>WWP2|NM_007014|3'UTR
   1 CCGAGGCCGCCCCTCCCACGCCCCCCAGCGCACATGTAGTCCTGAGTCCTCCCTGCCTGAGAGGCCACTGGCCCCGCAGC
  81 CCTTGGGAGGCCCCCGTGGATGTGGCCCTGTGTGGGACCACACTGTCATCTCGCTGCTGGCAGAAAAGCCTGATCCCAGG
 161 AGGCCCTGCAGTTCCCCCGACCCGCGGATGGCAGTCTGGAATAAAGCCCCCTAGTTGCCTTTGGCCCCACCTTTGCAAAG
 241 TTCCAGAGGGCTGACCCTCTCTGCAAAACTCTCCCCTGTCCTCTAGACCCCACCCTGGGTGTATGTGAGTGTGCAAGGGA
 321 AGGTGTTGCATCCCCAGGGGCTGCCGCAGAGGCCGGAGACCTCCTGGACTAGTTCGGCGAGGAGACTGGCCACTGGGGGT
 401 GGCTGTTCGGGACTGAGAGCGCCAAGGGTCTTTGCCAGCAAAGGAGGTTCTGCCTGTAATTGAGCCTCTCTGATGATGGA
 481 GATGAAGTGAAGGTCTGAGGGAGCGGGCCCTGGGGCGAGGCCATCTCTGCCTGCCTCCCTAGCAGGCGCCAGCGGTGGAG
 561 GCTGAGTCGCAGGACACATGCCGGCCAGTTAATTCATTCTCAGCCAATGAAGGTTTGTCTAAGCTGCCTGGGTATCCACG
 641 GGACAAAAACAGCAAACTCCCTCAGACTTTGTCCATGTATAAACTTGAAGTGGTTGTGTTGTAGGGTTGCAGGTTTTTTG
 721 TTACGCTGCTGTCACTTTCTGTCCAGGAGCTGGCACCCCAGGTGTTCTGAGACCTTGAGGGACCCAGACCTTTGGGTCCA
 801 AGAGTTTCCCAAACAGCCACGCCTCTCAGGAACCCACCTGGCGGTTCCGTGAGCTCAGGCAGGCCTGACCCGGCGGCACA
 881 GCCTGGCAGGGACCTCGTCCCCAAGCCTGGCAGAATGAGAGGGGTTGAGGTCCCGAGCGCCACTCCTAGCCTTGCCGCCT
 961 TCAATAGAGAAGAAATCCCTTTGCTAGATAGGGTCCCCCAGGCAGTCCCCAGTGGCGGGACACAGGGGTCCGGCTGTGGA
1041 GCTCCCCTGCCAGCCCCTGGAGCTCCAGGAGGGCCTGTTGGTCCCCTGTTCAGAATGGAGTGCAGCCCGCCAGCGGAAAG
1121 TGTTCATTCTGCATAGGTGTGAGGCTTTATCTGCACACAGGACATGAAAACCAGCAGAAAGGCCCTGAGCTGCTGCATAG
1201 CCCCATCTGATTTCTGCAGTTCCCGCCAGCCTCCAACACGGGGACTCTGCCGTAACTGGAATCTTCATAGGTCATATTGA
1281 AATCTTCAAGGTGACCATGCCCCACCGGGGTGCTGGGGCAGTAGTCATGGCAGACTCCCGGCCTGGGCCCCCAGGATTCT
1361 AGGACCCCCAGGCAGCCCCTTGGACTGGTCCCGGGTGCCTTCCAAGCACAGTCTCCATGCTCCCAGATTCTCGACCTTCC
1441 CCCGGCCCGGGAGGTGCAGCCTGCGTCTGCCTCTGTCGTGTGTGCTGATTTGAGTGGCTTAGCTTGCCACAGCGCAGCCT
1521 CTTCTGTCCCTTTCAGTCATTTGCTGTACTTCCCTGTGGCACGTTACCATGGAAGCCGCTCCAGGGTGGGTCAGGGTGCA
1601 AGCTGCTGGTGAGGTTTGGAAGCATCAGGCTCACGGGTGTTCATGTGTGTTCGTGCGTGTGTGTGCGTACGTGTATATAA
1681 CTGAAGTGTCTGTACGGAATGCCCTTTGCTAGCCATGGGCTGGTCACCAGATTGTTTTGTAATGCCCGCCCCTTGCCTCG
1761 ATATTGCCAGTTTCTTGTGCAATAAACAATCAGCAGCTGTGAAAAAAAAAAAAAAAAAA

ID	Duplex structure	Position	Score	MFE
1	miRNA 3' gggGGUGGUGGUGCGGGc 5' || |: |||||||| Target 5' ccgCCCCTCCCACGCCCc 3'	7 - 24	155.00	-25.20
2	miRNA 3' ggGGG--UGGUGGUGCGGGc 5' ||| || :|||||||: Target 5' ttCCCAAACAGCCACGCCTc 3'	806 - 825	142.00	-24.30
3	miRNA 3' ggggguggUGGUGCGGGc 5' ||||:|||| Target 5' tcaaggtgACCATGCCCc 3'	1286 - 1303	134.00	-15.50

Mutant ID	Mutant Position	Mutant Source
COSN1189947	20	COSMIC
COSN30503476	27	COSMIC
COSN13684771	30	COSMIC
COSN13684772	31	COSMIC
COSN30150016	40	COSMIC
COSN30156692	60	COSMIC
COSN30156702	70	COSMIC
COSN31505842	73	COSMIC
COSN30535899	122	COSMIC
COSN28189002	144	COSMIC
COSN30540375	180	COSMIC
COSN16131943	185	COSMIC
COSN5836717	187	COSMIC
COSN30166234	231	COSMIC
COSN31592761	409	COSMIC
COSN31578413	422	COSMIC
COSN31603827	526	COSMIC
COSN6092890	640	COSMIC
COSN28822579	897	COSMIC
COSN31565712	920	COSMIC
COSN31540556	947	COSMIC
COSN31603200	1344	COSMIC
COSN28478843	1393	COSMIC
COSN28654304	1427	COSMIC
COSN31600773	1450	COSMIC
COSN31540331	1465	COSMIC
COSN31593412	1466	COSMIC
COSN32055899	1479	COSMIC
COSN31603531	1578	COSMIC
COSN31577832	1628	COSMIC
COSN31574746	1668	COSMIC
COSN31564409	1669	COSMIC
COSN31605773	1732	COSMIC
COSN6092891	1748	COSMIC
COSN28646918	1789	COSMIC
rs3748387	704	GWAS

Mutant ID	Mutant Position	Mutant Source
rs180971731	3	dbSNP
rs774150015	4	dbSNP
rs761606433	9	dbSNP
rs767373799	10	dbSNP
rs750351965	11	dbSNP
rs374029799	13	dbSNP
rs772048213	14	dbSNP
rs756098646	20	dbSNP
rs368189035	21	dbSNP
rs1252541776	22	dbSNP
rs1290090768	23	dbSNP
rs752759351	26	dbSNP
rs550004825	28	dbSNP
rs758604668	30	dbSNP
rs371004702	31	dbSNP
rs928919362	35	dbSNP
rs956278339	40	dbSNP
rs1358722067	42	dbSNP
rs1462533952	43	dbSNP
rs1300466695	51	dbSNP
rs747312873	53	dbSNP
rs992032404	54	dbSNP
rs1024722603	65	dbSNP
rs914755374	71	dbSNP
rs947426990	75	dbSNP
rs1039551204	76	dbSNP
rs1240511272	77	dbSNP
rs969093615	80	dbSNP
rs1296647818	88	dbSNP
rs532273932	89	dbSNP
rs921949426	93	dbSNP
rs933357764	96	dbSNP
rs919578035	97	dbSNP
rs187148786	99	dbSNP
rs1004770555	101	dbSNP
rs142551098	103	dbSNP
rs899027911	110	dbSNP
rs1011986276	113	dbSNP
rs1302282563	122	dbSNP
rs1422581452	129	dbSNP
rs754886861	130	dbSNP
rs970416599	133	dbSNP
rs940857820	134	dbSNP
rs1003580892	139	dbSNP
rs1244979153	141	dbSNP
rs763933071	144	dbSNP
rs1490567687	145	dbSNP
rs1040551690	152	dbSNP
rs1484241975	153	dbSNP
rs1252343635	158	dbSNP
rs1323167077	167	dbSNP
rs1202060859	170	dbSNP
rs1250413775	171	dbSNP
rs1457870683	174	dbSNP
rs781112716	179	dbSNP
rs772851577	180	dbSNP
rs914724288	183	dbSNP
rs1478418674	184	dbSNP
rs1398386568	185	dbSNP
rs748150237	186	dbSNP
rs974854315	187	dbSNP
rs1178657016	189	dbSNP
rs1480840548	191	dbSNP
rs144814265	192	dbSNP
rs1001299232	195	dbSNP
rs749631853	201	dbSNP
rs933430213	206	dbSNP
rs1251726096	207	dbSNP
rs1052359636	214	dbSNP
rs1195627334	220	dbSNP
rs1052173000	228	dbSNP
rs1265606472	252	dbSNP
rs1168684482	255	dbSNP
rs907900181	256	dbSNP
rs548292304	257	dbSNP
rs1175929311	265	dbSNP
rs1205012693	270	dbSNP
rs1399817118	276	dbSNP
rs1323632800	282	dbSNP
rs1466221224	287	dbSNP
rs192495025	294	dbSNP
rs1337271176	296	dbSNP
rs1024775098	299	dbSNP
rs1371083168	300	dbSNP
rs969228068	305	dbSNP
rs1451760240	307	dbSNP
rs1001924788	308	dbSNP
rs774696446	314	dbSNP
rs1405466682	317	dbSNP
rs898996914	323	dbSNP
rs527928748	324	dbSNP
rs377569189	326	dbSNP
rs1044906941	328	dbSNP
rs906238198	331	dbSNP
rs1027179084	337	dbSNP
rs952393911	345	dbSNP
rs371077322	346	dbSNP
rs908108931	347	dbSNP
rs1461340728	355	dbSNP
rs962234161	356	dbSNP
rs1198273553	362	dbSNP
rs976305490	363	dbSNP
rs1294427219	366	dbSNP
rs571009963	376	dbSNP
rs1010479057	377	dbSNP
rs768372983	378	dbSNP
rs1050516735	379	dbSNP
rs372011074	380	dbSNP
rs112010616	387	dbSNP
rs767991582	389	dbSNP
rs141371236	390	dbSNP
rs1052831340	394	dbSNP
rs1334761464	395	dbSNP
rs1029176158	397	dbSNP
rs1158217041	401	dbSNP
rs1452008684	409	dbSNP
rs954936968	410	dbSNP
rs532675420	416	dbSNP
rs1241889195	418	dbSNP
rs1474011114	421	dbSNP
rs568465895	422	dbSNP
rs1261921645	426	dbSNP
rs117730544	446	dbSNP
rs1351181918	447	dbSNP
rs879049361	448	dbSNP
rs907869384	449	dbSNP
rs1478247644	453	dbSNP
rs554278499	466	dbSNP
rs1282425580	467	dbSNP
rs1172932064	469	dbSNP
rs1404059570	478	dbSNP
rs1046358577	483	dbSNP
rs181478010	485	dbSNP
rs1380777885	493	dbSNP
rs1367734791	495	dbSNP
rs1304112864	502	dbSNP
rs1424496704	505	dbSNP
rs150814804	506	dbSNP
rs948003067	508	dbSNP
rs1360118974	511	dbSNP
rs1026729907	516	dbSNP
rs1360770911	517	dbSNP
rs1373177489	522	dbSNP
rs1428394046	523	dbSNP
rs1045269953	524	dbSNP
rs1270671157	526	dbSNP
rs1222945647	546	dbSNP
rs1490126832	548	dbSNP
rs746235428	549	dbSNP
rs1003972903	554	dbSNP
rs1015635148	555	dbSNP
rs1269642611	565	dbSNP
rs965031142	569	dbSNP
rs1347611070	570	dbSNP
rs1284248317	579	dbSNP
rs879002753	583	dbSNP
rs1348520864	584	dbSNP
rs976292509	585	dbSNP
rs892128261	587	dbSNP
rs3748388	606	dbSNP
rs1476592959	609	dbSNP
rs576592287	624	dbSNP
rs544515365	628	dbSNP
rs1199715593	629	dbSNP
rs776125108	632	dbSNP
rs866285341	637	dbSNP
rs904745172	639	dbSNP
rs953545423	640	dbSNP
rs562617576	641	dbSNP
rs773291424	645	dbSNP
rs1196829646	652	dbSNP
rs986738367	654	dbSNP
rs1029560445	659	dbSNP
rs925484198	660	dbSNP
rs954930990	662	dbSNP
rs761311112	664	dbSNP
rs529727451	665	dbSNP
rs988263769	666	dbSNP
rs541450527	670	dbSNP
rs764808007	677	dbSNP
rs949392197	680	dbSNP
rs560240794	684	dbSNP
rs905147684	694	dbSNP
rs973340469	699	dbSNP
rs3748387	704	dbSNP
rs947939074	707	dbSNP
rs980736386	712	dbSNP
rs1232169830	714	dbSNP
rs1048669039	725	dbSNP
rs888288335	726	dbSNP
rs552262549	740	dbSNP
rs1004344712	742	dbSNP
rs1203165630	745	dbSNP
rs764226847	746	dbSNP
rs1286691048	748	dbSNP
rs1224619501	751	dbSNP
rs1401615202	754	dbSNP
rs1300973233	760	dbSNP
rs1307645836	761	dbSNP
rs1455085297	762	dbSNP
rs564686948	765	dbSNP
rs900829554	774	dbSNP
rs1436577104	777	dbSNP
rs997846513	783	dbSNP
rs1052180637	786	dbSNP
rs913621293	789	dbSNP
rs76061922	790	dbSNP
rs1401021033	792	dbSNP
rs899522891	800	dbSNP
rs369166433	806	dbSNP
rs554657380	810	dbSNP
rs986404176	812	dbSNP
rs141546398	814	dbSNP
rs3748386	817	dbSNP
rs1285887318	821	dbSNP
rs535886334	822	dbSNP
rs1219178950	824	dbSNP
rs1244003462	831	dbSNP
rs1267045643	841	dbSNP
rs1446745684	842	dbSNP
rs375396780	843	dbSNP
rs537495503	844	dbSNP
rs1248691337	845	dbSNP
rs113525332	849	dbSNP
rs914010211	850	dbSNP
rs1227184845	853	dbSNP
rs865953955	864	dbSNP
rs1248579700	872	dbSNP
rs536509822	873	dbSNP
rs759246601	875	dbSNP
rs1426386774	876	dbSNP
rs1385714447	880	dbSNP
rs1164009172	887	dbSNP
rs1158046447	892	dbSNP
rs767359680	896	dbSNP
rs375220060	897	dbSNP
rs1048324049	898	dbSNP
rs1421300817	900	dbSNP
rs1477606885	901	dbSNP
rs1261377538	902	dbSNP
rs1161364301	916	dbSNP
rs1490617956	924	dbSNP
rs62053264	931	dbSNP
rs1220037194	933	dbSNP
rs1386942844	934	dbSNP
rs1297065506	935	dbSNP
rs368232669	936	dbSNP
rs1036738764	939	dbSNP
rs373922674	940	dbSNP
rs1275916738	941	dbSNP
rs1445394154	942	dbSNP
rs1264745377	947	dbSNP
rs552893487	947	dbSNP
rs997898824	951	dbSNP
rs1027909412	957	dbSNP
rs889480133	958	dbSNP
rs369500889	962	dbSNP
rs367985081	965	dbSNP
rs1210704762	968	dbSNP
rs1267066688	975	dbSNP
rs1189868634	980	dbSNP
rs527829805	986	dbSNP
rs1481874950	988	dbSNP
rs576654631	990	dbSNP
rs1204603482	991	dbSNP
rs1316823572	1004	dbSNP
rs1292289168	1012	dbSNP
rs1008198028	1018	dbSNP
rs1032623064	1020	dbSNP
rs913755601	1024	dbSNP
rs958427999	1025	dbSNP
rs1300274414	1029	dbSNP
rs976337181	1030	dbSNP
rs1009774524	1032	dbSNP
rs77771398	1033	dbSNP
rs1465154608	1037	dbSNP
rs1398259138	1048	dbSNP
rs970767375	1064	dbSNP
rs920923985	1067	dbSNP
rs1470399399	1068	dbSNP
rs982194453	1074	dbSNP
rs1377301944	1082	dbSNP
rs926586055	1092	dbSNP
rs959412717	1094	dbSNP
rs1051206478	1110	dbSNP
rs1456907727	1112	dbSNP
rs890678100	1113	dbSNP
rs1205039602	1116	dbSNP
rs984427705	1118	dbSNP
rs1367728976	1121	dbSNP
rs1458189070	1122	dbSNP
rs545345905	1124	dbSNP
rs1488305096	1134	dbSNP
rs1445997935	1135	dbSNP
rs939841654	1137	dbSNP
rs1374606250	1141	dbSNP
rs1338720639	1150	dbSNP
rs1393855582	1159	dbSNP
rs1036791369	1163	dbSNP
rs537628040	1177	dbSNP
rs1401765755	1181	dbSNP
rs1464655637	1183	dbSNP
rs922445064	1187	dbSNP
rs933720788	1193	dbSNP
rs1331390761	1199	dbSNP
rs1049483071	1202	dbSNP
rs1171100016	1203	dbSNP
rs1191139589	1204	dbSNP
rs889438149	1206	dbSNP
rs1455652242	1210	dbSNP
rs1364779582	1212	dbSNP
rs1158451460	1213	dbSNP
rs1036462982	1217	dbSNP
rs1387644590	1219	dbSNP
rs1401696069	1225	dbSNP
rs898019895	1226	dbSNP
rs994868811	1229	dbSNP
rs1027771436	1231	dbSNP
rs1198418825	1238	dbSNP
rs556461945	1240	dbSNP
rs574641439	1241	dbSNP
rs73580178	1243	dbSNP
rs576132072	1252	dbSNP
rs960590088	1253	dbSNP
rs988080000	1269	dbSNP
rs894089936	1271	dbSNP
rs1339998851	1272	dbSNP
rs1332401441	1277	dbSNP
rs1316222840	1279	dbSNP
rs1009827754	1282	dbSNP
rs572037081	1284	dbSNP
rs58227376	1285	dbSNP
rs1297907917	1299	dbSNP
rs558843631	1311	dbSNP
rs1033796723	1316	dbSNP
rs1255376194	1318	dbSNP
rs1367420609	1321	dbSNP
rs959634815	1322	dbSNP
rs984173577	1340	dbSNP
rs1263466560	1341	dbSNP
rs1371017114	1349	dbSNP
rs1477265039	1351	dbSNP
rs564150146	1352	dbSNP
rs1355594675	1367	dbSNP
rs932400005	1373	dbSNP
rs75943235	1379	dbSNP
rs912245254	1381	dbSNP
rs972645720	1386	dbSNP
rs1398526343	1387	dbSNP
rs1347833457	1393	dbSNP
rs922413925	1394	dbSNP
rs1304244622	1395	dbSNP
rs1301667540	1396	dbSNP
rs1389228344	1399	dbSNP
rs550100284	1400	dbSNP
rs1463132645	1407	dbSNP
rs572229827	1407	dbSNP
rs772299867	1408	dbSNP
rs562454532	1410	dbSNP
rs1476700881	1411	dbSNP
rs1338739647	1412	dbSNP
rs1049449376	1415	dbSNP
rs911011240	1424	dbSNP
rs541059948	1427	dbSNP
rs1320172130	1428	dbSNP
rs897990464	1431	dbSNP
rs1197622741	1433	dbSNP
rs1054090375	1434	dbSNP
rs1347649314	1439	dbSNP
rs529566277	1440	dbSNP
rs1329856502	1442	dbSNP
rs1483497079	1444	dbSNP
rs1448327692	1445	dbSNP
rs1400443594	1449	dbSNP
rs891457779	1450	dbSNP
rs747476794	1454	dbSNP
rs1430993112	1459	dbSNP
rs1172877530	1460	dbSNP
rs1477612392	1464	dbSNP
rs548033451	1465	dbSNP
rs565756196	1466	dbSNP
rs1194020678	1467	dbSNP
rs1425310274	1468	dbSNP
rs539423999	1474	dbSNP
rs1430965490	1476	dbSNP
rs1196852298	1477	dbSNP
rs1325851719	1478	dbSNP
rs1003754588	1479	dbSNP
rs1377587061	1483	dbSNP
rs1343377217	1496	dbSNP
rs1466959426	1499	dbSNP
rs1241459796	1504	dbSNP
rs551492317	1514	dbSNP
rs569804020	1515	dbSNP
rs896517728	1517	dbSNP
rs1052429	1518	dbSNP
rs529739947	1525	dbSNP
rs967961562	1552	dbSNP
rs1160115909	1557	dbSNP
rs1440178033	1560	dbSNP
rs1379625296	1563	dbSNP
rs961374295	1564	dbSNP
rs370624389	1567	dbSNP
rs1238250458	1578	dbSNP
rs556088334	1579	dbSNP
rs1440943146	1593	dbSNP
rs1286725598	1596	dbSNP
rs190097585	1599	dbSNP
rs776420750	1607	dbSNP
rs972613128	1624	dbSNP
rs772790067	1627	dbSNP
rs1307799638	1628	dbSNP
rs955203356	1635	dbSNP
rs1380772668	1636	dbSNP
rs548485360	1640	dbSNP
rs1446778408	1644	dbSNP
rs953795936	1648	dbSNP
rs1300620056	1653	dbSNP
rs985343269	1653	dbSNP
rs986975699	1654	dbSNP
rs762373705	1657	dbSNP
rs935723177	1658	dbSNP
rs1156831941	1660	dbSNP
rs990323983	1665	dbSNP
rs1414576689	1667	dbSNP
rs912868160	1668	dbSNP
rs543072918	1671	dbSNP
rs760670277	1672	dbSNP
rs1488201494	1674	dbSNP
rs1284473988	1677	dbSNP
rs1352788757	1691	dbSNP
rs1216998129	1694	dbSNP
rs906818255	1696	dbSNP
rs912214104	1697	dbSNP
rs144809409	1705	dbSNP
rs1190146640	1713	dbSNP
rs939722638	1717	dbSNP
rs1339643461	1722	dbSNP
rs1055260820	1734	dbSNP
rs1434366162	1744	dbSNP
rs770542482	1748	dbSNP
rs144802638	1749	dbSNP
rs1403742688	1757	dbSNP
rs572100716	1761	dbSNP
rs1194712357	1767	dbSNP
rs1419491391	1771	dbSNP
rs1159555260	1776	dbSNP
rs1362722395	1777	dbSNP
rs1261427729	1779	dbSNP
rs1193306010	1783	dbSNP
rs3192882	1789	dbSNP
rs1265371405	1790	dbSNP
rs1220173993	1791	dbSNP
rs1319456429	1792	dbSNP
rs1259556769	1800	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.