332946215	369	dbSNP
rs928053261	371	dbSNP
rs962231959	372	dbSNP
rs1359125402	373	dbSNP
rs1311041098	375	dbSNP
rs939475790	377	dbSNP
rs1374674433	388	dbSNP
rs1470493662	389	dbSNP
rs1290650192	392	dbSNP
rs920664108	393	dbSNP
rs200781658	394	dbSNP
rs1303338787	395	dbSNP
rs1423610394	404	dbSNP
rs1055125141	408	dbSNP
rs892197667	410	dbSNP
rs1160997224	414	dbSNP
rs1009212217	415	dbSNP
rs1411913190	417	dbSNP
rs556700772	424	dbSNP
rs1407117394	427	dbSNP
rs1250990962	428	dbSNP
rs1179990065	429	dbSNP
rs568692604	430	dbSNP
rs1271185427	438	dbSNP
rs1184061745	442	dbSNP
rs946687905	443	dbSNP
rs1488286691	444	dbSNP
rs143082103	446	dbSNP
rs1263958950	450	dbSNP
rs1218380894	452	dbSNP
rs1317941986	455	dbSNP
rs1306849922	469	dbSNP
rs1227122703	470	dbSNP
rs575055340	472	dbSNP
rs1041626553	474	dbSNP
rs1283382336	475	dbSNP
rs1415483477	476	dbSNP
rs148209702	479	dbSNP
rs1365042174	481	dbSNP
rs1000018764	483	dbSNP
rs1454099831	485	dbSNP
rs1054219376	486	dbSNP
rs1156813742	487	dbSNP
rs902735650	488	dbSNP
rs1431472307	489	dbSNP
rs1306649638	494	dbSNP
rs1350428786	497	dbSNP
rs999707285	498	dbSNP
rs1051225741	499	dbSNP
rs186639406	502	dbSNP
rs73977769	508	dbSNP
rs1188559482	509	dbSNP
rs1486373785	512	dbSNP
rs971081243	520	dbSNP
rs1017354392	521	dbSNP
rs1207320219	525	dbSNP
rs1244268277	525	dbSNP
rs1326257187	529	dbSNP
rs1264374963	531	dbSNP
rs1004239909	532	dbSNP
rs1358474951	535	dbSNP
rs964398910	537	dbSNP
rs1015156831	538	dbSNP
rs994889805	539	dbSNP
rs555584481	540	dbSNP
rs147813431	543	dbSNP
rs1406727676	545	dbSNP
rs950650282	545	dbSNP
rs1207258167	551	dbSNP
rs1255109969	557	dbSNP
rs1423050896	558	dbSNP
rs574052389	562	dbSNP
rs1175669443	565	dbSNP
rs544834542	566	dbSNP
rs1027713329	568	dbSNP
rs1369844679	569	dbSNP
rs1172715752	570	dbSNP
rs553761392	571	dbSNP
rs1429350345	578	dbSNP
rs191438558	581	dbSNP
rs1462965948	586	dbSNP
rs1474109468	590	dbSNP
rs983382961	597	dbSNP
rs1046021424	603	dbSNP
rs1200404030	604	dbSNP
rs1167403883	605	dbSNP
rs563109395	606	dbSNP
rs1370714187	607	dbSNP
rs960514294	610	dbSNP
rs944707317	615	dbSNP
rs906806890	617	dbSNP
rs578214690	618	dbSNP
rs990887082	619	dbSNP
rs916640066	620	dbSNP
rs1310408689	621	dbSNP
rs1054253850	626	dbSNP
rs758253355	637	dbSNP
rs1299950632	645	dbSNP
rs1462620817	648	dbSNP
rs1400460017	652	dbSNP
rs946750862	655	dbSNP
rs1386283858	656	dbSNP
rs1313634607	664	dbSNP
rs1441206433	665	dbSNP
rs1044084077	670	dbSNP
rs1253355534	671	dbSNP
rs1342472318	672	dbSNP
rs182807741	673	dbSNP
rs906885927	678	dbSNP
rs1224282270	680	dbSNP
rs1359800927	680	dbSNP
rs1283393317	681	dbSNP
rs560795973	682	dbSNP
rs528076978	686	dbSNP
rs370441062	689	dbSNP
rs1230458007	690	dbSNP
rs1307666391	691	dbSNP
rs1410491430	692	dbSNP
rs1370051946	693	dbSNP
rs1415645334	693	dbSNP
rs1015602413	695	dbSNP
rs898056155	696	dbSNP
rs1163028598	697	dbSNP
rs1472053157	698	dbSNP
rs924219466	699	dbSNP
rs546545286	700	dbSNP
rs373980193	701	dbSNP
rs1258081782	702	dbSNP
rs1249027035	704	dbSNP
rs1002377042	712	dbSNP
rs1444922357	717	dbSNP
rs1224178298	720	dbSNP
rs1490406834	721	dbSNP
rs1207808186	723	dbSNP
rs1288783648	723	dbSNP
rs1051340933	724	dbSNP
rs891330336	725	dbSNP
rs994967987	728	dbSNP
rs1286548725	729	dbSNP
rs1406907835	732	dbSNP
rs1027744423	735	dbSNP
rs1007046154	736	dbSNP
rs1170953540	741	dbSNP
rs1403936078	744	dbSNP
rs1038822795	745	dbSNP
rs1466027693	752	dbSNP
rs1303785852	755	dbSNP
rs561641238	758	dbSNP
rs986217270	759	dbSNP
rs1457187566	761	dbSNP
rs1410468716	764	dbSNP
rs528986286	765	dbSNP
rs1480498829	768	dbSNP
rs1245748245	770	dbSNP
rs1448475909	773	dbSNP
rs550241844	773	dbSNP
rs966454515	778	dbSNP
rs1207971277	782	dbSNP
rs1265003731	794	dbSNP
rs1326981045	794	dbSNP
rs977425550	797	dbSNP
rs1345871480	801	dbSNP
rs924526415	802	dbSNP
rs935871781	803	dbSNP
rs1321626126	809	dbSNP
rs1027770607	810	dbSNP
rs950403676	812	dbSNP
rs1414493042	813	dbSNP
rs1437375858	814	dbSNP
rs990060704	818	dbSNP
rs1005235452	821	dbSNP
rs753895277	821	dbSNP
rs1034880558	823	dbSNP
rs796217721	829	dbSNP
rs960546567	833	dbSNP
rs1463409428	835	dbSNP
rs1233967641	843	dbSNP
rs1244874044	844	dbSNP
rs1204252524	845	dbSNP
rs1443037640	845	dbSNP
rs572150707	846	dbSNP
rs1257513222	857	dbSNP
rs1023683192	861	dbSNP
rs1228092707	870	dbSNP
rs1207664391	873	dbSNP
rs188228843	886	dbSNP
rs112843870	887	dbSNP
rs34157498	887	dbSNP
rs397817394	887	dbSNP
rs906920626	887	dbSNP
rs577422500	892	dbSNP
rs939697662	892	dbSNP
rs898090231	893	dbSNP
rs1386898783	895	dbSNP
rs1447387341	895	dbSNP
rs1472436050	896	dbSNP
rs746433772	896	dbSNP
rs1235728185	897	dbSNP
rs1208068475	899	dbSNP
rs1027858687	900	dbSNP
rs1275555882	903	dbSNP
rs1204741038	904	dbSNP
rs1266134810	905	dbSNP
rs889312193	906	dbSNP
rs1229309930	909	dbSNP
rs1282985466	910	dbSNP
rs1379077713	910	dbSNP
rs1443715375	912	dbSNP
rs1177486298	918	dbSNP
rs1370664437	920	dbSNP
rs1306985254	923	dbSNP
rs756911866	923	dbSNP
rs368100502	926	dbSNP
rs1165208529	936	dbSNP
rs923972752	937	dbSNP
rs1411499550	941	dbSNP
rs1423065907	941	dbSNP
rs1158621508	954	dbSNP
rs935334148	961	dbSNP
rs1019466700	964	dbSNP
rs1389679932	969	dbSNP
rs1181656791	971	dbSNP
rs564453391	972	dbSNP
rs1482188429	973	dbSNP
rs11553167	975	dbSNP
rs1437620514	983	dbSNP
rs558592456	997	dbSNP
rs987075821	1000	dbSNP
rs1367049980	1001	dbSNP
rs999271848	1002	dbSNP
rs1031707610	1004	dbSNP
rs1288292670	1006	dbSNP
rs1226013274	1007	dbSNP
rs1350501832	1010	dbSNP
rs539241061	1012	dbSNP
rs1387259732	1021	dbSNP
rs4791855	1030	dbSNP
rs942861900	1031	dbSNP
rs1039864045	1037	dbSNP
rs898658883	1046	dbSNP
rs930420967	1047	dbSNP
rs915815816	1051	dbSNP
rs1048788671	1053	dbSNP
rs1161114501	1056	dbSNP
rs1227566694	1057	dbSNP
rs1411225302	1058	dbSNP
rs1158517543	1060	dbSNP
rs1471675663	1061	dbSNP
rs886126069	1063	dbSNP
rs1488338533	1064	dbSNP
rs969890135	1067	dbSNP
rs1211065782	1086	dbSNP
rs1330416969	1089	dbSNP
rs1268588735	1094	dbSNP
rs1268091882	1100	dbSNP
rs1226013810	1104	dbSNP
rs1325094936	1105	dbSNP
rs371945892	1107	dbSNP
rs981273114	1110	dbSNP
rs1034911754	1114	dbSNP
rs896373344	1115	dbSNP
rs566713372	1120	dbSNP
rs1012038050	1121	dbSNP
rs1435627455	1126	dbSNP
rs1387780746	1128	dbSNP
rs1156919126	1131	dbSNP
rs939752765	1132	dbSNP
rs1023929110	1133	dbSNP
rs1192241563	1139	dbSNP
rs967899844	1139	dbSNP
rs1037180680	1145	dbSNP
rs1432838238	1153	dbSNP
rs766375767	1156	dbSNP
rs1031067435	1157	dbSNP
rs1247896108	1160	dbSNP
rs1207420258	1162	dbSNP
rs1483906273	1164	dbSNP
rs919631733	1170	dbSNP
rs533962815	1175	dbSNP
rs1049315571	1178	dbSNP
rs1063746	1181	dbSNP
rs1228840887	1184	dbSNP
rs1318415058	1187	dbSNP
rs1364219125	1187	dbSNP
rs1413249005	1187	dbSNP
rs1454520430	1188	dbSNP
rs751631671	1192	dbSNP
rs1404379031	1196	dbSNP
rs1303488783	1199	dbSNP
rs1458992459	1200	dbSNP
rs986772231	1207	dbSNP
rs912828422	1209	dbSNP
rs1349328902	1211	dbSNP
rs1450430397	1216	dbSNP
rs1389947916	1218	dbSNP
rs1008144152	1219	dbSNP
rs1426059868	1220	dbSNP
rs1040511706	1221	dbSNP
rs902003256	1224	dbSNP
rs1295153761	1225	dbSNP
rs1205469232	1230	dbSNP
rs1341115136	1231	dbSNP
rs754964115	1236	dbSNP
rs1295150759	1244	dbSNP
rs550093679	1249	dbSNP
rs998991081	1252	dbSNP
rs1311977481	1255	dbSNP
rs1031744504	1264	dbSNP
rs1352151277	1267	dbSNP
rs1011553040	1268	dbSNP
rs957388248	1268	dbSNP
rs1430656475	1269	dbSNP
rs1226210124	1273	dbSNP
rs573936345	1276	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.

- 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.