ID	Duplex structure	Position	Score	MFE
1	miRNA 3' gauugaaguacaaGUUAGAUUu 5' |||||||| Target 5' ggacagcaacaacCAATCTAAt 3'	186 - 207	145.00	-7.40
2	miRNA 3' gaUUGAAGUACAA--------GUUAGAUuu 5' ||||| | ||| ||||| | Target 5' gaAACTT-AGGTTTTTCCACGCAATCGAtg 3'	799 - 827	105.00	-6.66
3	miRNA 3' gauUGAAGUACA--AGUUAGAuuu 5' |:||: ||| :|||:| Target 5' cctATTTTCTGTAAATAATTTtct 3'	38 - 61	101.00	-5.52

Mutant ID	Mutant Position	Mutant Source
COSN1083265	16	COSMIC
COSN31497986	21	COSMIC
COSN30117858	70	COSMIC
COSN30142920	129	COSMIC
COSN19325937	166	COSMIC
COSN30532316	191	COSMIC
COSN30138567	216	COSMIC
COSN15624452	254	COSMIC
COSN26958313	270	COSMIC
COSN20117441	276	COSMIC
COSN31536879	322	COSMIC
COSN30162379	432	COSMIC
COSN15624453	610	COSMIC
COSN30532799	614	COSMIC
COSN31529179	670	COSMIC
COSN31570128	674	COSMIC
COSN26430763	728	COSMIC
COSN30127909	981	COSMIC
COSN26601302	984	COSMIC
COSN27549588	991	COSMIC
COSN26553330	1004	COSMIC
COSN8904864	1010	COSMIC
COSN26958314	1095	COSMIC
COSN31553490	1144	COSMIC
COSN30116996	1154	COSMIC
COSN31516152	1162	COSMIC
COSN16659259	1243	COSMIC
COSN31568387	1261	COSMIC
rs5845353	269	GWAS

Mutant ID	Mutant Position	Mutant Source
rs778264424	2	dbSNP
rs1407961991	7	dbSNP
rs762508334	8	dbSNP
rs1290822104	10	dbSNP
rs1243430823	11	dbSNP
rs768151082	14	dbSNP
rs1266067379	16	dbSNP
rs369827028	21	dbSNP
rs761193074	22	dbSNP
rs1381172687	24	dbSNP
rs1426451028	25	dbSNP
rs1045468757	30	dbSNP
rs747571332	31	dbSNP
rs766868103	32	dbSNP
rs1391978409	39	dbSNP
rs374321557	42	dbSNP
rs765433480	47	dbSNP
rs1364982393	49	dbSNP
rs1400719323	53	dbSNP
rs1364516542	58	dbSNP
rs937461564	59	dbSNP
rs1347155849	60	dbSNP
rs1431947170	61	dbSNP
rs1038531381	64	dbSNP
rs1220347101	64	dbSNP
rs1391343023	64	dbSNP
rs1170434562	74	dbSNP
rs1427250143	83	dbSNP
rs1269607727	85	dbSNP
rs1191818883	87	dbSNP
rs898770276	90	dbSNP
rs1266989509	92	dbSNP
rs1219981097	93	dbSNP
rs1275067711	97	dbSNP
rs1038457671	100	dbSNP
rs1278588978	102	dbSNP
rs994825940	108	dbSNP
rs1302796397	111	dbSNP
rs1219266877	116	dbSNP
rs1047093397	117	dbSNP
rs766133967	119	dbSNP
rs753029207	129	dbSNP
rs1200986788	130	dbSNP
rs898541286	131	dbSNP
rs1411266264	136	dbSNP
rs1371635290	142	dbSNP
rs1297929327	143	dbSNP
rs556109728	144	dbSNP
rs1008272055	149	dbSNP
rs1379825310	152	dbSNP
rs1176918476	155	dbSNP
rs1457944031	160	dbSNP
rs1427477985	163	dbSNP
rs145575097	166	dbSNP
rs1184680499	180	dbSNP
rs1029222196	183	dbSNP
rs188218991	191	dbSNP
rs1230705259	196	dbSNP
rs1257625821	196	dbSNP
rs774182032	200	dbSNP
rs1322296456	204	dbSNP
rs560871492	225	dbSNP
rs1350701852	226	dbSNP
rs995995606	242	dbSNP
rs1389986467	245	dbSNP
rs1404989114	252	dbSNP
rs1303877561	255	dbSNP
rs6000898	264	dbSNP
rs1404083491	268	dbSNP
rs5845353	268	dbSNP
rs869083632	268	dbSNP
rs957343460	269	dbSNP
rs546462313	270	dbSNP
rs1172565104	271	dbSNP
rs1400689473	272	dbSNP
rs564670907	274	dbSNP
rs1465325955	275	dbSNP
rs199983827	276	dbSNP
rs34537258	291	dbSNP
rs1417026802	294	dbSNP
rs1327053867	303	dbSNP
rs138070396	305	dbSNP
rs980986429	307	dbSNP
rs781348760	309	dbSNP
rs1210000742	312	dbSNP
rs1259709346	313	dbSNP
rs1329466507	313	dbSNP
rs544337602	320	dbSNP
rs1274329686	322	dbSNP
rs562451656	324	dbSNP
rs939639866	332	dbSNP
rs992368861	337	dbSNP
rs1452601216	345	dbSNP
rs1381163050	347	dbSNP
rs1322681883	349	dbSNP
rs1457777191	355	dbSNP
rs1344176456	360	dbSNP
rs529721010	377	dbSNP
rs1157111001	379	dbSNP
rs1459641005	381	dbSNP
rs1259135991	386	dbSNP
rs937054184	409	dbSNP
rs1894644	417	dbSNP
rs1241151588	432	dbSNP
rs1197103178	436	dbSNP
rs1189943363	445	dbSNP
rs920082286	451	dbSNP
rs1270503514	452	dbSNP
rs1452961235	454	dbSNP
rs755591730	456	dbSNP
rs149530054	461	dbSNP
rs1292988727	462	dbSNP
rs1245651091	464	dbSNP
rs564513505	465	dbSNP
rs1245559703	472	dbSNP
rs1047724497	480	dbSNP
rs1326001594	483	dbSNP
rs1316278629	485	dbSNP
rs891148228	492	dbSNP
rs1388798307	494	dbSNP
rs1391659075	497	dbSNP
rs944012675	499	dbSNP
rs1039667342	506	dbSNP
rs1894645	507	dbSNP
rs1050305651	509	dbSNP
rs1475696960	509	dbSNP
rs551908391	510	dbSNP
rs1424111960	518	dbSNP
rs1464943755	519	dbSNP
rs531244846	521	dbSNP
rs1222237302	524	dbSNP
rs1040321011	525	dbSNP
rs1406100828	527	dbSNP
rs1322987040	532	dbSNP
rs1277209715	535	dbSNP
rs1215715795	538	dbSNP
rs1339283066	544	dbSNP
rs892920665	547	dbSNP
rs1268510247	548	dbSNP
rs1235458231	557	dbSNP
rs537915688	559	dbSNP
rs1346389639	568	dbSNP
rs1302718031	570	dbSNP
rs556276859	576	dbSNP
rs1403319767	577	dbSNP
rs1020589954	582	dbSNP
rs1894646	599	dbSNP
rs1022359465	600	dbSNP
rs1402431148	604	dbSNP
rs981126671	605	dbSNP
rs1429367655	606	dbSNP
rs1198329410	614	dbSNP
rs143155064	618	dbSNP
rs1340424017	624	dbSNP
rs1225765705	629	dbSNP
rs148246524	630	dbSNP
rs1205609257	633	dbSNP
rs779395965	634	dbSNP
rs749197940	637	dbSNP
rs1210006413	642	dbSNP
rs974197803	649	dbSNP
rs920111301	651	dbSNP
rs1290432697	653	dbSNP
rs1033848327	655	dbSNP
rs1479223471	661	dbSNP
rs1282719720	667	dbSNP
rs1221955044	670	dbSNP
rs1352538082	673	dbSNP
rs960864830	675	dbSNP
rs1442583849	676	dbSNP
rs1353873430	683	dbSNP
rs1263877976	685	dbSNP
rs1416100620	692	dbSNP
rs930114962	693	dbSNP
rs185448090	698	dbSNP
rs908813928	699	dbSNP
rs1413658407	702	dbSNP
rs1178140046	703	dbSNP
rs961586331	708	dbSNP
rs1231515885	717	dbSNP
rs1190300209	730	dbSNP
rs983067627	732	dbSNP
rs1262641513	740	dbSNP
rs1201799580	741	dbSNP
rs1331491072	742	dbSNP
rs1369920409	751	dbSNP
rs1428164321	751	dbSNP
rs1473261350	752	dbSNP
rs1162849434	755	dbSNP
rs1223420616	756	dbSNP
rs143916364	757	dbSNP
rs912835711	758	dbSNP
rs564843237	759	dbSNP
rs1039719777	760	dbSNP
rs932788547	768	dbSNP
rs1335539196	777	dbSNP
rs1346607156	779	dbSNP
rs1383581606	780	dbSNP
rs147261789	784	dbSNP
rs1399748449	789	dbSNP
rs1406290985	791	dbSNP
rs80219930	792	dbSNP
rs1054256709	797	dbSNP
rs73411582	804	dbSNP
rs1010511224	815	dbSNP
rs1466357405	816	dbSNP
rs1336576505	822	dbSNP
rs1215389841	823	dbSNP
rs780269772	824	dbSNP
rs1281919163	826	dbSNP
rs1245111854	830	dbSNP
rs1314216452	838	dbSNP
rs1360074054	838	dbSNP
rs1313977781	846	dbSNP
rs1243662357	847	dbSNP
rs1363537891	847	dbSNP
rs764824828	847	dbSNP
rs907156754	852	dbSNP
rs1429650641	858	dbSNP
rs1356796590	871	dbSNP
rs1343022399	875	dbSNP
rs1305371841	876	dbSNP
rs1241761805	879	dbSNP
rs1286106878	886	dbSNP
rs758697213	887	dbSNP
rs1043433143	889	dbSNP
rs903515611	890	dbSNP
rs1001838698	892	dbSNP
rs1420381944	892	dbSNP
rs142971115	894	dbSNP
rs1185958084	895	dbSNP
rs1002781131	900	dbSNP
rs1034026043	909	dbSNP
rs1224455263	927	dbSNP
rs958321952	933	dbSNP
rs747257116	935	dbSNP
rs1442829643	936	dbSNP
rs995287625	938	dbSNP
rs1033398299	939	dbSNP
rs1290749582	945	dbSNP
rs1027124843	949	dbSNP
rs1383679830	952	dbSNP
rs1295700317	956	dbSNP
rs960416882	957	dbSNP
rs1013726781	961	dbSNP
rs1284868478	971	dbSNP
rs527396863	973	dbSNP
rs1301656263	974	dbSNP
rs1379710106	974	dbSNP
rs1464001478	975	dbSNP
rs1355586411	979	dbSNP
rs768777607	980	dbSNP
rs1200498983	982	dbSNP
rs1452290130	983	dbSNP
rs961683640	986	dbSNP
rs1174789166	987	dbSNP
rs1481593213	990	dbSNP
rs1403496131	993	dbSNP
rs912728234	997	dbSNP
rs974725866	999	dbSNP
rs1344425136	1005	dbSNP
rs1281811306	1006	dbSNP
rs965634510	1008	dbSNP
rs1393437619	1012	dbSNP
rs190553770	1014	dbSNP
rs1298160528	1017	dbSNP
rs541767765	1018	dbSNP
rs1177212073	1019	dbSNP
rs912668125	1022	dbSNP
rs921281662	1024	dbSNP
rs1196487523	1026	dbSNP
rs192459911	1029	dbSNP
rs1250966181	1042	dbSNP
rs1053776701	1065	dbSNP
rs559705827	1072	dbSNP
rs191509238	1082	dbSNP
rs913729309	1085	dbSNP
rs1203707957	1093	dbSNP
rs536090839	1096	dbSNP
rs1260805592	1112	dbSNP
rs945477959	1131	dbSNP
rs1317964022	1138	dbSNP
rs1306694633	1140	dbSNP
rs527555427	1145	dbSNP
rs907002805	1147	dbSNP
rs1002794176	1151	dbSNP
rs1385550372	1152	dbSNP
rs1044038156	1156	dbSNP
rs552069887	1157	dbSNP
rs1257739539	1158	dbSNP
rs903736097	1159	dbSNP
rs1160582665	1168	dbSNP
rs937688304	1174	dbSNP
rs894159705	1177	dbSNP
rs1240967182	1180	dbSNP
rs15973	1190	dbSNP
rs1244829289	1191	dbSNP
rs1026635006	1199	dbSNP
rs1183687128	1203	dbSNP
rs71324880	1203	dbSNP
rs896130117	1203	dbSNP
rs1316276587	1204	dbSNP
rs1179441591	1206	dbSNP
rs1380727673	1207	dbSNP
rs566172878	1207	dbSNP
rs1383012123	1210	dbSNP
rs1384474673	1210	dbSNP
rs529447236	1211	dbSNP
rs1288074574	1212	dbSNP
rs56665907	1212	dbSNP
rs1050466	1213	dbSNP
rs1201067719	1214	dbSNP
rs1194638902	1217	dbSNP
rs1165709780	1219	dbSNP
rs1015761846	1222	dbSNP
rs1260527007	1225	dbSNP
rs897400299	1233	dbSNP
rs1003959686	1235	dbSNP
rs1019742130	1238	dbSNP
rs183751019	1240	dbSNP
rs975647803	1243	dbSNP
rs1222463460	1244	dbSNP
rs1354800924	1258	dbSNP
rs995809517	1260	dbSNP
rs1228157398	1261	dbSNP
rs568582594	1264	dbSNP
rs1293773763	1267	dbSNP
rs921545337	1268	dbSNP
rs1367262693	1275	dbSNP
rs1303512818	1279	dbSNP
rs958296853	1280	dbSNP
rs1388441091	1284	dbSNP
rs1466887789	1289	dbSNP
rs1169148849	1296	dbSNP
rs989926767	1297	dbSNP
rs954262760	1298	dbSNP

- Nature, 2013

Circular RNAs (circRNAs) in animals are an enigmatic class of RNA with unknown function. To explore circRNAs systematically, we sequenced and computationally analysed human, mouse and nematode RNA. We detected thousands of well-expressed, stable circRNAs, often showing tissue/developmental-stage-specific expression. Sequence analysis indicated important regulatory functions for circRNAs. We found that a human circRNA, antisense to the cerebellar degeneration-related protein 1 transcript (CDR1as), is densely bound by microRNA (miRNA) effector complexes and harbours 63 conserved binding sites for the ancient miRNA miR-7. Further analyses indicated that CDR1as functions to bind miR-7 in neuronal tissues. Human CDR1as expression in zebrafish impaired midbrain development, similar to knocking down miR-7, suggesting that CDR1as is a miRNA antagonist with a miRNA-binding capacity ten times higher than any other known transcript. Together, our data provide evidence that circRNAs form a large class of post-transcriptional regulators. Numerous circRNAs form by head-to-tail splicing of exons, suggesting previously unrecognized regulatory potential of coding sequences.

- 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.