>MYC|NM_002467|3'UTR
   1 GGAAAAGTAAGGAAAACGATTCCTTCTAACAGAAATGTCCTGAGCAATCACCTATGAACTTGTTTCAAATGCATGATCAA
  81 ATGCAACCTCACAACCTTGGCTGAGTCTTGAGACTGAAAGATTTAGCCATAATGTAAACTGCCTCAAATTGGACTTTGGG
 161 CATAAAAGAACTTTTTTATGCTTACCATCTTTTTTTTTTCTTTAACAGATTTGTATTTAAGAATTGTTTTTAAAAAATTT
 241 TAAGATTTACACAATGTTTCTCTGTAAATATTGCCATTAAATGTAAATAACTTTAATAAAACGTTTATAGCAGTTACACA
 321 GAATTTCAATCCTAGTATATAGTACCTAGTATTATAGGTACTATAAACCCTAATTTTTTTTATTTAAGTACATTTTGCTT
 401 TTTAAAGTTGATTTTTTTCTATTGTTTTTAGAAAAAATAAAATAACTGGCAAATATATCATTGAGCCAAATCTTAAAAAA
 481 AAAAAAAAA

ID	Duplex structure	Position	Score	MFE
1	miRNA 3' auuucGUCGUGUCAUUAUAAcc 5' :||:|| ||:|||| Target 5' gtataTAGTAC-CTAGTATTat 3'	335 - 355	120.00	-6.70
2	miRNA 3' auUUC---GUCGUGUCAUUAUAacc 5' ||| :||| || ||||:| Target 5' gaAAGATTTAGC-CA-TAATGTaaa 3'	116 - 138	102.00	-5.72
3	miRNA 3' auuUCGUC---GUGUCAUUAUAacc 5' ||||| ||||| ||| | Target 5' tatAGCAGTTACACAG-AATTTcaa 3'	306 - 329	98.00	-9.93

Mutant ID	Mutant Position	Mutant Source
COSN14324859	18	COSMIC
COSN31491901	25	COSMIC
COSN31573866	36	COSMIC
COSN30461269	41	COSMIC
COSN15315257	51	COSMIC
COSN30479950	53	COSMIC
COSN30646181	68	COSMIC
COSN9597076	69	COSMIC
COSN30496495	79	COSMIC
COSN31530358	79	COSMIC
COSN5674198	107	COSMIC
COSN30452818	115	COSMIC
COSN9255250	126	COSMIC
COSN9597077	129	COSMIC
COSN9597078	133	COSMIC
COSN18733201	179	COSMIC
COSN15664850	200	COSMIC
COSN31602668	230	COSMIC
COSN31772579	238	COSMIC
COSN30175029	293	COSMIC
COSN1359443	320	COSMIC
COSN14898034	357	COSMIC
COSN28763683	387	COSMIC
COSN31772580	450	COSMIC

Mutant ID	Mutant Position	Mutant Source
rs1362443865	2	dbSNP
rs779751378	6	dbSNP
rs200447778	10	dbSNP
rs1331275161	11	dbSNP
rs1452207357	13	dbSNP
rs768701719	16	dbSNP
rs373561075	18	dbSNP
rs367692900	19	dbSNP
rs1438303994	21	dbSNP
rs1281624150	29	dbSNP
rs931069152	30	dbSNP
rs774015583	31	dbSNP
rs747913772	33	dbSNP
rs181048497	41	dbSNP
rs1353515183	44	dbSNP
rs35524866	45	dbSNP
rs546100354	45	dbSNP
rs949093702	46	dbSNP
rs200570465	47	dbSNP
rs907487353	49	dbSNP
rs759911200	50	dbSNP
rs2070583	51	dbSNP
rs576408843	52	dbSNP
rs1245476064	53	dbSNP
rs1003352425	54	dbSNP
rs1031845666	55	dbSNP
rs893273346	56	dbSNP
rs1190366265	57	dbSNP
rs1388324174	58	dbSNP
rs1474451314	59	dbSNP
rs760393718	69	dbSNP
rs1391577072	91	dbSNP
rs149534345	95	dbSNP
rs1028803920	97	dbSNP
rs1363132641	106	dbSNP
rs544605712	107	dbSNP
rs14607	110	dbSNP
rs1006494666	111	dbSNP
rs1436355649	115	dbSNP
rs185650723	128	dbSNP
rs4645970	130	dbSNP
rs1427861623	133	dbSNP
rs987235223	139	dbSNP
rs1226030225	143	dbSNP
rs542316783	144	dbSNP
rs1019568567	160	dbSNP
rs1192842372	163	dbSNP
rs961317581	169	dbSNP
rs1266830942	173	dbSNP
rs975108386	179	dbSNP
rs1483468160	183	dbSNP
rs1028404221	186	dbSNP
rs1307281064	190	dbSNP
rs371119850	190	dbSNP
rs986942649	190	dbSNP
rs924487690	201	dbSNP
rs560444505	205	dbSNP
rs1301946221	231	dbSNP
rs1371960357	232	dbSNP
rs934456533	232	dbSNP
rs990034221	233	dbSNP
rs753508752	237	dbSNP
rs1461351266	238	dbSNP
rs972586894	239	dbSNP
rs919772233	252	dbSNP
rs143895359	254	dbSNP
rs1210404336	255	dbSNP
rs931114049	256	dbSNP
rs990648738	257	dbSNP
rs1246093632	259	dbSNP
rs1472952830	266	dbSNP
rs1254330747	277	dbSNP
rs1427804412	290	dbSNP
rs1188205475	291	dbSNP
rs907186988	303	dbSNP
rs552525496	304	dbSNP
rs1321949168	313	dbSNP
rs564425416	321	dbSNP
rs949155742	322	dbSNP
rs190322311	338	dbSNP
rs778430083	339	dbSNP
rs923561358	344	dbSNP
rs1304464370	360	dbSNP
rs934906579	361	dbSNP
rs1053336677	362	dbSNP
rs752036530	364	dbSNP
rs1163039403	368	dbSNP
rs1468183786	370	dbSNP
rs1016431498	374	dbSNP
rs886607980	374	dbSNP
rs893327404	374	dbSNP
rs1179956021	387	dbSNP
rs900793735	387	dbSNP
rs550160158	392	dbSNP
rs1049908801	398	dbSNP
rs1185749197	399	dbSNP
rs889904780	399	dbSNP
rs568518631	408	dbSNP
rs1330660879	412	dbSNP
rs562624244	412	dbSNP
rs955185283	412	dbSNP
rs1258379502	414	dbSNP
rs535929859	420	dbSNP
rs1019578422	421	dbSNP
rs529405092	426	dbSNP
rs1031804737	432	dbSNP
rs1314420816	432	dbSNP
rs1382114180	432	dbSNP
rs1381732668	434	dbSNP
rs755565767	444	dbSNP
rs1341676481	448	dbSNP
rs1242050026	450	dbSNP
rs1156821729	451	dbSNP
rs994062577	451	dbSNP
rs955782808	458	dbSNP
rs989981761	460	dbSNP
rs1359749415	461	dbSNP
rs914389805	462	dbSNP
rs1242892491	470	dbSNP
rs1189793239	486	dbSNP
rs781405135	487	dbSNP
rs1026880159	491	dbSNP
rs1229881592	496	dbSNP
rs548284320	497	dbSNP
rs1243296011	503	dbSNP
rs1266883844	503	dbSNP
rs991092766	507	dbSNP
rs916415070	508	dbSNP
rs1258251930	510	dbSNP
rs1437194341	511	dbSNP
rs928673770	525	dbSNP
rs1381787358	526	dbSNP
rs970886207	537	dbSNP
rs566471603	543	dbSNP
rs923613724	544	dbSNP
rs148188362	546	dbSNP
rs1037895418	547	dbSNP
rs1371921454	559	dbSNP
rs34682115	560	dbSNP
rs1473013197	565	dbSNP
rs1193066431	573	dbSNP
rs541510321	575	dbSNP
rs1270355743	580	dbSNP
rs1362352940	580	dbSNP
rs1219836396	582	dbSNP
rs1490065537	588	dbSNP
rs1275106389	590	dbSNP
rs914837117	591	dbSNP
rs996455670	593	dbSNP
rs1030961340	596	dbSNP
rs1269564322	605	dbSNP
rs890805369	608	dbSNP
rs1331774956	609	dbSNP
rs1173655072	616	dbSNP
rs1304985662	625	dbSNP
rs947656300	634	dbSNP
rs558826267	637	dbSNP
rs1365254438	648	dbSNP
rs889924017	650	dbSNP
rs778102478	654	dbSNP
rs376385237	658	dbSNP
rs1394760437	660	dbSNP
rs955814959	661	dbSNP
rs1011269784	662	dbSNP
rs1021428607	663	dbSNP
rs969843417	665	dbSNP
rs749564337	672	dbSNP
rs560392947	678	dbSNP
rs928506151	679	dbSNP
rs1411208748	682	dbSNP
rs1435911709	685	dbSNP
rs1286086243	687	dbSNP
rs1041083667	693	dbSNP
rs141503199	702	dbSNP
rs983896024	703	dbSNP
rs907855814	711	dbSNP
rs1221837881	717	dbSNP
rs994155868	719	dbSNP
rs1280413062	723	dbSNP
rs1037759950	730	dbSNP
rs1210102346	731	dbSNP
rs1328524787	733	dbSNP
rs1026932841	735	dbSNP
rs181649764	742	dbSNP
rs1409016604	752	dbSNP
rs1174895022	753	dbSNP
rs186781003	754	dbSNP
rs1412032870	755	dbSNP
rs574790380	757	dbSNP
rs1483423768	758	dbSNP
rs932109332	768	dbSNP
rs1012126869	779	dbSNP
rs774632440	781	dbSNP
rs1051930848	789	dbSNP
rs1462486047	790	dbSNP
rs1023896394	795	dbSNP
rs890742830	798	dbSNP
rs1322949403	799	dbSNP
rs572241574	807	dbSNP
rs1284998838	820	dbSNP
rs541930040	821	dbSNP
rs1225690294	823	dbSNP
rs999765993	827	dbSNP
rs970557438	836	dbSNP
rs1248752892	840	dbSNP
rs981876945	842	dbSNP
rs923710357	843	dbSNP
rs1453917788	844	dbSNP
rs192089690	849	dbSNP
rs1335376628	852	dbSNP
rs989180728	855	dbSNP
rs1052750043	862	dbSNP
rs1160564541	871	dbSNP
rs1398605629	876	dbSNP
rs1200087225	880	dbSNP
rs1163449352	885	dbSNP
rs906824192	886	dbSNP
rs369999379	888	dbSNP
rs1182946577	889	dbSNP
rs1021292790	893	dbSNP
rs1173571178	894	dbSNP
rs1242791369	896	dbSNP
rs1218110368	898	dbSNP
rs554217507	900	dbSNP
rs1001806624	901	dbSNP
rs1431165657	905	dbSNP
rs1296091102	909	dbSNP
rs1313317196	914	dbSNP
rs183850214	924	dbSNP
rs944231870	925	dbSNP
rs1303073506	927	dbSNP
rs983373244	928	dbSNP
rs1368554361	929	dbSNP
rs1303407544	931	dbSNP
rs545977969	938	dbSNP
rs1383161009	944	dbSNP
rs4645971	949	dbSNP
rs775305295	950	dbSNP
rs1421646129	957	dbSNP
rs1184673670	959	dbSNP
rs1484961887	960	dbSNP
rs1241542155	962	dbSNP
rs963350284	963	dbSNP
rs186425113	967	dbSNP
rs543718581	972	dbSNP
rs1245769786	974	dbSNP
rs1207461493	999	dbSNP
rs1249803703	1001	dbSNP
rs1213278724	1003	dbSNP
rs932082900	1005	dbSNP
rs562110890	1011	dbSNP
rs888419381	1012	dbSNP
rs1210697326	1026	dbSNP
rs1269835976	1028	dbSNP
rs1052388785	1029	dbSNP
rs529667999	1031	dbSNP
rs1391398654	1033	dbSNP
rs1450761255	1035	dbSNP
rs1356038076	1038	dbSNP
rs1168263489	1045	dbSNP
rs1427808502	1046	dbSNP
rs544395121	1052	dbSNP
rs139159192	1053	dbSNP
rs765476985	1058	dbSNP
rs1222000513	1065	dbSNP
rs906426058	1065	dbSNP
rs1003407494	1070	dbSNP
rs566549822	1075	dbSNP
rs527438788	1076	dbSNP
rs1307368804	1084	dbSNP
rs1298233794	1088	dbSNP
rs143798928	1096	dbSNP
rs764712948	1098	dbSNP
rs773551317	1104	dbSNP
rs1212759760	1107	dbSNP
rs4645972	1108	dbSNP
rs189649721	1109	dbSNP
rs1391560030	1122	dbSNP
rs986180555	1124	dbSNP
rs1296167448	1130	dbSNP
rs1461428658	1137	dbSNP
rs146363336	1144	dbSNP
rs1406808798	1147	dbSNP
rs1245727201	1156	dbSNP
rs911505936	1162	dbSNP
rs1467414589	1167	dbSNP
rs1198467607	1178	dbSNP
rs944284119	1185	dbSNP
rs973440966	1190	dbSNP
rs1175907738	1192	dbSNP
rs116768771	1193	dbSNP
rs953617444	1195	dbSNP
rs1320830991	1199	dbSNP
rs182295576	1209	dbSNP
rs912067388	1221	dbSNP
rs930070349	1223	dbSNP
rs1418082464	1224	dbSNP
rs1048444140	1226	dbSNP
rs186907577	1229	dbSNP
rs915529914	1232	dbSNP
rs1166451335	1241	dbSNP
rs1450311714	1245	dbSNP
rs768009219	1248	dbSNP
rs878955999	1254	dbSNP
rs572499713	1256	dbSNP
rs71520682	1287	dbSNP
rs1460697118	1288	dbSNP
rs906483805	1292	dbSNP
rs1042729184	1308	dbSNP
rs1003460090	1312	dbSNP
rs905515204	1317	dbSNP
rs557892493	1331	dbSNP
rs549762957	1348	dbSNP
rs1390605046	1349	dbSNP
rs1428475908	1350	dbSNP
rs1439524655	1352	dbSNP
rs892272524	1354	dbSNP
rs1185999262	1356	dbSNP
rs4645973	1360	dbSNP
rs778333249	1362	dbSNP
rs1258625748	1364	dbSNP
rs370221716	1364	dbSNP
rs1022023630	1365	dbSNP
rs1359932909	1367	dbSNP
rs1316814165	1375	dbSNP
rs953234060	1376	dbSNP
rs1382018014	1383	dbSNP
rs1295318461	1384	dbSNP
rs749509425	1396	dbSNP
rs985847052	1405	dbSNP
rs757623398	1413	dbSNP
rs139430896	1417	dbSNP
rs562389011	1418	dbSNP
rs529598316	1420	dbSNP
rs1214201921	1421	dbSNP
rs745907253	1424	dbSNP
rs1385900463	1426	dbSNP
rs541802702	1427	dbSNP
rs559893073	1428	dbSNP
rs1029419944	1433	dbSNP
rs953379919	1437	dbSNP
rs984676885	1443	dbSNP
rs909996855	1448	dbSNP
rs183498027	1450	dbSNP
rs1490395875	1451	dbSNP
rs1045111964	1460	dbSNP
rs375266627	1467	dbSNP
rs927911672	1474	dbSNP
rs939259613	1475	dbSNP
rs1052325211	1479	dbSNP
rs1229458144	1484	dbSNP
rs4645974	1486	dbSNP
rs981019285	1493	dbSNP
rs926970808	1498	dbSNP
rs1413833784	1508	dbSNP
rs1398799140	1513	dbSNP
rs1158284340	1514	dbSNP
rs1010765105	1519	dbSNP
rs1423170080	1520	dbSNP
rs1448821393	1520	dbSNP
rs936984498	1523	dbSNP
rs1390434454	1524	dbSNP
rs1314776240	1526	dbSNP
rs565975495	1531	dbSNP
rs1476638471	1535	dbSNP
rs768048008	1541	dbSNP
rs1192381206	1548	dbSNP
rs1480475870	1555	dbSNP
rs895605998	1556	dbSNP
rs1196809999	1557	dbSNP
rs940402694	1560	dbSNP
rs1273394514	1564	dbSNP
rs1353674635	1569	dbSNP
rs1337302482	1573	dbSNP
rs1257331219	1588	dbSNP
rs570631438	1590	dbSNP
rs370450661	1602	dbSNP
rs1289234004	1614	dbSNP
rs1043940792	1616	dbSNP
rs1346192556	1624	dbSNP
rs370934681	1626	dbSNP
rs1403280540	1635	dbSNP
rs374076133	1638	dbSNP
rs1007679957	1639	dbSNP
rs1411991446	1642	dbSNP
rs1395054662	1643	dbSNP
rs898968610	1645	dbSNP
rs994773032	1653	dbSNP
rs1050320374	1656	dbSNP
rs1196878432	1657	dbSNP
rs1313345023	1659	dbSNP
rs4645975	1668	dbSNP
rs576210279	1678	dbSNP
rs1435856709	1682	dbSNP
rs965655026	1684	dbSNP
rs998410064	1688	dbSNP
rs1025875179	1696	dbSNP
rs1485068519	1703	dbSNP
rs775454005	1707	dbSNP
rs1182440846	1708	dbSNP
rs956812868	1712	dbSNP
rs1468381800	1720	dbSNP
rs1324394335	1722	dbSNP
rs1265014829	1726	dbSNP
rs1176456458	1741	dbSNP
rs951619162	1749	dbSNP
rs1425637769	1753	dbSNP
rs1344654504	1757	dbSNP
rs1009595034	1764	dbSNP
rs4645976	1765	dbSNP
rs1416062962	1770	dbSNP
rs1375124491	1771	dbSNP
rs1171686446	1786	dbSNP
rs746955010	1796	dbSNP
rs1022433552	1801	dbSNP
rs188398428	1802	dbSNP
rs1407659732	1805	dbSNP
rs910038577	1814	dbSNP
rs1173555274	1817	dbSNP
rs1413392428	1819	dbSNP
rs1408344995	1822	dbSNP
rs1373648518	1836	dbSNP
rs1159906509	1840	dbSNP
rs1468453235	1846	dbSNP
rs1379401057	1848	dbSNP
rs1184165028	1851	dbSNP
rs1434245624	1858	dbSNP
rs968164535	1862	dbSNP
rs1208191763	1868	dbSNP
rs981434654	1869	dbSNP
rs193204061	1872	dbSNP
rs981232062	1875	dbSNP
rs1225637793	1877	dbSNP
rs927966274	1880	dbSNP
rs62515808	1884	dbSNP
rs756756340	1889	dbSNP
rs1247360445	1893	dbSNP
rs77023277	1896	dbSNP
rs1368758532	1897	dbSNP
rs565952481	1898	dbSNP
rs1043567498	1899	dbSNP
rs888911114	1906	dbSNP
rs1007321773	1907	dbSNP
rs920426524	1914	dbSNP
rs1398551203	1916	dbSNP
rs1040076536	1921	dbSNP
rs901581696	1929	dbSNP
rs930426921	1935	dbSNP
rs539515638	1936	dbSNP
rs993152114	1939	dbSNP
rs557853775	1945	dbSNP
rs1472524506	1953	dbSNP
rs1242737990	1958	dbSNP
rs1218223151	1960	dbSNP
rs1487396802	1963	dbSNP
rs1285560206	1968	dbSNP
rs1274654133	1974	dbSNP
rs764801483	1979	dbSNP
rs1361995158	1984	dbSNP
rs889080895	1989	dbSNP
rs1203420196	1994	dbSNP

- 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.