>ARHGAP39|NM_025251|3'UTR
   1 CGGGGGCGCCCGGGGACAGGAGGGATGTCCTGCCGCCCCCAGCCAGGCCGAACTCCGCACTCGCTCTCCCGGCAGAGGGG
  81 CCAGAATCGCCCGGCCCAGCCCTGGAGCCCCCTCCACTCCCCCAGGCCCCTGGCCCCGGCGCTCCCCACGTCTTCTGCCT
 161 GGTCTGAGGGTGCAGCCAGGGCACAGCAGCGGCGGGGAGGGCGCCTCTGGCCCCCCACCTCACGGCCAGTTCCCGCGGGC
 241 ACCGCCTCGCCCTCCGCTGGCCGCGGGTCAGCTCCGAGAAAGTGCCTTCTGTGTCCTGGAGCCGAGCGACGCTGCCTCCT
 321 TGGGGCCGGGCTGCCTCCCTGTGGCTCCTGCGCGCCCTGGCCTGGGCCTTGCCCAGCCGCCCCGGTCTCTCCTTCCCTTT
 401 CTCCTGTCCTCGTCCTGGCCTGCAGCTCTTCCCAGCCCCGAGAGAGCTTCCCGACCTGTCCCCGCCTCCTCTCCCTCCCT
 481 CGGCCCGTGGTCCCCAGCTGGTGACTGCTCAGGAGTTTGGGGGCTCCAGGACAGTGGGCCCGGGGCCTGGCAGGCTCTCG
 561 GTGGGTGGGGTGGGGGCCCCCAAACCAAAGTCCTCTGGGGTAGGGAGCAGGGCTGGGCAGGCATTCTGGGGGCAGGGTGG
 641 GGGAGGGGCGAGAGTATTTTTTTCTTCGTGTAACTGTAAATCCAGAATCTATCCTGCATCGCAGCCCACCGTGTATAGAG
 721 ATATAAATAGAGGGAAAGATATAAGAACTAAATTTGCTAATGACATAGTTTTAACCTAAATGCTATTTATCTCTGAGCCG
 801 TCCCCGTCCTCCGTGCAGAGCAAGTTGAGGTCATTCCTTCTTTTCTTCTCCGATCTTTTTTCTTGGCTTCTGACCAAAAA
 881 CCAAGCTCTACCCCATCCCCATCCCAGACCTGCAGGAGACGAGCGAGCGGGAAGGCGCCGGGCCCGGGACTGTCCGTTCT
 961 CGGGGCCAGAGCTGCTGGGGGACCGAGTTTGTACATTTTCCATTTTGGAATTTTGAGTTCCAATTGTTGTAAAACTTAAT
1041 TTCTCCCCAGTTTTTATATATATATTTTTTAGAGTTCCGTTTTTATTTATTAAAAACAAAAGCCCCAGCCCTGCCGAGGC
1121 CTGGGCGGCGTCCTCAGTCGGGTGGTCCCGGGGCCTTTGCGGTCCCGCCCGGCTGAGACGCTCGCCCCGACGCATGGACC
1201 CGAGAGGCGACGACACGAGTGAATAAAGTGCACATGGACCCTGAAAAAAAAAAAAAAAAA

ID	Duplex structure	Position	Score	MFE
1	miRNA 3' gguugguuacuuucUUACGAa 5' |||||| Target 5' atagttttaacctaAATGCTa 3'	765 - 785	120.00	-5.40
2	miRNA 3' gguuGGUUACUUUCUUACGAa 5' |||: :: || |||| Target 5' gtccCCAGCTGGTGACTGCTc 3'	490 - 510	117.00	-12.10
3	miRNA 3' gguUGGUUACUU-UCUUACGaa 5' || |:|||| | |:||| Target 5' gacACGAGTGAATAAAGTGCac 3'	1212 - 1233	102.00	-9.20

Mutant ID	Mutant Position	Mutant Source
COSN30118080	4	COSMIC
COSN30477309	10	COSMIC
COSN31480651	75	COSMIC
COSN14825004	116	COSMIC
COSN30126699	140	COSMIC
COSN8074328	244	COSMIC
COSN22890953	361	COSMIC
COSN24593045	439	COSMIC
COSN24490161	504	COSMIC
COSN20091882	540	COSMIC
COSN22432240	775	COSMIC
COSN27474996	832	COSMIC
COSN32116662	1202	COSMIC

Mutant ID	Mutant Position	Mutant Source
rs199861857	2	dbSNP
rs376486769	3	dbSNP
rs200191602	4	dbSNP
rs1433113131	5	dbSNP
rs779114975	6	dbSNP
rs755419370	9	dbSNP
rs1448434603	12	dbSNP
rs1456087654	14	dbSNP
rs754099493	15	dbSNP
rs780491500	16	dbSNP
rs1341106359	18	dbSNP
rs1457998126	22	dbSNP
rs1162172903	23	dbSNP
rs1052034699	25	dbSNP
rs745906509	25	dbSNP
rs1254022207	27	dbSNP
rs756409961	29	dbSNP
rs1232264175	30	dbSNP
rs1371560950	31	dbSNP
rs368076363	32	dbSNP
rs1443139907	33	dbSNP
rs750473274	34	dbSNP
rs1328333708	35	dbSNP
rs1410737005	37	dbSNP
rs767659192	39	dbSNP
rs933466469	40	dbSNP
rs922104740	43	dbSNP
rs1323768998	46	dbSNP
rs781302056	47	dbSNP
rs752723117	49	dbSNP
rs764923005	50	dbSNP
rs1258207845	54	dbSNP
rs557280896	58	dbSNP
rs1035431875	62	dbSNP
rs535471095	63	dbSNP
rs190879743	64	dbSNP
rs925742475	71	dbSNP
rs1464750180	77	dbSNP
rs1304196618	79	dbSNP
rs372296531	81	dbSNP
rs978817907	83	dbSNP
rs1411089158	84	dbSNP
rs1415024709	87	dbSNP
rs1025273442	94	dbSNP
rs995408611	96	dbSNP
rs1412858869	99	dbSNP
rs992778608	101	dbSNP
rs1455413252	102	dbSNP
rs959822498	105	dbSNP
rs367737984	108	dbSNP
rs1034194018	109	dbSNP
rs377151963	111	dbSNP
rs114845297	112	dbSNP
rs1016378460	117	dbSNP
rs142534226	122	dbSNP
rs552357594	123	dbSNP
rs532824477	131	dbSNP
rs1258198911	132	dbSNP
rs1483371226	133	dbSNP
rs1199537514	134	dbSNP
rs562436455	137	dbSNP
rs1052407164	138	dbSNP
rs1182318858	139	dbSNP
rs1051217642	140	dbSNP
rs1411115237	145	dbSNP
rs1473585294	147	dbSNP
rs997730161	149	dbSNP
rs1359528794	150	dbSNP
rs1466695984	153	dbSNP
rs900795074	155	dbSNP
rs1373672306	156	dbSNP
rs1252642300	158	dbSNP
rs935403127	168	dbSNP
rs1411711993	169	dbSNP
rs1871537	170	dbSNP
rs1043757918	171	dbSNP
rs946965032	172	dbSNP
rs916840830	173	dbSNP
rs1232024992	175	dbSNP
rs1277711594	181	dbSNP
rs1258678657	188	dbSNP
rs1002527450	198	dbSNP
rs1205232457	202	dbSNP
rs990989226	204	dbSNP
rs1201430129	211	dbSNP
rs1350448809	217	dbSNP
rs907470348	217	dbSNP
rs1479577681	223	dbSNP
rs1192866766	225	dbSNP
rs1425550200	239	dbSNP
rs1258534385	243	dbSNP
rs139043473	245	dbSNP
rs928139924	246	dbSNP
rs1042827081	251	dbSNP
rs945681029	255	dbSNP
rs776286021	261	dbSNP
rs992710972	264	dbSNP
rs1368965681	265	dbSNP
rs1440600619	267	dbSNP
rs1301766054	273	dbSNP
rs1343846670	275	dbSNP
rs1342242493	278	dbSNP
rs1228684453	286	dbSNP
rs1334527596	292	dbSNP
rs951148717	295	dbSNP
rs1025241637	301	dbSNP
rs1382535879	302	dbSNP
rs974171634	307	dbSNP
rs773570142	319	dbSNP
rs561755084	322	dbSNP
rs1164366119	324	dbSNP
rs1472079340	327	dbSNP
rs1249731789	328	dbSNP
rs927235208	331	dbSNP
rs746824766	332	dbSNP
rs1418841668	339	dbSNP
rs779797408	342	dbSNP
rs1370665131	344	dbSNP
rs1006724546	345	dbSNP
rs1188883280	346	dbSNP
rs963220747	347	dbSNP
rs955149678	348	dbSNP
rs1016736187	350	dbSNP
rs1004970975	351	dbSNP
rs950740992	352	dbSNP
rs1260096426	354	dbSNP
rs1029507603	356	dbSNP
rs1465112420	357	dbSNP
rs999580150	364	dbSNP
rs1359486455	375	dbSNP
rs900742829	375	dbSNP
rs1290042201	378	dbSNP
rs1321045959	379	dbSNP
rs902616558	380	dbSNP
rs772114503	382	dbSNP
rs1465205639	383	dbSNP
rs1357882901	384	dbSNP
rs1043713528	385	dbSNP
rs1474582839	386	dbSNP
rs1183662263	387	dbSNP
rs1011352495	397	dbSNP
rs1000962468	400	dbSNP
rs904040978	402	dbSNP
rs540496692	403	dbSNP
rs1055746251	404	dbSNP
rs1318136990	408	dbSNP
rs116738744	409	dbSNP
rs1449863980	411	dbSNP
rs1284206089	414	dbSNP
rs1437520781	418	dbSNP
rs1389714754	420	dbSNP
rs1231331534	422	dbSNP
rs1290101525	422	dbSNP
rs928108845	425	dbSNP
rs1204318711	426	dbSNP
rs1403630950	433	dbSNP
rs763237543	434	dbSNP
rs1474940712	439	dbSNP
rs1047903971	440	dbSNP
rs557936597	441	dbSNP
rs918366534	442	dbSNP
rs973759096	444	dbSNP
rs962734359	447	dbSNP
rs772346260	448	dbSNP
rs1158348450	452	dbSNP
rs1406247766	457	dbSNP
rs910889920	462	dbSNP
rs985744564	463	dbSNP
rs1374514308	465	dbSNP
rs1412357560	466	dbSNP
rs955285127	467	dbSNP
rs546029780	468	dbSNP
rs999382149	469	dbSNP
rs966771233	471	dbSNP
rs983722720	474	dbSNP
rs1022834752	475	dbSNP
rs1221111658	477	dbSNP
rs1010904175	478	dbSNP
rs1281271912	479	dbSNP
rs1030853384	486	dbSNP
rs1208806638	490	dbSNP
rs1452776041	491	dbSNP
rs997462088	494	dbSNP
rs940910041	497	dbSNP
rs1181739269	501	dbSNP
rs545436229	504	dbSNP
rs575434690	507	dbSNP
rs1479228118	509	dbSNP
rs895105059	510	dbSNP
rs1173575885	512	dbSNP
rs1394086877	515	dbSNP
rs1055145733	521	dbSNP
rs1003727782	522	dbSNP
rs1001077080	523	dbSNP
rs903986627	526	dbSNP
rs1021115733	527	dbSNP
rs1010188878	529	dbSNP
rs906818499	537	dbSNP
rs1347429005	539	dbSNP
rs557171858	540	dbSNP
rs929507903	541	dbSNP
rs1228819384	545	dbSNP
rs918337746	547	dbSNP
rs1056914519	548	dbSNP
rs1340181481	554	dbSNP
rs1195692827	559	dbSNP
rs60512843	564	dbSNP
rs905529161	567	dbSNP
rs1044301686	576	dbSNP
rs941948703	577	dbSNP
rs909159274	579	dbSNP
rs1190134792	580	dbSNP
rs1390211823	587	dbSNP
rs941130582	592	dbSNP
rs929157431	593	dbSNP
rs534384921	594	dbSNP
rs752930375	595	dbSNP
rs985162946	596	dbSNP
rs1324342900	602	dbSNP
rs1438923613	603	dbSNP
rs1300142019	604	dbSNP
rs1409871439	607	dbSNP
rs1327291112	608	dbSNP
rs1226764110	613	dbSNP
rs1249754357	620	dbSNP
rs955257725	626	dbSNP
rs1214873410	628	dbSNP
rs1369285890	634	dbSNP
rs568329980	636	dbSNP
rs1261972866	637	dbSNP
rs933487197	637	dbSNP
rs1427618632	638	dbSNP
rs977912508	647	dbSNP
rs968326370	652	dbSNP
rs1475463659	654	dbSNP
rs1021649510	655	dbSNP
rs552971909	656	dbSNP
rs1321043723	660	dbSNP
rs1381863991	665	dbSNP
rs1430745359	665	dbSNP
rs1022131459	667	dbSNP
rs1293445977	668	dbSNP
rs896664592	670	dbSNP
rs141687296	678	dbSNP
rs1394868328	683	dbSNP
rs781483737	684	dbSNP
rs1210957044	687	dbSNP
rs959502394	688	dbSNP
rs1485303219	692	dbSNP
rs1034076971	693	dbSNP
rs375870879	694	dbSNP
rs1180521649	695	dbSNP
rs576430822	700	dbSNP
rs906784322	702	dbSNP
rs1159475684	705	dbSNP
rs1363021514	706	dbSNP
rs1002631635	708	dbSNP
rs1026562130	710	dbSNP
rs570819852	711	dbSNP
rs1404668999	712	dbSNP
rs1044080423	716	dbSNP
rs552495058	718	dbSNP
rs993711329	720	dbSNP
rs1230778777	721	dbSNP
rs941713840	722	dbSNP
rs1316724457	723	dbSNP
rs1346792499	724	dbSNP
rs531008520	729	dbSNP
rs887686642	730	dbSNP
rs899297850	732	dbSNP
rs1257367122	733	dbSNP
rs1485823939	733	dbSNP
rs1048123011	734	dbSNP
rs929133357	737	dbSNP
rs141813045	738	dbSNP
rs550391749	742	dbSNP
rs943449414	747	dbSNP
rs1417049447	749	dbSNP
rs1178025035	754	dbSNP
rs1397101507	757	dbSNP
rs528997272	767	dbSNP
rs558158896	768	dbSNP
rs889568284	769	dbSNP
rs1441520665	775	dbSNP
rs910676164	776	dbSNP
rs1049412485	783	dbSNP
rs561495452	785	dbSNP
rs979439757	788	dbSNP
rs762017990	789	dbSNP
rs1310330718	791	dbSNP
rs933679223	792	dbSNP
rs371288035	802	dbSNP
rs1375217557	803	dbSNP
rs977964743	808	dbSNP
rs945288973	809	dbSNP
rs1415790018	811	dbSNP
rs915034874	812	dbSNP
rs960830378	821	dbSNP
rs2620649	825	dbSNP
rs138692736	829	dbSNP
rs564362126	830	dbSNP
rs546165715	835	dbSNP
rs959707367	836	dbSNP
rs1471289962	837	dbSNP
rs1192704750	840	dbSNP
rs1253400832	843	dbSNP
rs568599243	848	dbSNP
rs575323873	848	dbSNP
rs1228815122	851	dbSNP
rs1171286819	852	dbSNP
rs1033801556	853	dbSNP
rs969775346	855	dbSNP
rs1460919542	858	dbSNP
rs113488941	860	dbSNP
rs982074373	862	dbSNP
rs1372204321	868	dbSNP
rs970661608	870	dbSNP
rs1358458021	874	dbSNP
rs1485334751	880	dbSNP
rs1300764431	893	dbSNP
rs563532721	903	dbSNP
rs1235504883	906	dbSNP
rs1271756838	907	dbSNP
rs1005855044	908	dbSNP
rs1212027566	909	dbSNP
rs1026278708	916	dbSNP
rs541930346	921	dbSNP
rs1279541812	924	dbSNP
rs899434894	924	dbSNP
rs1016828783	925	dbSNP
rs1211635236	926	dbSNP
rs1007757066	928	dbSNP
rs1047603116	929	dbSNP
rs889527890	941	dbSNP
rs1049545615	942	dbSNP
rs1167772129	944	dbSNP
rs187567154	946	dbSNP
rs900805249	952	dbSNP
rs115814584	955	dbSNP
rs572914680	958	dbSNP
rs1450571652	962	dbSNP
rs534690118	967	dbSNP
rs1360122234	969	dbSNP
rs1431021125	972	dbSNP
rs1269023363	981	dbSNP
rs1359283089	982	dbSNP
rs943229985	983	dbSNP
rs1293803696	984	dbSNP
rs1334134670	990	dbSNP
rs915189833	995	dbSNP
rs1231214798	1000	dbSNP
rs1269862934	1004	dbSNP
rs1317113012	1008	dbSNP
rs1455374078	1014	dbSNP
rs1448895401	1015	dbSNP
rs1054019058	1018	dbSNP
rs576875885	1023	dbSNP
rs926458995	1025	dbSNP
rs1484914388	1026	dbSNP
rs1411487571	1031	dbSNP
rs1190212587	1032	dbSNP
rs1419194404	1037	dbSNP
rs111567232	1044	dbSNP
rs1475204913	1045	dbSNP
rs1163143233	1046	dbSNP
rs946698588	1047	dbSNP
rs1183553123	1050	dbSNP
rs913898672	1052	dbSNP
rs1472971892	1054	dbSNP
rs982125206	1056	dbSNP
rs970801955	1057	dbSNP
rs960944465	1058	dbSNP
rs1281020214	1063	dbSNP
rs928223101	1064	dbSNP
rs919238799	1065	dbSNP
rs969556528	1066	dbSNP
rs980920579	1066	dbSNP
rs1351853211	1071	dbSNP
rs972064219	1078	dbSNP
rs1209393678	1082	dbSNP
rs766787639	1084	dbSNP
rs1186453362	1086	dbSNP
rs1016551782	1089	dbSNP
rs1450488621	1092	dbSNP
rs758940718	1100	dbSNP
rs1158405388	1102	dbSNP
rs1382152533	1103	dbSNP
rs879273799	1105	dbSNP
rs1230528854	1107	dbSNP
rs901750091	1109	dbSNP
rs1040298125	1115	dbSNP
rs953533329	1117	dbSNP
rs1330768817	1118	dbSNP
rs558804730	1119	dbSNP
rs1030512697	1123	dbSNP
rs1441190218	1126	dbSNP
rs997911096	1130	dbSNP
rs1432410545	1132	dbSNP
rs888951178	1134	dbSNP
rs749909836	1149	dbSNP
rs1042061440	1161	dbSNP
rs1347285362	1165	dbSNP
rs1198841921	1169	dbSNP
rs946782426	1171	dbSNP
rs1347628528	1172	dbSNP
rs537786461	1175	dbSNP
rs570113065	1180	dbSNP
rs1009268114	1184	dbSNP
rs184108569	1185	dbSNP
rs893711107	1186	dbSNP
rs116480921	1188	dbSNP
rs1186497064	1194	dbSNP
rs928170920	1195	dbSNP
rs1396439176	1196	dbSNP
rs1443329486	1199	dbSNP
rs981036911	1200	dbSNP
rs1250081285	1206	dbSNP
rs948165132	1208	dbSNP
rs1189469992	1211	dbSNP
rs937931851	1212	dbSNP
rs149527055	1213	dbSNP
rs1224406840	1215	dbSNP
rs1322899880	1217	dbSNP
rs1274323515	1220	dbSNP
rs1194613020	1225	dbSNP
rs1226602846	1230	dbSNP
rs745405372	1231	dbSNP
rs1026088481	1232	dbSNP
rs778609369	1233	dbSNP
rs949455770	1234	dbSNP
rs1461751596	1235	dbSNP
rs919373187	1237	dbSNP
rs1394025800	1240	dbSNP
rs79956544	1243	dbSNP
rs1320308665	1244	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.