>SAP18|NM_005870|3'UTR
   1 ATTCTATTTACTATTTGTTGAATTTATTTTTCCGTCAGTTATGTAAAATAAACATACTCTTCTTCCTCCCCTGATTATTG
  81 CCATTAAGCCTTTAAATTCTAAACAAATTATAATGCATCATCTATTTAGGAGTTAGATTTGGATGTGCTATTGTATGATT
 161 ACGAATAGTCTGTATGTTTCAAGCCCTTCTGTAAAATATGAAGAAAAGTGCTCTTAGCATTCTGTGTAAAACTGTACTGT
 241 TAAATATATGTGTGTAATCAGCCTGAGTGTGAAAGTTAATGGAGGCCTGGGAACAGGGTTTATACTAAGTAGTGGAGGAG
 321 CGTATGGTTAAGCCCAAAGGGGCAGAACAAGAAAGCCACGGGATTGTATGAAATCAAACATGAGTTTGTGGTGTAGACTG
 401 CTGTATGCAGTTGGAAAGGACACGTGAGAGTGAGCTCAAGTGGCAGCAGAGGCAGTTTGGAATAAGCTGCGGCAAGTTGA
 481 AGAAGCTGTGTTGGACGAGATTGCCCCGCCTTGATCAGGGTACCATGACATAAAAGGTTAAAGAACAGGCAACACAATGA
 561 GCACTTAAGTTTTTAACATGTGGGGAATAGGGCATTTTAAAGGCTGGAACCAGTTCAGAGGAAACAAGGGTTTGGGTAGA
 641 GGTAGAAAGGTTTAATTAACCCTGGAGATCTGCAAATGGAGGGAGGGGTGAAGGAGGAATCTTAAGACCGAGGGAGAAGA
 721 GCCAAGGACAAGGTCAGGTTGAATGAGTAGGAGGTGTTCACACATCCTCTTGTGTGCTAGGTAGTGGCGTGCATCTGATC
 801 TGAGAGGCAGTAAAGCAGTGATGAAGACAGTGCAGCAGAACATTGAAGTCCTGATTGCAGCAGTGACTCTGCAACCTTGG
 881 ATAAATTATTTCAATCTTTATTTTGTAAAACGGAGATAACGGCCTATAGGATTGTTAAGACTGAATATTTTAAAAGAGCT
 961 TAGAATGGTGCCTGACAAATGAGAAACAATAAATACTGATTATTGGCCATAAAGTGGTATTAAAACTGGATCTCTTTTCT
1041 TCCATGGCACTACTCTCATTTTGAAGTTTATGAACAGTACGACAGTGTATTGTAAATTCCCTTTAGTTTGTTACAGTAGC
1121 CAATTGAAAATGTATATCCCAAAATTTAAAAAAAAAAGTACCAGCAGCAATAAAATTGCACTAGTTTTATCTGGTACATA
1201 CAAAAACAGCCATTTAAAATCTGATGATTCTGTGGAATTGGTGTCCCTGTTAGCAATGGCAGAGACCAGCCTGGAGCCTA
1281 GATCTGGTGCTTCTTCTGTGCTGTGGTTTACCCCAAACCTTTAGGTTGTTTATTCATTCAGATTAGATAGACTGGAGCCA
1361 TAAAGTTAATTTGCACCTAGCTTTTTGGAGAATAGCCATGATTAACTGCTATTCGTGGTGGGGGTGGGGGGGAACCCTAT
1441 GATTTACTATGCAGATGAAGAGGGTAGGAACTAAATAAAGGACTTTGTAAGCCAAAGTGGTTGGGCTGCTTTGTCAAATT
1521 CCACCCTTTGCTTGGTTCCAACATGGAATTTCTCCTTTAAAGATTTCAATATCCCATCAAAAGTACAGTTAGAGAATACC
1601 TAGTGAATTTATTGAATATAATGCTAAGAATCAAAAGACTTGTACTAGTTTACCTCTGGCTTTGGTAAGTGTGGCTTTGA
1681 GTAATAACTGAGCTGTTTCCCCGCATATAAAATAGAAATAAATAAGTAGTCATCATGACAGCAAAAAAAAAAAAAAAAAA

ID	Duplex structure	Position	Score	MFE
1	miRNA 3' uaagcUACUGAGUCAGAGAAGAa 5' || | || ||||||| Target 5' gtaaaAT-AAACATACTCTTCTt 3'	43 - 64	145.00	-9.40
2	miRNA 3' uaagcuacUGAGUCAGAGAAGAa 5' ||| : ||||||:| Target 5' gtattaaaACTGGATCTCTTTTc 3'	1017 - 1039	139.00	-9.50
3	miRNA 3' uaagcuaCUGAGUCA--GAGAAGAa 5' ||: ::|| :|||||| Target 5' gagcctaGATCTGGTGCTTCTTCTg 3'	1274 - 1298	134.00	-9.90

Mutant ID	Mutant Position	Mutant Source
COSM8917748	1	COSMIC
COSN510542	21	COSMIC
COSN55846	38	COSMIC
COSN30160744	64	COSMIC
COSN30524872	66	COSMIC
COSN30113504	96	COSMIC
COSN30136836	97	COSMIC
COSN30473764	120	COSMIC
COSN30510016	121	COSMIC
COSN9743665	221	COSMIC
COSN28880411	225	COSMIC
COSN30165219	266	COSMIC
COSN195649	591	COSMIC
COSN20110416	703	COSMIC
COSN27087356	710	COSMIC
COSN32061989	714	COSMIC
COSN27085519	1077	COSMIC
COSN17375105	1149	COSMIC
COSN27613205	1163	COSMIC
COSN4734941	1373	COSMIC
COSN6223403	1585	COSMIC

Mutant ID	Mutant Position	Mutant Source
rs768581538	7	dbSNP
rs559646955	14	dbSNP
rs1015191156	15	dbSNP
rs747652682	20	dbSNP
rs771451387	33	dbSNP
rs201857690	34	dbSNP
rs760386842	35	dbSNP
rs369167136	38	dbSNP
rs962258295	39	dbSNP
rs1177831148	41	dbSNP
rs770851175	44	dbSNP
rs574647621	49	dbSNP
rs1168959752	50	dbSNP
rs542068070	53	dbSNP
rs941203755	56	dbSNP
rs1037776824	60	dbSNP
rs1314451439	63	dbSNP
rs1243919089	64	dbSNP
rs1360368568	71	dbSNP
rs930943774	75	dbSNP
rs1381384361	107	dbSNP
rs1294484368	108	dbSNP
rs563489887	110	dbSNP
rs1326657132	114	dbSNP
rs1290477917	116	dbSNP
rs765853412	125	dbSNP
rs1260730027	126	dbSNP
rs113356811	132	dbSNP
rs552331513	136	dbSNP
rs35433859	141	dbSNP
rs1445963780	144	dbSNP
rs138835313	146	dbSNP
rs1484803780	154	dbSNP
rs1446717845	155	dbSNP
rs1260081779	161	dbSNP
rs555282436	163	dbSNP
rs183906377	164	dbSNP
rs1220285492	169	dbSNP
rs1361697145	171	dbSNP
rs1262085480	172	dbSNP
rs1478934146	173	dbSNP
rs1284930048	187	dbSNP
rs754651769	194	dbSNP
rs1324962315	199	dbSNP
rs1197479283	203	dbSNP
rs900642077	205	dbSNP
rs142661589	214	dbSNP
rs1364845628	220	dbSNP
rs1470329352	225	dbSNP
rs1178936096	233	dbSNP
rs904532971	236	dbSNP
rs1474215693	240	dbSNP
rs1453587435	244	dbSNP
rs996141378	248	dbSNP
rs1342714371	249	dbSNP
rs1478365213	253	dbSNP
rs1401495231	267	dbSNP
rs1029099404	283	dbSNP
rs1220910029	288	dbSNP
rs1280935235	297	dbSNP
rs535786713	298	dbSNP
rs1032705076	308	dbSNP
rs1195346322	308	dbSNP
rs1337656177	310	dbSNP
rs955829600	312	dbSNP
rs1218965827	315	dbSNP
rs1009098578	320	dbSNP
rs550832904	322	dbSNP
rs1303407158	323	dbSNP
rs200312611	336	dbSNP
rs1406693588	338	dbSNP
rs1214916145	340	dbSNP
rs995055769	343	dbSNP
rs1407742313	345	dbSNP
rs1027821479	346	dbSNP
rs1168150348	349	dbSNP
rs1466406154	352	dbSNP
rs1261118286	353	dbSNP
rs146031677	360	dbSNP
rs980147500	361	dbSNP
rs1481691281	374	dbSNP
rs1268425704	375	dbSNP
rs1181129110	378	dbSNP
rs189083319	379	dbSNP
rs980021937	381	dbSNP
rs755794737	385	dbSNP
rs1405803665	407	dbSNP
rs192066903	408	dbSNP
rs1160413167	410	dbSNP
rs1362886627	412	dbSNP
rs1278909994	418	dbSNP
rs1345594195	418	dbSNP
rs992714820	421	dbSNP
rs913050083	424	dbSNP
rs945828582	425	dbSNP
rs1331519082	427	dbSNP
rs973939476	428	dbSNP
rs1042998013	430	dbSNP
rs1174686255	444	dbSNP
rs920666960	471	dbSNP
rs1426431866	474	dbSNP
rs1158512948	476	dbSNP
rs929341623	479	dbSNP
rs1047844621	483	dbSNP
rs925839685	484	dbSNP
rs534252868	487	dbSNP
rs1050845840	488	dbSNP
rs1179401649	489	dbSNP
rs1461022211	493	dbSNP
rs1241577365	497	dbSNP
rs911871663	498	dbSNP
rs1370479507	500	dbSNP
rs117922086	501	dbSNP
rs1222000017	506	dbSNP
rs1009387466	508	dbSNP
rs573945849	509	dbSNP
rs1244652650	511	dbSNP
rs897998747	513	dbSNP
rs1355653887	514	dbSNP
rs1338323168	520	dbSNP
rs542168779	525	dbSNP
rs1450565999	530	dbSNP
rs1243485599	538	dbSNP
rs1318162778	542	dbSNP
rs1399452922	555	dbSNP
rs900775145	557	dbSNP
rs1159297760	560	dbSNP
rs563554731	562	dbSNP
rs757457330	563	dbSNP
rs1452415518	564	dbSNP
rs1383557449	565	dbSNP
rs1185658356	567	dbSNP
rs544429500	568	dbSNP
rs185876417	571	dbSNP
rs556100633	578	dbSNP
rs1480330700	579	dbSNP
rs1448626993	597	dbSNP
rs994939688	609	dbSNP
rs1286686506	612	dbSNP
rs891974611	617	dbSNP
rs1356664855	621	dbSNP
rs1178334020	626	dbSNP
rs1316635923	626	dbSNP
rs1027874997	630	dbSNP
rs969599522	638	dbSNP
rs1001231138	646	dbSNP
rs190199548	650	dbSNP
rs1386192356	652	dbSNP
rs1405620489	654	dbSNP
rs1299368291	656	dbSNP
rs1325070611	657	dbSNP
rs1363783118	661	dbSNP
rs959852177	663	dbSNP
rs564223302	671	dbSNP
rs35145794	673	dbSNP
rs868225407	684	dbSNP
rs1167076712	689	dbSNP
rs746135655	690	dbSNP
rs772353436	692	dbSNP
rs906853670	698	dbSNP
rs528180390	701	dbSNP
rs71677346	702	dbSNP
rs967224211	705	dbSNP
rs540285613	709	dbSNP
rs748998476	709	dbSNP
rs1046530	710	dbSNP
rs528858644	711	dbSNP
rs1230278173	713	dbSNP
rs1213129672	720	dbSNP
rs1342775614	721	dbSNP
rs1050482147	722	dbSNP
rs1279304992	725	dbSNP
rs911888248	732	dbSNP
rs944682705	736	dbSNP
rs1295328120	742	dbSNP
rs1458499486	744	dbSNP
rs1354105045	749	dbSNP
rs572510680	755	dbSNP
rs1466933824	756	dbSNP
rs1424071904	759	dbSNP
rs1175518973	762	dbSNP
rs944705949	763	dbSNP
rs1036870700	765	dbSNP
rs922200595	766	dbSNP
rs897884344	770	dbSNP
rs930842557	774	dbSNP
rs17062935	782	dbSNP
rs1200133538	783	dbSNP
rs905490970	789	dbSNP
rs71427921	790	dbSNP
rs1321977930	802	dbSNP
rs569198150	802	dbSNP
rs768851740	805	dbSNP
rs533393747	806	dbSNP
rs1387364298	816	dbSNP
rs1164687134	826	dbSNP
rs1013898818	829	dbSNP
rs148332414	829	dbSNP
rs1401368688	831	dbSNP
rs1020061558	832	dbSNP
rs115703922	837	dbSNP
rs112350274	840	dbSNP
rs1170783373	852	dbSNP
rs543037631	857	dbSNP
rs1401777527	863	dbSNP
rs1032845215	864	dbSNP
rs527754057	867	dbSNP
rs953204205	876	dbSNP
rs534524849	885	dbSNP
rs911787399	889	dbSNP
rs1203381354	890	dbSNP
rs951180204	891	dbSNP
rs986656659	894	dbSNP
rs139897635	895	dbSNP
rs1242457874	897	dbSNP
rs966561269	897	dbSNP
rs1377880524	900	dbSNP
rs974864022	903	dbSNP
rs1450118880	907	dbSNP
rs1303268311	912	dbSNP
rs1404094404	912	dbSNP
rs555804299	913	dbSNP
rs919366505	920	dbSNP
rs372846432	921	dbSNP
rs1260103427	922	dbSNP
rs17062936	927	dbSNP
rs1181373291	929	dbSNP
rs1425257725	931	dbSNP
rs1049252683	935	dbSNP
rs990334392	943	dbSNP
rs905368438	944	dbSNP
rs913508763	945	dbSNP
rs557335004	946	dbSNP
rs1279929680	951	dbSNP
rs946214804	952	dbSNP
rs938154576	955	dbSNP
rs117811759	959	dbSNP
rs1354522978	963	dbSNP
rs1314551840	964	dbSNP
rs1242863151	972	dbSNP
rs896708193	976	dbSNP
rs546076414	977	dbSNP
rs561657334	978	dbSNP
rs1014369343	981	dbSNP
rs1191487456	984	dbSNP
rs771913633	986	dbSNP
rs1299976736	988	dbSNP
rs760520538	988	dbSNP
rs1419701541	991	dbSNP
rs1364400801	992	dbSNP
rs928825081	996	dbSNP
rs762275297	1002	dbSNP
rs1241827616	1003	dbSNP
rs902975914	1016	dbSNP
rs1188632718	1019	dbSNP
rs766331769	1027	dbSNP
rs1261587135	1029	dbSNP
rs999952296	1034	dbSNP
rs1488943012	1035	dbSNP
rs200382580	1035	dbSNP
rs1208173233	1037	dbSNP
rs1358683280	1049	dbSNP
rs770494556	1050	dbSNP
rs12862079	1052	dbSNP
rs1226344928	1053	dbSNP
rs377195565	1053	dbSNP
rs953349721	1054	dbSNP
rs115052118	1058	dbSNP
rs1400523274	1060	dbSNP
rs1046997470	1064	dbSNP
rs1315976966	1071	dbSNP
rs1344337313	1074	dbSNP
rs1019308110	1075	dbSNP
rs965970657	1076	dbSNP
rs3088071	1077	dbSNP
rs180950342	1081	dbSNP
rs1173334111	1082	dbSNP
rs752246050	1082	dbSNP
rs1478415329	1084	dbSNP
rs984844881	1091	dbSNP
rs1196782471	1106	dbSNP
rs1453414292	1110	dbSNP
rs1268236906	1113	dbSNP
rs1343775403	1114	dbSNP
rs1222971484	1118	dbSNP
rs1276034965	1121	dbSNP
rs1322682562	1124	dbSNP
rs926705436	1125	dbSNP
rs561804286	1134	dbSNP
rs201532150	1145	dbSNP
rs1347762201	1146	dbSNP
rs1029092917	1148	dbSNP
rs112480850	1148	dbSNP
rs957355948	1148	dbSNP
rs1056624367	1149	dbSNP
rs78333745	1158	dbSNP
rs78237939	1159	dbSNP
rs79753577	1160	dbSNP
rs1046537	1163	dbSNP
rs565817508	1172	dbSNP
rs967567126	1179	dbSNP
rs551072055	1181	dbSNP
rs1216943904	1182	dbSNP
rs78370106	1183	dbSNP
rs1181243585	1191	dbSNP
rs566220746	1195	dbSNP
rs199721628	1202	dbSNP
rs1198988677	1212	dbSNP
rs1460718984	1224	dbSNP
rs1276342745	1225	dbSNP
rs1197555441	1227	dbSNP
rs999836213	1230	dbSNP
rs1345708737	1247	dbSNP
rs1278411016	1248	dbSNP
rs1377640949	1249	dbSNP
rs919697424	1256	dbSNP
rs1054217242	1258	dbSNP
rs1156703467	1263	dbSNP
rs1407033091	1264	dbSNP
rs888856832	1267	dbSNP
rs1358941205	1270	dbSNP
rs1332670931	1282	dbSNP
rs1416632390	1285	dbSNP
rs1007827345	1288	dbSNP
rs539422314	1290	dbSNP
rs1208287138	1291	dbSNP
rs141765434	1293	dbSNP
rs1382341461	1294	dbSNP
rs1281854731	1295	dbSNP
rs1179505357	1296	dbSNP
rs1320636927	1307	dbSNP
rs185821441	1312	dbSNP
rs1212036374	1318	dbSNP
rs993382307	1323	dbSNP
rs1283501350	1324	dbSNP
rs527864744	1325	dbSNP
rs1355228444	1327	dbSNP
rs1279463860	1333	dbSNP
rs1286190355	1335	dbSNP
rs1026150211	1337	dbSNP
rs1244772028	1341	dbSNP
rs1376578824	1345	dbSNP
rs549247113	1352	dbSNP
rs899638000	1353	dbSNP
rs567741835	1366	dbSNP
rs188197221	1369	dbSNP
rs926730157	1371	dbSNP
rs959468162	1375	dbSNP
rs1417871253	1382	dbSNP
rs1029487109	1383	dbSNP
rs992777316	1404	dbSNP
rs757247515	1409	dbSNP
rs1411935342	1412	dbSNP
rs1489727441	1414	dbSNP
rs1183328588	1415	dbSNP
rs778938077	1415	dbSNP
rs945486791	1416	dbSNP
rs1191412710	1417	dbSNP
rs957484491	1419	dbSNP
rs1221142107	1420	dbSNP
rs1267480511	1420	dbSNP
rs1011622625	1425	dbSNP
rs750521800	1425	dbSNP
rs1230331253	1426	dbSNP
rs1357503105	1426	dbSNP
rs141460548	1426	dbSNP
rs1042678268	1427	dbSNP
rs1298855482	1429	dbSNP
rs925495764	1431	dbSNP
rs1237483524	1433	dbSNP
rs982072397	1435	dbSNP
rs556603494	1436	dbSNP
rs1406237928	1437	dbSNP
rs758372021	1438	dbSNP
rs1168333317	1441	dbSNP
rs1478743366	1458	dbSNP
rs755152348	1470	dbSNP
rs1383094491	1472	dbSNP
rs1054108795	1474	dbSNP
rs1487227116	1478	dbSNP
rs1248027988	1482	dbSNP
rs959108146	1487	dbSNP
rs1457618735	1488	dbSNP
rs1164014954	1490	dbSNP
rs781290344	1495	dbSNP
rs919668914	1500	dbSNP
rs571631162	1503	dbSNP
rs1257801715	1510	dbSNP
rs1217231061	1516	dbSNP
rs539763985	1518	dbSNP
rs982532466	1521	dbSNP
rs558007972	1522	dbSNP
rs35719665	1524	dbSNP
rs1040493509	1526	dbSNP
rs1437429778	1534	dbSNP
rs572985931	1536	dbSNP
rs1449168989	1538	dbSNP
rs1328994661	1539	dbSNP
rs901687875	1544	dbSNP
rs1424182457	1545	dbSNP
rs181381894	1563	dbSNP
rs1431436478	1564	dbSNP
rs1313162755	1573	dbSNP
rs1191321815	1586	dbSNP
rs1026202800	1587	dbSNP
rs1236017725	1587	dbSNP
rs1197076140	1592	dbSNP
rs780343595	1595	dbSNP
rs1006204151	1601	dbSNP
rs1252320976	1604	dbSNP
rs1210010149	1605	dbSNP
rs1311005718	1607	dbSNP
rs943734304	1613	dbSNP
rs1033683897	1616	dbSNP
rs548554365	1625	dbSNP
rs1265833234	1633	dbSNP
rs866716345	1638	dbSNP
rs992265563	1639	dbSNP
rs574280799	1640	dbSNP
rs1400753011	1645	dbSNP
rs769727644	1654	dbSNP
rs868785628	1660	dbSNP
rs1053516773	1666	dbSNP
rs1194008254	1666	dbSNP
rs966879128	1675	dbSNP
rs185666567	1691	dbSNP
rs893640556	1692	dbSNP
rs190820843	1697	dbSNP
rs372814374	1703	dbSNP
rs769048745	1704	dbSNP
rs936904362	1706	dbSNP
rs990255585	1712	dbSNP
rs138297818	1716	dbSNP
rs372979387	1716	dbSNP
rs1258310397	1718	dbSNP
rs781533023	1719	dbSNP
rs1370570971	1720	dbSNP
rs562160301	1722	dbSNP
rs183229638	1723	dbSNP
rs992160407	1724	dbSNP
rs1040143460	1727	dbSNP
rs1311712017	1739	dbSNP
rs1394108015	1743	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.

- 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.

- 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.