>MYO1C|NM_001080779|3'UTR
   1 TAAAGGCGCCCACTGGACCCTCCCAACGCCCAATGCTTTGCTTTTCTCCTCCTCCCCTTCCCAGTTACCAAAGACTCGAA
  81 CTTCCAGACAGGGACCCAGGGACACCCCGAAGCCCACCTGCAATCTCCCACCTCCTGCCCATCCCTCTCTTGAGGGAGCA
 161 GCAGGGGCCAGGAGCTACCCCAGGAGTGGGCCAGGCCGGGCCACAGCAATAGGAAAGCCAGGGCCAGAGCGAGCCATGCC
 241 AGCCCTACTGCCGATGCCAAATATTTGAGAGAAGGGAACTTTTGCTGAGGTTTTCTCTGAGGTTTTTTTGATGCTTTATA
 321 GGAAACTATTTTTTAAAAAAAGCCATTTCCCACCCAAGGACACAGTGGATGTGTTTTCCCTGACTCCAGCAGGGCAAGGA
 401 ATGTAGCCGAGAGGTTGTGTGGGCTGGGCTCTGGTGCCCTCTTCCCTGGCCAGGACACCTCTCCTCCTGATTCCCTTGGC
 481 ACCTTGTCTTTCTGTCTGTTTACCTGTCTCCCTGCCTGCCCATCTGCATCTTTTGCAGCCCACTCTGACTTCCATCTGGG
 561 GGCTGAGACCACCCTTGCCTGCCCCCTTCTTTCTGCCTTAAGAATGTCCTTTTAGGCTGGGCATGGTGGCTCACGCCTGT
 641 AACCCCAGCACTTTGGGAGGCGGAGACGGGCAGATAACCTGAGGTCAGGATTTCGAGACCAACCTGACCTACATGGAGAA
 721 ACTCCGCCTCTAGTAAAAATACAAAATTAGCCGGGCATGGTGGTGCACGCCTCTAATCCCAGCTACTCGGGAGGCTGAGG
 801 CAGGAGAATCACTTGAACCCGGGAAGTGGAGGTTGCAGTGAGCCAAGAGTACACCACTGCACTCCAGCCTGGGCAACAGA
 881 GCGAGACTCCGTCTTAAAAAAAAAAAAAAAGAACGCCCTTTTACTGTCCTCATCATCCCAGTTTGAGGCAGTGCTGGAGT
 961 GGGGAAGGCCGTCTTAGACCATAGAGGTTGGAAGACGCTGAGAGATCATCCAGCCCAGCCCCTTGATGTTACAGAGCAGA
1041 AGACAGATGCCCAAACAGGAGAAGGCACTTGCCCACGGTCATACGGCAGGTTGCCACAAAACCAAGATGGCAGCCCTTCC
1121 TCAGCGTGCCTCACTGCCACTCCCAGAGCCAGGGAGCCCCATAAAACCCACATCATGTCTTAAGAGTATATCTGGCTCCT
1201 TGACCAGCAATCGGCCCTGGGAGCCACCAGGTGGGAAAAGCGCCTCTGCCAGAGTCCAGGCCTTGGGATGACAGACAGCT
1281 TGCCCGCACACTCGGGCCCCACTCAAGGATGTAGGGCCTTTTCTGGCCCCTGACCCCTCCCTGGCATGGGAGCGTGGGGA
1361 CGGGGCTGGCCTTGGGAGGAGCGGCAGGGGCATCACCTCCTTCTGCTGCTTCTCCCTGCTCCTACCCTCAAGGGCCTGGG
1441 GGCTGCCCAGCTGCCTCTATGCCCTTCTGGGGGTCTCAGCCCACTGCTGACACTTCTGCAATCCAGAGAAACACTAAATA
1521 AAGCAATACGTGTTTGCCAAAAAAAAAAAAAAAAAAAAAAA

ID	Duplex structure	Position	Score	MFE
1	miRNA 3' gauucugguucGGA--GGAAGGGa 5' ||| ||||||| Target 5' gcttttctcctCCTCCCCTTCCCa 3'	40 - 63	145.00	-16.00
2	miRNA 3' gaUUCUGGUUCGG-----AGGAAGGGa 5' || |||||| : ||||||: Target 5' acAAAACCAAGATGGCAGCCCTTCCTc 3'	1096 - 1122	140.00	-15.60
3	miRNA 3' gauucugguuCGGAGGAAGGGa 5' ||| :|||||| Target 5' gggctctggtGCCCTCTTCCCt 3'	426 - 447	136.00	-18.80

Mutant ID	Mutant Position	Mutant Source
1183863	197	ClinVar
COSN28882938	10	COSMIC
COSN30163224	22	COSMIC
COSN20060348	27	COSMIC
COSN31602132	125	COSMIC
COSN30481334	127	COSMIC
COSN30580662	158	COSMIC
COSN30136542	167	COSMIC
COSN26601933	201	COSMIC
COSN31579867	250	COSMIC
COSN31601383	252	COSMIC
COSN21767487	334	COSMIC
COSN22158181	335	COSMIC
COSN26664238	616	COSMIC
COSN26567342	619	COSMIC
COSN30544845	635	COSMIC
COSN8831701	668	COSMIC
COSN28162908	890	COSMIC
COSN21503955	917	COSMIC
COSN30175929	997	COSMIC
COSN8240340	1018	COSMIC
COSN31514872	1126	COSMIC
COSN26509527	1206	COSMIC
COSN28726267	1221	COSMIC
COSN30165157	1307	COSMIC
COSN31595002	1469	COSMIC
COSN31555585	1486	COSMIC

Mutant ID	Mutant Position	Mutant Source
rs772871115	1	dbSNP
rs769839215	3	dbSNP
rs769837724	5	dbSNP
rs761710266	6	dbSNP
rs779020986	6	dbSNP
rs548792139	7	dbSNP
rs373989989	8	dbSNP
rs746482131	10	dbSNP
rs1036506968	13	dbSNP
rs1161187830	18	dbSNP
rs779681383	19	dbSNP
rs771562248	27	dbSNP
rs372318243	28	dbSNP
rs777992599	31	dbSNP
rs958609717	32	dbSNP
rs371622828	33	dbSNP
rs1449829152	34	dbSNP
rs753281962	41	dbSNP
rs556221831	42	dbSNP
rs755114267	46	dbSNP
rs1445144322	48	dbSNP
rs751636919	49	dbSNP
rs766685895	51	dbSNP
rs989444316	52	dbSNP
rs1239827425	56	dbSNP
rs967123854	56	dbSNP
rs370234417	60	dbSNP
rs1030896809	63	dbSNP
rs563141164	75	dbSNP
rs965613046	77	dbSNP
rs377690275	78	dbSNP
rs1402712020	86	dbSNP
rs1050657404	89	dbSNP
rs1316220801	90	dbSNP
rs1291929907	93	dbSNP
rs1324749445	95	dbSNP
rs1437384277	100	dbSNP
rs1208720633	108	dbSNP
rs74477362	109	dbSNP
rs1369564227	117	dbSNP
rs1370569550	118	dbSNP
rs888168985	134	dbSNP
rs565548397	136	dbSNP
rs545652606	139	dbSNP
rs901821706	143	dbSNP
rs1346196831	144	dbSNP
rs1205053482	150	dbSNP
rs1282833452	151	dbSNP
rs1471832855	152	dbSNP
rs1465812004	154	dbSNP
rs764277066	155	dbSNP
rs1251941615	160	dbSNP
rs940700657	168	dbSNP
rs557172939	170	dbSNP
rs573466740	172	dbSNP
rs559846706	179	dbSNP
rs760701365	181	dbSNP
rs919796678	189	dbSNP
rs11538162	197	dbSNP
rs1207552644	198	dbSNP
rs574042046	204	dbSNP
rs1321325110	207	dbSNP
rs1393894457	208	dbSNP
rs958674545	213	dbSNP
rs906732254	214	dbSNP
rs1332025114	221	dbSNP
rs1045226167	231	dbSNP
rs928554119	233	dbSNP
rs1331873823	234	dbSNP
rs1229604545	236	dbSNP
rs948141398	243	dbSNP
rs1002416367	246	dbSNP
rs967448712	252	dbSNP
rs11538164	253	dbSNP
rs989497088	262	dbSNP
rs935350678	267	dbSNP
rs781083014	271	dbSNP
rs557096082	292	dbSNP
rs923921257	301	dbSNP
rs1029188342	302	dbSNP
rs757389559	304	dbSNP
rs1414031705	309	dbSNP
rs1472863658	310	dbSNP
rs537425881	312	dbSNP
rs1164175301	313	dbSNP
rs1417241050	319	dbSNP
rs866219951	332	dbSNP
rs577542349	334	dbSNP
rs878944818	335	dbSNP
rs1004846430	342	dbSNP
rs985272710	344	dbSNP
rs886449820	347	dbSNP
rs1352761705	356	dbSNP
rs1299392949	363	dbSNP
rs1293279421	377	dbSNP
rs1331959723	380	dbSNP
rs1246357474	382	dbSNP
rs188847316	384	dbSNP
rs1338368694	385	dbSNP
rs1026662168	386	dbSNP
rs1193766053	400	dbSNP
rs993864597	402	dbSNP
rs534545283	403	dbSNP
rs896849054	408	dbSNP
rs1255333210	409	dbSNP
rs1422059388	415	dbSNP
rs1035315074	419	dbSNP
rs1004234826	425	dbSNP
rs1369180936	427	dbSNP
rs898317638	428	dbSNP
rs906748875	429	dbSNP
rs1167023274	434	dbSNP
rs1372787306	441	dbSNP
rs1327971394	444	dbSNP
rs1045640627	445	dbSNP
rs774926934	448	dbSNP
rs1377663776	451	dbSNP
rs1397219642	453	dbSNP
rs1055522335	456	dbSNP
rs1325386417	466	dbSNP
rs1224783395	469	dbSNP
rs1276403159	473	dbSNP
rs937187688	474	dbSNP
rs928528685	479	dbSNP
rs553012656	482	dbSNP
rs565533302	486	dbSNP
rs1278046429	491	dbSNP
rs146109048	495	dbSNP
rs537979117	496	dbSNP
rs945724233	502	dbSNP
rs912941106	503	dbSNP
rs893968339	510	dbSNP
rs1053898060	516	dbSNP
rs957136448	521	dbSNP
rs1365193459	532	dbSNP
rs1028760934	535	dbSNP
rs935401504	538	dbSNP
rs974916417	555	dbSNP
rs966613886	558	dbSNP
rs1432206770	583	dbSNP
rs1383600157	586	dbSNP
rs1019159955	595	dbSNP
rs1299271038	603	dbSNP
rs142945535	606	dbSNP
rs976746221	608	dbSNP
rs1463541688	609	dbSNP
rs1267355259	610	dbSNP
rs1313812392	613	dbSNP
rs569698386	618	dbSNP
rs1260090924	622	dbSNP
rs1352514748	623	dbSNP
rs1027638161	634	dbSNP
rs943956331	635	dbSNP
rs138624977	646	dbSNP
rs911117231	651	dbSNP
rs184606761	661	dbSNP
rs1055137327	662	dbSNP
rs937154774	666	dbSNP
rs759924946	667	dbSNP
rs907062574	668	dbSNP
rs1177350126	670	dbSNP
rs1363729543	674	dbSNP
rs778109356	687	dbSNP
rs1321995030	688	dbSNP
rs1331875847	694	dbSNP
rs1439706344	695	dbSNP
rs945976737	699	dbSNP
rs1138599	702	dbSNP
rs1369394944	706	dbSNP
rs1219589737	707	dbSNP
rs192120099	709	dbSNP
rs1327028574	710	dbSNP
rs989787354	712	dbSNP
rs1365102036	713	dbSNP
rs747678054	714	dbSNP
rs867703940	718	dbSNP
rs1321738900	722	dbSNP
rs144651285	725	dbSNP
rs528749137	726	dbSNP
rs1035770733	727	dbSNP
rs1138603	732	dbSNP
rs1138604	736	dbSNP
rs1138605	737	dbSNP
rs1138606	738	dbSNP
rs1002501367	740	dbSNP
rs1138607	741	dbSNP
rs1250367656	742	dbSNP
rs1172339833	745	dbSNP
rs974906340	748	dbSNP
rs1465288612	750	dbSNP
rs971402621	752	dbSNP
rs1023921329	753	dbSNP
rs1012896784	755	dbSNP
rs1460482062	763	dbSNP
rs1162185298	766	dbSNP
rs894020307	768	dbSNP
rs1053952765	769	dbSNP
rs780621861	773	dbSNP
rs966231585	782	dbSNP
rs999619456	785	dbSNP
rs187495378	788	dbSNP
rs1193759331	789	dbSNP
rs754629969	797	dbSNP
rs1138626	802	dbSNP
rs1199649133	803	dbSNP
rs1138627	808	dbSNP
rs994755962	817	dbSNP
rs751207950	818	dbSNP
rs543174713	820	dbSNP
rs1004074966	821	dbSNP
rs1138638	825	dbSNP
rs1253175859	826	dbSNP
rs1474572517	830	dbSNP
rs944024311	837	dbSNP
rs911200111	838	dbSNP
rs1415396169	842	dbSNP
rs1405562637	848	dbSNP
rs1169388780	850	dbSNP
rs549335507	852	dbSNP
rs931226157	853	dbSNP
rs919792117	858	dbSNP
rs140741038	862	dbSNP
rs1341482926	863	dbSNP
rs1447320088	867	dbSNP
rs1282477071	874	dbSNP
rs1381479473	874	dbSNP
rs961111964	875	dbSNP
rs928378815	883	dbSNP
rs1299027757	888	dbSNP
rs1274211467	889	dbSNP
rs1340403200	890	dbSNP
rs1207783867	891	dbSNP
rs1275914534	892	dbSNP
rs74487886	893	dbSNP
rs74409989	894	dbSNP
rs1427368031	895	dbSNP
rs74354330	896	dbSNP
rs1238698638	906	dbSNP
rs1472873063	906	dbSNP
rs1185514845	907	dbSNP
rs10655321	910	dbSNP
rs1451054824	910	dbSNP
rs1169007114	911	dbSNP
rs1336159629	911	dbSNP
rs1374674686	911	dbSNP
rs1412653194	911	dbSNP
rs201219288	911	dbSNP
rs557106289	911	dbSNP
rs1054377856	913	dbSNP
rs1344834372	914	dbSNP
rs1442424797	914	dbSNP
rs981588392	914	dbSNP
rs1245763270	915	dbSNP
rs1465954431	918	dbSNP
rs1339217313	926	dbSNP
rs372875944	929	dbSNP
rs1023052244	931	dbSNP
rs1476928413	934	dbSNP
rs1012539970	935	dbSNP
rs1425830647	941	dbSNP
rs1375694384	943	dbSNP
rs1175076677	944	dbSNP
rs1386597356	954	dbSNP
rs958243499	956	dbSNP
rs1437545079	957	dbSNP
rs1321538376	959	dbSNP
rs1389056855	960	dbSNP
rs1330823800	968	dbSNP
rs1231533460	970	dbSNP
rs766246646	971	dbSNP
rs115607969	982	dbSNP
rs758098121	984	dbSNP
rs902610625	987	dbSNP
rs754880297	996	dbSNP
rs1208904791	999	dbSNP
rs1041164223	1007	dbSNP
rs950885845	1025	dbSNP
rs1008710599	1027	dbSNP
rs536186509	1034	dbSNP
rs182867532	1037	dbSNP
rs1050182933	1047	dbSNP
rs14269	1052	dbSNP
rs534604960	1055	dbSNP
rs1390328572	1059	dbSNP
rs1385404397	1061	dbSNP
rs569514314	1062	dbSNP
rs1332077856	1066	dbSNP
rs1234311154	1068	dbSNP
rs919802880	1072	dbSNP
rs1287067216	1076	dbSNP
rs1036841919	1077	dbSNP
rs939825780	1081	dbSNP
rs928442164	1084	dbSNP
rs766060179	1085	dbSNP
rs1290324257	1093	dbSNP
rs981255418	1113	dbSNP
rs1253890774	1114	dbSNP
rs555288657	1116	dbSNP
rs1182648147	1121	dbSNP
rs970205088	1122	dbSNP
rs1456551342	1123	dbSNP
rs1369544147	1125	dbSNP
rs535608410	1126	dbSNP
rs879094841	1129	dbSNP
rs1411088863	1134	dbSNP
rs569677692	1136	dbSNP
rs971190248	1144	dbSNP
rs958294601	1156	dbSNP
rs1032567246	1161	dbSNP
rs1352892532	1162	dbSNP
rs1162531296	1169	dbSNP
rs978326246	1170	dbSNP
rs1475428441	1174	dbSNP
rs1425626512	1179	dbSNP
rs1246519649	1185	dbSNP
rs1284440438	1186	dbSNP
rs1010035333	1208	dbSNP
rs941456806	1210	dbSNP
rs569121463	1212	dbSNP
rs1008344886	1213	dbSNP
rs889832709	1215	dbSNP
rs556214496	1216	dbSNP
rs1054366476	1217	dbSNP
rs1028282386	1221	dbSNP
rs1422192753	1223	dbSNP
rs1189805806	1230	dbSNP
rs995441795	1241	dbSNP
rs550839340	1244	dbSNP
rs900149853	1252	dbSNP
rs898429167	1253	dbSNP
rs1036935027	1254	dbSNP
rs1039139981	1256	dbSNP
rs1233602531	1263	dbSNP
rs939933022	1270	dbSNP
rs1302835018	1273	dbSNP
rs1206736275	1276	dbSNP
rs1449889476	1279	dbSNP
rs1397277135	1285	dbSNP
rs111518969	1286	dbSNP
rs911590692	1290	dbSNP
rs1337558444	1291	dbSNP
rs765111540	1293	dbSNP
rs948501411	1294	dbSNP
rs1342688635	1296	dbSNP
rs1232421145	1299	dbSNP
rs1254187225	1309	dbSNP
rs1228159551	1315	dbSNP
rs1482296292	1320	dbSNP
rs1372161411	1322	dbSNP
rs1243880177	1331	dbSNP
rs1279710499	1336	dbSNP
rs1186982842	1341	dbSNP
rs1392402110	1342	dbSNP
rs1443764867	1350	dbSNP
rs1429497173	1353	dbSNP
rs377283936	1354	dbSNP
rs915623764	1358	dbSNP
rs929466738	1361	dbSNP
rs920800356	1362	dbSNP
rs1461953879	1363	dbSNP
rs1432434582	1366	dbSNP
rs775718708	1369	dbSNP
rs570465173	1376	dbSNP
rs1156694322	1382	dbSNP
rs1472110922	1383	dbSNP
rs78635371	1384	dbSNP
rs1179131054	1385	dbSNP
rs1477145349	1387	dbSNP
rs978378781	1390	dbSNP
rs1328648817	1391	dbSNP
rs1246252565	1394	dbSNP
rs967355500	1398	dbSNP
rs926906699	1399	dbSNP
rs190206678	1402	dbSNP
rs1208509697	1405	dbSNP
rs1317844310	1416	dbSNP
rs970756599	1418	dbSNP
rs57305444	1419	dbSNP
rs879461107	1420	dbSNP
rs955855919	1423	dbSNP
rs1457138872	1426	dbSNP
rs1032871474	1428	dbSNP
rs1369548176	1434	dbSNP
rs759900227	1438	dbSNP
rs1225152922	1440	dbSNP
rs549341388	1442	dbSNP
rs1028333243	1445	dbSNP
rs995534621	1448	dbSNP
rs900390871	1459	dbSNP
rs1302146640	1461	dbSNP
rs1317717885	1461	dbSNP
rs1440924545	1462	dbSNP
rs898543514	1463	dbSNP
rs1489705004	1464	dbSNP
rs564981961	1467	dbSNP
rs1251733730	1473	dbSNP
rs1452831764	1474	dbSNP
rs1471300720	1474	dbSNP
rs1015542677	1483	dbSNP
rs1183689430	1493	dbSNP
rs1408130420	1496	dbSNP
rs1004142860	1497	dbSNP
rs907077304	1517	dbSNP
rs1351349772	1523	dbSNP
rs774689703	1529	dbSNP
rs1307298759	1530	dbSNP
rs1368656385	1532	dbSNP
rs1047464311	1535	dbSNP
rs529472964	1540	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.

- mBio, 2013

UNLABELLED: The question of how HIV-1 interfaces with cellular microRNA (miRNA) biogenesis and effector mechanisms has been highly controversial. Here, we first used deep sequencing of small RNAs present in two different infected cell lines (TZM-bl and C8166) and two types of primary human cells (CD4(+) peripheral blood mononuclear cells [PBMCs] and macrophages) to unequivocally demonstrate that HIV-1 does not encode any viral miRNAs. Perhaps surprisingly, we also observed that infection of T cells by HIV-1 has only a modest effect on the expression of cellular miRNAs at early times after infection. Comprehensive analysis of miRNA binding to the HIV-1 genome using the photoactivatable ribonucleoside-induced cross-linking and immunoprecipitation (PAR-CLIP) technique revealed several binding sites for cellular miRNAs, a subset of which were shown to be capable of mediating miRNA-mediated repression of gene expression. However, the main finding from this analysis is that HIV-1 transcripts are largely refractory to miRNA binding, most probably due to extensive viral RNA secondary structure. Together, these data demonstrate that HIV-1 neither encodes viral miRNAs nor strongly influences cellular miRNA expression, at least early after infection, and imply that HIV-1 transcripts have evolved to avoid inhibition by preexisting cellular miRNAs by adopting extensive RNA secondary structures that occlude most potential miRNA binding sites. IMPORTANCE: MicroRNAs (miRNAs) are a ubiquitous class of small regulatory RNAs that serve as posttranscriptional regulators of gene expression. Previous work has suggested that HIV-1 might subvert the function of the cellular miRNA machinery by expressing viral miRNAs or by dramatically altering the level of cellular miRNA expression. Using very sensitive approaches, we now demonstrate that neither of these ideas is in fact correct. Moreover, HIV-1 transcripts appear to largely avoid regulation by cellular miRNAs by adopting an extensive RNA secondary structure that occludes the ability of cellular miRNAs to interact with viral mRNAs. Together, these data suggest that HIV-1, rather than seeking to control miRNA function in infected cells, has instead evolved a mechanism to become largely invisible to cellular miRNA effector mechanisms.

- 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.