>ARID1A|NM_006015|3'UTR
   1 CAGCCGTGGGACACCTCCCCCCCCCGTGTGTGTGTGCGTGTGTGGAGAACTTAGAAACTGACTGTTGCCCTTTATTTATG
  81 CAAAACCACCTCAGAATCCAGTTTACCCTGTGCTGTCCAGCTTCTCCCTTGGGAAAAAGTCTCTCCTGTTTCTCTCTCCT
 161 CCTTCCACCTCCCCTCCCTCCATCACCTCACGCCTTTCTGTTCCTTGTCCTCACCTTACTCCCCTCAGGACCCTACCCCA
 241 CCCTCTTTGAAAAGACAAAGCTCTGCCTACATAGAAGACTTTTTTTATTTTAACCAAAGTTACTGTTGTTTACAGTGAGT
 321 TTGGGGAAAAAAAATAAAATAAAAATGGCTTTCCCAGTCCTTGCATCAACGGGATGCCACATTTCATAACTGTTTTTAAT
 401 GGTAAAAAAAAAAAAAAAAAATACAAAAAAAAATTCTGAAGGACAAAAAAGGTGACTGCTGAACTGTGTGTGGTTTATTG
 481 TTGTACATTCACAATCTTGCAGGAGCCAAGAAGTTCGCAGTTGTGAACAGACCCTGTTCACTGGAGAGGCCTGTGCAGTA
 561 GAGTGTAGACCCTTTCATGTACTGTACTGTACACCTGATACTGTAAACATACTGTAATAATAATGTCTCACATGGAAACA
 641 GAAAACGCTGGGTCAGCAGCAAGCTGTAGTTTTTAAAAATGTTTTTAGTTAAACGTTGAGGAGAAAAAAAAAAAAGGCTT
 721 TTCCCCCAAAGTATCATGTGTGAACCTACAACACCCTGACCTCTTTCTCTCCTCCTTGATTGTATGAATAACCCTGAGAT
 801 CACCTCTTAGAACTGGTTTTAACCTTTAGCTGCAGCGGCTACGCTGCCACGTGTGTATATATATGACGTTGTACATTGCA
 881 CATACCCTTGGATCCCCACAGTTTGGTCCTCCTCCCAGCTACCCCTTTATAGTATGACGAGTTAACAAGTTGGTGACCTG
 961 CACAAAGCGAGACACAGCTATTTAATCTCTTGCCAGATATCGCCCCTCTTGGTGCGATGCTGTACAGGTCTCTGTAAAAA
1041 GTCCTTGCTGTCTCAGCAGCCAATCAACTTATAGTTTATTTTTTTCTGGGTTTTTGTTTTGTTTTGTTTTCTTTCTAATC
1121 GAGGTGTGAAAAAGTTCTAGGTTCAGTTGAAGTTCTGATGAAGAAACACAATTGAGATTTTTTCAGTGATAAAATCTGCA
1201 TATTTGTATTTCAACAATGTAGCTAAAACTTGATGTAAATTCCTCCTTTTTTTCCTTTTTTGGCTTAATGAATATCATTT
1281 ATTCAGTATGAAATCTTTATACTATATGTTCCACGTGTTAAGAATAAATGTACATTAAATCTTGGTAAGACTTT

ID	Duplex structure	Position	Score	MFE
1	miRNA 3' acauccgaccCCUAUUUACUUAu 5' || | ||||||| Target 5' ttccttttttGGCTTAATGAATa 3'	1252 - 1274	149.00	-8.00
2	miRNA 3' acauccgaccccuauuUACUUAu 5' |||||| Target 5' tctcctccttgattgtATGAATa 3'	768 - 790	120.00	-5.70
3	miRNA 3' acaUCCGACCCC---UAUUUACUUau 5' || :||||| | |||| || Target 5' gtgAGTTTGGGGAAAAAAAATAAAat 3'	315 - 340	116.00	-12.00

Mutant ID	Mutant Position	Mutant Source
1192736	6	ClinVar
1197106	11	ClinVar
COSN31594347	6	COSMIC
COSN30468855	18	COSMIC
COSN30552090	25	COSMIC
COSN30548382	26	COSMIC
COSN20074011	38	COSMIC
COSN30097813	93	COSMIC
COSN25846364	140	COSMIC
COSN31541229	196	COSMIC
COSN31596748	270	COSMIC
COSN30170887	271	COSMIC
COSN31594795	335	COSMIC
COSN19365852	422	COSMIC
COSN30174930	526	COSMIC
COSN22872902	608	COSMIC
COSN19304313	621	COSMIC
COSN28578908	675	COSMIC
COSN27402416	716	COSMIC
COSN29066575	716	COSMIC
COSN31769385	737	COSMIC
COSN31532324	811	COSMIC
COSN31513608	847	COSMIC
COSN31960201	852	COSMIC
COSN31535903	856	COSMIC
COSN31484548	970	COSMIC
COSN31556897	990	COSMIC
COSN31565426	1002	COSMIC
COSN26509054	1009	COSMIC
COSN26677618	1013	COSMIC
COSN31523204	1029	COSMIC
COSN31593976	1063	COSMIC
COSN31523201	1074	COSMIC
COSN31769386	1183	COSMIC
COSN31568545	1185	COSMIC
COSN31769390	1187	COSMIC
COSN31769393	1191	COSMIC
COSN32061019	1198	COSMIC
COSN31606438	1272	COSMIC

Mutant ID	Mutant Position	Mutant Source
rs748607027	2	dbSNP
rs768407935	3	dbSNP
rs201289176	6	dbSNP
rs761262959	7	dbSNP
rs572794512	8	dbSNP
rs372029026	11	dbSNP
rs763359043	14	dbSNP
rs1371743129	16	dbSNP
rs1491421314	17	dbSNP
rs369896037	17	dbSNP
rs551176418	17	dbSNP
rs745390232	17	dbSNP
rs377238538	18	dbSNP
rs755516865	19	dbSNP
rs1263075449	21	dbSNP
rs774971536	21	dbSNP
rs377624643	22	dbSNP
rs760439531	22	dbSNP
rs763858866	23	dbSNP
rs778187938	23	dbSNP
rs200568725	24	dbSNP
rs776428236	24	dbSNP
rs1441882203	25	dbSNP
rs1491399260	25	dbSNP
rs201547182	26	dbSNP
rs3841356	26	dbSNP
rs750470371	26	dbSNP
rs199555039	27	dbSNP
rs1314517111	29	dbSNP
rs761352508	35	dbSNP
rs769273623	36	dbSNP
rs375168652	38	dbSNP
rs114615474	39	dbSNP
rs751971163	43	dbSNP
rs759773973	46	dbSNP
rs915071595	48	dbSNP
rs1387972191	55	dbSNP
rs994830363	59	dbSNP
rs1462055512	64	dbSNP
rs1328126265	69	dbSNP
rs1454399182	83	dbSNP
rs193200602	87	dbSNP
rs1028353479	99	dbSNP
rs1239740672	106	dbSNP
rs953605214	108	dbSNP
rs570966006	111	dbSNP
rs1288293349	113	dbSNP
rs1007771911	119	dbSNP
rs1264000698	129	dbSNP
rs1462893445	130	dbSNP
rs1019086140	134	dbSNP
rs965796800	140	dbSNP
rs1250317878	150	dbSNP
rs201874010	151	dbSNP
rs969224680	153	dbSNP
rs981247939	167	dbSNP
rs762599015	169	dbSNP
rs185013013	170	dbSNP
rs1479178017	179	dbSNP
rs1181304090	191	dbSNP
rs1205766877	192	dbSNP
rs751706703	193	dbSNP
rs1406403111	201	dbSNP
rs1470776155	204	dbSNP
rs989824139	207	dbSNP
rs377690379	213	dbSNP
rs928091627	217	dbSNP
rs939320870	220	dbSNP
rs1395579085	225	dbSNP
rs1036374197	233	dbSNP
rs868709218	234	dbSNP
rs1391892783	238	dbSNP
rs190650562	239	dbSNP
rs948598431	240	dbSNP
rs1408417706	241	dbSNP
rs1307887735	245	dbSNP
rs930879662	252	dbSNP
rs1235734781	255	dbSNP
rs1309946194	256	dbSNP
rs1320638749	263	dbSNP
rs928443330	266	dbSNP
rs757365605	268	dbSNP
rs566849047	269	dbSNP
rs1227680069	272	dbSNP
rs889275126	273	dbSNP
rs1481929277	275	dbSNP
rs766238144	280	dbSNP
rs939470085	280	dbSNP
rs1486603790	282	dbSNP
rs1044113	288	dbSNP
rs1223004626	300	dbSNP
rs1180113728	313	dbSNP
rs1411692272	320	dbSNP
rs1171345252	327	dbSNP
rs1284114092	327	dbSNP
rs369865650	327	dbSNP
rs1325901660	330	dbSNP
rs1392259519	331	dbSNP
rs550131155	331	dbSNP
rs1168337088	335	dbSNP
rs1376510290	336	dbSNP
rs897898640	342	dbSNP
rs1007749223	346	dbSNP
rs1301660848	353	dbSNP
rs1049058386	358	dbSNP
rs1382332074	360	dbSNP
rs144625506	371	dbSNP
rs1339653193	372	dbSNP
rs1481169558	375	dbSNP
rs1198014666	383	dbSNP
rs1187195724	387	dbSNP
rs1250042738	390	dbSNP
rs1188206844	391	dbSNP
rs1447878196	391	dbSNP
rs1396050280	393	dbSNP
rs1007784903	403	dbSNP
rs140784604	403	dbSNP
rs1174528243	404	dbSNP
rs1217268548	404	dbSNP
rs1372859595	404	dbSNP
rs531891434	404	dbSNP
rs533673675	404	dbSNP
rs71007893	404	dbSNP
rs71582803	404	dbSNP
rs879190726	404	dbSNP
rs1019140683	405	dbSNP
rs966221010	408	dbSNP
rs1429436211	413	dbSNP
rs1481204994	415	dbSNP
rs999017389	420	dbSNP
rs1188114808	421	dbSNP
rs140247425	422	dbSNP
rs879067977	423	dbSNP
rs1385781858	425	dbSNP
rs1424979331	425	dbSNP
rs201576837	425	dbSNP
rs957140373	425	dbSNP
rs990224567	425	dbSNP
rs1022551333	427	dbSNP
rs969962710	429	dbSNP
rs1036660091	437	dbSNP
rs981301637	438	dbSNP
rs1274019817	443	dbSNP
rs552617811	447	dbSNP
rs192390664	449	dbSNP
rs139737956	455	dbSNP
rs972587229	481	dbSNP
rs1303826808	482	dbSNP
rs919377839	485	dbSNP
rs1453530028	487	dbSNP
rs1219728139	489	dbSNP
rs1246460797	491	dbSNP
rs866265719	503	dbSNP
rs1184917444	509	dbSNP
rs1049101049	517	dbSNP
rs750577664	518	dbSNP
rs1164990786	520	dbSNP
rs1415411446	525	dbSNP
rs1295149514	534	dbSNP
rs1322530817	535	dbSNP
rs1030625284	540	dbSNP
rs1354846836	542	dbSNP
rs1411465866	557	dbSNP
rs1306038878	564	dbSNP
rs183673478	566	dbSNP
rs1230115951	572	dbSNP
rs1284851133	577	dbSNP
rs1264096542	578	dbSNP
rs943331229	578	dbSNP
rs1226801481	579	dbSNP
rs1289460947	580	dbSNP
rs1010767671	587	dbSNP
rs1207755836	588	dbSNP
rs1040674568	589	dbSNP
rs145352087	611	dbSNP
rs1189316316	615	dbSNP
rs1268970655	615	dbSNP
rs1471534613	619	dbSNP
rs1162241813	620	dbSNP
rs999468120	628	dbSNP
rs1431346731	629	dbSNP
rs1031799251	640	dbSNP
rs1260631745	647	dbSNP
rs1415289971	648	dbSNP
rs969606409	671	dbSNP
rs1336146483	675	dbSNP
rs1428849870	680	dbSNP
rs1342294407	685	dbSNP
rs1172224910	690	dbSNP
rs1445917538	694	dbSNP
rs892884880	695	dbSNP
rs573932625	696	dbSNP
rs1230974226	698	dbSNP
rs1272887783	699	dbSNP
rs1383216996	701	dbSNP
rs1423928995	702	dbSNP
rs1164141784	703	dbSNP
rs1011294855	704	dbSNP
rs1022606208	704	dbSNP
rs1212161198	704	dbSNP
rs760723895	704	dbSNP
rs1367469673	705	dbSNP
rs1428749539	720	dbSNP
rs969719142	736	dbSNP
rs981060933	737	dbSNP
rs1174211102	738	dbSNP
rs980644703	741	dbSNP
rs755982730	749	dbSNP
rs1333587077	751	dbSNP
rs779697055	762	dbSNP
rs1437514380	764	dbSNP
rs1295704549	766	dbSNP
rs972982682	766	dbSNP
rs960826442	768	dbSNP
rs546236808	770	dbSNP
rs1382588716	775	dbSNP
rs1343482452	778	dbSNP
rs749310830	781	dbSNP
rs1200457346	783	dbSNP
rs919252408	785	dbSNP
rs930659273	787	dbSNP
rs1465901163	794	dbSNP
rs1206385837	798	dbSNP
rs1454506677	804	dbSNP
rs930738590	804	dbSNP
rs1200715643	806	dbSNP
rs984895434	825	dbSNP
rs1477638772	833	dbSNP
rs985022973	835	dbSNP
rs910824315	838	dbSNP
rs943503949	842	dbSNP
rs1358365430	843	dbSNP
rs1388199644	844	dbSNP
rs1040553727	852	dbSNP
rs1303861925	856	dbSNP
rs902095027	860	dbSNP
rs900878195	864	dbSNP
rs1187969128	868	dbSNP
rs536545312	868	dbSNP
rs1052168297	869	dbSNP
rs1289548913	876	dbSNP
rs60798877	893	dbSNP
rs1226045973	895	dbSNP
rs1184076490	899	dbSNP
rs1010549686	901	dbSNP
rs1387049545	902	dbSNP
rs1488599804	905	dbSNP
rs1022141064	907	dbSNP
rs905118899	911	dbSNP
rs1264975363	912	dbSNP
rs893281882	914	dbSNP
rs778763188	915	dbSNP
rs1158452685	917	dbSNP
rs566545995	920	dbSNP
rs1414093032	922	dbSNP
rs1455533630	923	dbSNP
rs1473582132	928	dbSNP
rs1157021071	937	dbSNP
rs1411417459	939	dbSNP
rs1022699450	940	dbSNP
rs1388965067	944	dbSNP
rs1002408607	945	dbSNP
rs1334971301	947	dbSNP
rs1002535806	948	dbSNP
rs747678001	950	dbSNP
rs960857696	953	dbSNP
rs1352852079	960	dbSNP
rs572778412	969	dbSNP
rs1026425035	970	dbSNP
rs952002276	974	dbSNP
rs1246467690	975	dbSNP
rs1263340752	976	dbSNP
rs1355294489	979	dbSNP
rs1205622967	981	dbSNP
rs746879215	982	dbSNP
rs1317726068	996	dbSNP
rs1375287195	998	dbSNP
rs12685	999	dbSNP
rs1181420844	1000	dbSNP
rs1249887927	1002	dbSNP
rs1424496245	1003	dbSNP
rs910760044	1004	dbSNP
rs994071818	1005	dbSNP
rs1027296882	1009	dbSNP
rs943634804	1014	dbSNP
rs976778050	1016	dbSNP
rs1408513780	1023	dbSNP
rs188298594	1026	dbSNP
rs1460677655	1042	dbSNP
rs985282134	1046	dbSNP
rs1244800396	1051	dbSNP
rs923453125	1053	dbSNP
rs1310061934	1061	dbSNP
rs1339498312	1064	dbSNP
rs1468526124	1067	dbSNP
rs772969127	1073	dbSNP
rs1276480547	1078	dbSNP
rs1339867681	1078	dbSNP
rs964750452	1081	dbSNP
rs36117735	1086	dbSNP
rs1256548522	1087	dbSNP
rs747724215	1092	dbSNP
rs976087309	1092	dbSNP
rs1408722599	1105	dbSNP
rs1420966563	1110	dbSNP
rs1174480077	1111	dbSNP
rs1428252222	1112	dbSNP
rs528990173	1113	dbSNP
rs934925108	1115	dbSNP
rs1470448228	1121	dbSNP
rs760232227	1122	dbSNP
rs1299399036	1127	dbSNP
rs548634719	1131	dbSNP
rs544354417	1138	dbSNP
rs1301827326	1143	dbSNP
rs1313870762	1144	dbSNP
rs914796227	1146	dbSNP
rs1254308225	1158	dbSNP
rs762673189	1160	dbSNP
rs558794605	1166	dbSNP
rs1044541667	1169	dbSNP
rs555311641	1170	dbSNP
rs1280862191	1173	dbSNP
rs1322377873	1178	dbSNP
rs1426400378	1178	dbSNP
rs1435396043	1184	dbSNP
rs1223811004	1192	dbSNP
rs1264768228	1196	dbSNP
rs147234817	1201	dbSNP
rs1322061358	1216	dbSNP
rs904897761	1218	dbSNP
rs994223697	1218	dbSNP
rs1002119988	1219	dbSNP
rs1035378243	1223	dbSNP
rs1293862975	1224	dbSNP
rs567162533	1230	dbSNP
rs1481632983	1236	dbSNP
rs1197324707	1241	dbSNP
rs1322828742	1243	dbSNP
rs1229101269	1246	dbSNP
rs756317726	1246	dbSNP
rs866177135	1246	dbSNP
rs1463707738	1247	dbSNP
rs1428741691	1255	dbSNP
rs1480877517	1256	dbSNP
rs952603391	1259	dbSNP
rs1489685103	1260	dbSNP
rs1178860619	1263	dbSNP
rs1417742913	1264	dbSNP
rs1409773858	1265	dbSNP
rs1429209967	1266	dbSNP
rs537890755	1267	dbSNP
rs180769241	1269	dbSNP
rs1356760783	1273	dbSNP
rs1399732242	1275	dbSNP
rs77103907	1279	dbSNP
rs1165063956	1285	dbSNP
rs1351360742	1289	dbSNP
rs1434029488	1297	dbSNP
rs1018085560	1298	dbSNP
rs964802993	1298	dbSNP
rs1411656473	1305	dbSNP
rs547256040	1307	dbSNP
rs1300734152	1308	dbSNP
rs1290258585	1312	dbSNP
rs1327225341	1314	dbSNP
rs1223384334	1315	dbSNP
rs896302585	1316	dbSNP
rs1323815558	1329	dbSNP
rs976141554	1345	dbSNP
rs923333401	1349	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.