>CCDC86|NM_024098|3'UTR
   1 GCTCAGGACGGCCCGAGGCCTTCCATGGCCAACAACCATGTCAGACACAGCACCTCAGGCCGCTGCTCAGATGCCTCTGC
  81 TGGAGCTGGCACTCCAAACCCATGGCTCCAGAACAGGGACCCCCACCCCGACCGGGGCTCCTCGGCCTTTGAAGGCTTCC
 161 AGGCAGGTCTGTGTGGGACAGAAGCCCAGAGGGGGCCTGGGACCTGGCAGAGATGGGGGCGGGAAGAGATTCAGCTCCCA
 241 TCCCTCCTTCCTCTCCTTCTCCAAGTGCCTTCAAACCAAGAACTGTACATTCTTCTGGTTCCTCAGTGAGCTGGTGACTG
 321 GCAGGTGACTCCCTCAGCAGTGTATGCCCTTTCTCAGCATCCTAGGTCCATCCCAGGCCTGGAGGCTGACAGTTGGGAAT
 401 CCAGCTTCCCCCACACCTTCCCAAAGGCTGCTCTGAGCACCTCCACACCCCACTGCCTCTGTCCCCAGCAAACTGAATCC
 481 GGTTCCTCTCCACTTTTCAATACTGAAAGATTAAAATGGGGAGGTTGCAGGGAGCAGAGCTTTTCCCTAGCACCCACTTT
 561 CCCAAACCAGTCTCTGCAGAAGCCCCAGAGAATCTAACTCATGCCTGTCCAGTCTACAGCAAAAATATTTATTGAGTGCC
 641 TGTTGCATACAGGCACAATCCTAGGCACCGGCAAATACAGACAATAGACCAAAGTCCCTGCCCTCGAGGAGCTTTCATTC
 721 TGATGGAGAGAAAACATAATAAACAAGCAAAATGCACCACGTGAAAAAAA

ID	Duplex structure	Position	Score	MFE
1	miRNA 3' guCCGUGCCCUCGAGUCCacu 5' | ||| | | |||||| Target 5' caGACACAGCACCTCAGGccg 3'	42 - 62	123.00	-13.22
2	miRNA 3' guccgugcccucgaGUCCACu 5' |||||| Target 5' gagctggtgactggCAGGTGa 3'	308 - 328	120.00	-15.70
3	miRNA 3' guccgugcccuCGAGUCCacu 5' ||||||| Target 5' -----------GCTCAGGacg 3'	1 - 10	110.00	-9.62

Mutant ID	Mutant Position	Mutant Source
COSM348487	1	COSMIC
COSN26969583	11	COSMIC
COSN28186888	14	COSMIC
COSN26969584	15	COSMIC
COSN26969585	15	COSMIC
COSN31494721	26	COSMIC
COSN31592280	36	COSMIC
COSN18735918	37	COSMIC
COSN30168843	45	COSMIC
COSN30466016	57	COSMIC
COSN30168987	69	COSMIC
COSN30465198	78	COSMIC
COSN31543784	134	COSMIC
COSN20108309	188	COSMIC
COSN8584367	219	COSMIC
COSN31606614	221	COSMIC
COSN17037801	306	COSMIC
COSN28752663	337	COSMIC
COSN31542498	363	COSMIC
COSN23263360	738	COSMIC

Mutant ID	Mutant Position	Mutant Source
rs779720765	5	dbSNP
rs746574946	10	dbSNP
rs372627966	11	dbSNP
rs200607901	13	dbSNP
rs1397499156	14	dbSNP
rs117062491	15	dbSNP
rs376394070	16	dbSNP
rs1292162632	24	dbSNP
rs897214253	26	dbSNP
rs1373810112	27	dbSNP
rs530963	37	dbSNP
rs772225825	38	dbSNP
rs1334943836	39	dbSNP
rs775680026	40	dbSNP
rs760813351	41	dbSNP
rs1348511480	44	dbSNP
rs764054311	47	dbSNP
rs202099467	48	dbSNP
rs1157161939	53	dbSNP
rs891181093	57	dbSNP
rs1413036473	62	dbSNP
rs952682473	63	dbSNP
rs1001745720	64	dbSNP
rs1127038	67	dbSNP
rs1422205167	87	dbSNP
rs1034541723	88	dbSNP
rs1201545085	99	dbSNP
rs1485708885	107	dbSNP
rs7125995	116	dbSNP
rs755976572	123	dbSNP
rs1210155498	126	dbSNP
rs1208379268	128	dbSNP
rs531936657	130	dbSNP
rs41321144	131	dbSNP
rs369158439	134	dbSNP
rs959241507	135	dbSNP
rs1381608209	138	dbSNP
rs534840733	138	dbSNP
rs493176	145	dbSNP
rs925616864	164	dbSNP
rs1322270042	169	dbSNP
rs917741838	172	dbSNP
rs1162949500	176	dbSNP
rs201480424	185	dbSNP
rs747024962	186	dbSNP
rs386754105	187	dbSNP
rs7932772	188	dbSNP
rs41404547	190	dbSNP
rs781748765	191	dbSNP
rs41373648	192	dbSNP
rs1428467494	193	dbSNP
rs386754106	194	dbSNP
rs41530751	196	dbSNP
rs1465674198	197	dbSNP
rs931596533	205	dbSNP
rs923648937	213	dbSNP
rs1357795308	215	dbSNP
rs775640151	219	dbSNP
rs1265551022	220	dbSNP
rs1161203112	221	dbSNP
rs1339949866	234	dbSNP
rs1398194061	237	dbSNP
rs911786831	238	dbSNP
rs577318342	245	dbSNP
rs751367318	256	dbSNP
rs796489246	256	dbSNP
rs1369983515	289	dbSNP
rs944579924	290	dbSNP
rs763223324	293	dbSNP
rs1054722513	296	dbSNP
rs897274542	302	dbSNP
rs1388838287	305	dbSNP
rs932854062	323	dbSNP
rs890780119	327	dbSNP
rs1050371183	331	dbSNP
rs1171108916	335	dbSNP
rs7167	337	dbSNP
rs1252790903	342	dbSNP
rs1048427728	343	dbSNP
rs1196262507	345	dbSNP
rs888467834	346	dbSNP
rs1186757160	347	dbSNP
rs1008349275	349	dbSNP
rs1267676806	356	dbSNP
rs1194726168	361	dbSNP
rs553522484	369	dbSNP
rs1294463121	371	dbSNP
rs1037114281	374	dbSNP
rs1034592020	378	dbSNP
rs896036137	399	dbSNP
rs1346818879	400	dbSNP
rs1253389900	404	dbSNP
rs1014461569	410	dbSNP
rs1195442805	411	dbSNP
rs1020863368	415	dbSNP
rs967538037	417	dbSNP
rs1333025581	418	dbSNP
rs1272627194	428	dbSNP
rs1409278007	433	dbSNP
rs1368790473	434	dbSNP
rs1486682093	444	dbSNP
rs1430989285	445	dbSNP
rs1188687638	447	dbSNP
rs978509556	453	dbSNP
rs1032737329	459	dbSNP
rs558701633	461	dbSNP
rs953054323	471	dbSNP
rs634933	472	dbSNP
rs911852869	480	dbSNP
rs41372745	481	dbSNP
rs553242616	482	dbSNP
rs1462213879	494	dbSNP
rs895080715	512	dbSNP
rs1201946750	517	dbSNP
rs150468620	530	dbSNP
rs1345529638	531	dbSNP
rs1167545657	533	dbSNP
rs1275588858	537	dbSNP
rs1228044343	541	dbSNP
rs1348670291	555	dbSNP
rs1012154601	558	dbSNP
rs971974673	562	dbSNP
rs775715987	571	dbSNP
rs1025263437	573	dbSNP
rs1416454490	578	dbSNP
rs1368262696	579	dbSNP
rs1403372694	594	dbSNP
rs758029285	598	dbSNP
rs760728112	603	dbSNP
rs1312881927	606	dbSNP
rs1182239552	610	dbSNP
rs1472210225	615	dbSNP
rs1235657477	617	dbSNP
rs1379096148	620	dbSNP
rs919089640	621	dbSNP
rs970532659	630	dbSNP
rs1394790544	632	dbSNP
rs372611424	633	dbSNP
rs977815369	634	dbSNP
rs930456673	640	dbSNP
rs1327361654	644	dbSNP
rs1228012398	647	dbSNP
rs575794040	653	dbSNP
rs138444219	655	dbSNP
rs937364603	657	dbSNP
rs989526895	661	dbSNP
rs1378539558	664	dbSNP
rs766370934	669	dbSNP
rs148839456	670	dbSNP
rs932924232	671	dbSNP
rs571853221	681	dbSNP
rs184623748	682	dbSNP
rs912773108	686	dbSNP
rs944147374	690	dbSNP
rs1390365364	692	dbSNP
rs545365765	697	dbSNP
rs559280561	699	dbSNP
rs1411006239	706	dbSNP
rs903367311	710	dbSNP
rs753683564	711	dbSNP
rs1032786430	717	dbSNP
rs1428917527	718	dbSNP
rs1473069408	720	dbSNP
rs931369184	722	dbSNP
rs953106526	727	dbSNP
rs759189168	728	dbSNP
rs1019036403	731	dbSNP
rs371857294	741	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.