>ALDH3B1|NM_000694|3'UTR
   1 GCCCTTCCCCAGGCCCAGGCTGTAGACCACCATGACAGCTGTCGCCTGCGGCTGGTGGAGACGGGGCCTGGGCTCCCGGG
  81 CCCGAGGAGGAAAAGGATTGCCAAGGCTCCAGGGCACCCCTCAAAGCAGCGCCTGCCTCCTCCCTCCTGGGTCTTCCCTC
 161 TCCCTGCCTCAGCCTCCTCCCTCAGCCGCTCCCAACCATGAGAGCCGAGGTGGGAGGCATGGGAAACAGTGCAGTGACTC
 241 ACCCCCTGCCCCCGCACCAACCACCCATATTCAGGAGAAGAGGACAGACACGGCACCTCTGAGTCACCCCTCTCCTGTGG
 321 AGCGGGCGTCCGAGGGGCCCTGGCATCTGACTCAGGCCACACCATGGAATCACTGCATCCAAGGCCATTCCTGCCCTCTC
 401 TGAGTCTCAGTTTTTCCATTTGTTCAGTGGAGAGAATTAACCATTGATACCTCCTGGCTGGGTGAGGCGGCTCACACCTG
 481 TAATCCCAGCACTTTGGGAGGCCGAGGCAGGCGGATCACCTGAAATCAGGAGTTCAAGATCAGCCTGGCTAACATGGCGA
 561 AACCCCGTCTCTACTAAAAATACAAAAATTAGCCTGGCGTGGTGGCGCATGCCTGTAATCCCAGCTACTCAGGAGGCTAA
 641 GGCAGGAGAATCGCTTGAACCCGGGAGGTGGAGGTTGCCGTGAGCTGAGATTGCGTCACTGAACTCCGGCCTGGGTGACA
 721 GAAGGAGGCTCTGCCTTAAAAAAAAAAAAAAAAAAAACCTCCTGGGACTGTTGCAAGGATGAAATGAAGGATTGAGGGAT
 801 TGAGGGATTGCTGAGCTGGAGCTCCAGGTGTCCTATCTTTCTCAGTGGGGTGGCACGGAGCGGGGCCGCCTCCCTCTTCT
 881 CTCCAGGCAGGTGGGGCTGTGGTTATGCGATAGGGTCTCCCTTCCCTCCAGCCCATGCCAGAGGAGCTTGTAACTCTTTA
 961 TCCTCATGGTGCCCACTACGAGTCATACTCTTCCCCATGCTGCTCATCCTCCTGGGCCCCATCCACTCAGCCAAAGCAGA
1041 ATGCAGGGTTTCCTGCCTGACAACCCTTCTCACCTCCCAAGTCCCACTTTTGAACAAGCTGATGATTCTGAAACTGGCCC
1121 AATTTCCTAACAAGCCGGATGCTTGAGAAACCTACATTTGGACAATGAGAGGCTGCTCCTGCGGCCTGCGGGCCACCTCC
1201 TCTTCCTTGGCTCCTGCTTTCTTTTTAGACTATATCAACCTACAACTTTAGTCGGGAAGAGGGACAGGGGTGGACCTGAG
1281 TTTCGTCTCCTGTCTCTCTGGCTGATGTCACCTGAATAAAGCCTTCTTCCCTGGCAATACTTAAAAAAAAAAAAAAAAAA

ID	Duplex structure	Position	Score	MFE
1	miRNA 3' gugagucgcCGGCAAAGGGGUu 5' ||| ||||||| Target 5' ---------GCC-CTTCCCCAg 3'	1 - 12	144.00	-13.80
2	miRNA 3' guGAGUCGC-CGGCA----AAGGGGUu 5' | | || |:| | ||||||| Target 5' ccCACTACGAGTCATACTCTTCCCCAt 3'	972 - 998	142.00	-16.10
3	miRNA 3' guGAGUCGCCGGCAAAGGGGUu 5' || ||: | ||||::||| Target 5' ctCTGAGTCTCAGTTTTTCCAt 3'	398 - 419	132.00	-12.90

Mutant ID	Mutant Position	Mutant Source
COSN19701948	39	COSMIC
COSN31563410	50	COSMIC
COSN31531017	57	COSMIC
COSN26965780	85	COSMIC
COSN30178891	88	COSMIC
COSN31493416	123	COSMIC
COSN30484719	157	COSMIC
COSN30541635	173	COSMIC
COSN30509103	198	COSMIC
COSN17519390	207	COSMIC
COSN28798721	208	COSMIC
COSN30465996	219	COSMIC
COSN16129066	251	COSMIC
COSN31564581	255	COSMIC
COSN7017677	325	COSMIC
COSN10090927	822	COSMIC
COSN26317657	1170	COSMIC
COSN194278	1190	COSMIC
rs3751081	208	GWAS

Mutant ID	Mutant Position	Mutant Source
rs778759508	1	dbSNP
rs1382206130	4	dbSNP
rs1418527376	5	dbSNP
rs753798617	10	dbSNP
rs1357317411	11	dbSNP
rs1412798945	22	dbSNP
rs1311753904	32	dbSNP
rs144879452	34	dbSNP
rs1194028547	37	dbSNP
rs567436201	39	dbSNP
rs1262679060	40	dbSNP
rs751776553	44	dbSNP
rs757480205	45	dbSNP
rs965883993	46	dbSNP
rs1281055369	47	dbSNP
rs781479683	50	dbSNP
rs142085281	51	dbSNP
rs1227584895	53	dbSNP
rs950615309	57	dbSNP
rs777232783	58	dbSNP
rs932530075	63	dbSNP
rs563096242	64	dbSNP
rs1420027999	66	dbSNP
rs780683696	67	dbSNP
rs1365897547	69	dbSNP
rs1361737467	71	dbSNP
rs749849588	73	dbSNP
rs1422793101	74	dbSNP
rs768274330	76	dbSNP
rs1376676466	78	dbSNP
rs541303778	79	dbSNP
rs1021688203	81	dbSNP
rs761396208	82	dbSNP
rs111444623	84	dbSNP
rs772953072	85	dbSNP
rs1374970621	86	dbSNP
rs977402743	88	dbSNP
rs1251499635	90	dbSNP
rs760340602	97	dbSNP
rs766214326	101	dbSNP
rs1231769509	102	dbSNP
rs1053403305	106	dbSNP
rs753745570	107	dbSNP
rs1197952001	109	dbSNP
rs759539471	110	dbSNP
rs1457048620	112	dbSNP
rs561264104	113	dbSNP
rs528280364	116	dbSNP
rs757388912	121	dbSNP
rs752663585	126	dbSNP
rs949847487	127	dbSNP
rs1373592783	128	dbSNP
rs781222499	129	dbSNP
rs1296245431	130	dbSNP
rs750705047	131	dbSNP
rs756402514	132	dbSNP
rs916069002	135	dbSNP
rs546784642	136	dbSNP
rs1044047110	140	dbSNP
rs1326799759	143	dbSNP
rs538075662	144	dbSNP
rs769224164	145	dbSNP
rs758252408	146	dbSNP
rs182409890	148	dbSNP
rs147792238	151	dbSNP
rs1230182100	159	dbSNP
rs1288123398	162	dbSNP
rs747575974	163	dbSNP
rs771636296	164	dbSNP
rs1470406425	168	dbSNP
rs772720034	174	dbSNP
rs551064911	175	dbSNP
rs770709387	181	dbSNP
rs776468909	182	dbSNP
rs1261729496	183	dbSNP
rs759341232	188	dbSNP
rs186248863	189	dbSNP
rs888719695	192	dbSNP
rs1036429208	196	dbSNP
rs536699902	199	dbSNP
rs768703170	200	dbSNP
rs1234758261	206	dbSNP
rs770326306	207	dbSNP
rs3751081	208	dbSNP
rs965454922	214	dbSNP
rs756458825	222	dbSNP
rs766719292	223	dbSNP
rs763295304	224	dbSNP
rs1028254803	230	dbSNP
rs566786820	231	dbSNP
rs1234306219	232	dbSNP
rs1275375062	237	dbSNP
rs1319554428	241	dbSNP
rs779242232	243	dbSNP
rs1260862396	245	dbSNP
rs748742349	246	dbSNP
rs757819965	250	dbSNP
rs190665404	254	dbSNP
rs558677709	255	dbSNP
rs988628527	268	dbSNP
rs1409115496	273	dbSNP
rs1163076142	283	dbSNP
rs1470009140	292	dbSNP
rs1387688162	293	dbSNP
rs1184891931	294	dbSNP
rs774494608	295	dbSNP
rs570719358	297	dbSNP
rs1448399747	299	dbSNP
rs1456225021	305	dbSNP
rs1044183426	306	dbSNP
rs1032097403	310	dbSNP
rs960031381	311	dbSNP
rs1357169092	317	dbSNP
rs1289408983	324	dbSNP
rs761740175	325	dbSNP
rs538336763	327	dbSNP
rs930276344	328	dbSNP
rs1023189921	329	dbSNP
rs182803449	332	dbSNP
rs984249242	333	dbSNP
rs367832472	346	dbSNP
rs11605214	348	dbSNP
rs1164701213	353	dbSNP
rs963104089	363	dbSNP
rs542642099	379	dbSNP
rs1184297773	384	dbSNP
rs1015721237	391	dbSNP
rs1476176172	394	dbSNP
rs1242397393	395	dbSNP
rs1221453230	396	dbSNP
rs1327225228	396	dbSNP
rs554283866	399	dbSNP
rs757444727	408	dbSNP
rs998194100	427	dbSNP
rs1487152058	433	dbSNP
rs1028347892	434	dbSNP
rs1052143397	443	dbSNP
rs1208519546	451	dbSNP
rs1293487647	459	dbSNP
rs1216456012	462	dbSNP
rs1268634971	467	dbSNP
rs185753052	469	dbSNP
rs978726193	472	dbSNP
rs141801807	483	dbSNP
rs1403341181	486	dbSNP
rs943223262	497	dbSNP
rs1304162350	500	dbSNP
rs955944221	504	dbSNP
rs989153202	505	dbSNP
rs917061203	513	dbSNP
rs540537847	514	dbSNP
rs979954681	518	dbSNP
rs927026402	522	dbSNP
rs1042903992	526	dbSNP
rs1159224947	528	dbSNP
rs1364965435	531	dbSNP
rs1270733281	533	dbSNP
rs1199935603	535	dbSNP
rs565033325	537	dbSNP
rs1249606372	539	dbSNP
rs904322872	544	dbSNP
rs1308085222	545	dbSNP
rs1262606401	551	dbSNP
rs1221871442	555	dbSNP
rs999348586	556	dbSNP
rs1284300228	560	dbSNP
rs532391270	565	dbSNP
rs1391236647	567	dbSNP
rs930413694	568	dbSNP
rs1300345224	583	dbSNP
rs1462953087	597	dbSNP
rs1400326070	599	dbSNP
rs767511986	600	dbSNP
rs1175131962	604	dbSNP
rs544379891	607	dbSNP
rs750319109	608	dbSNP
rs1431042016	611	dbSNP
rs1176871679	614	dbSNP
rs1053189189	618	dbSNP
rs907535704	620	dbSNP
rs895820531	621	dbSNP
rs1178819711	627	dbSNP
rs756012891	634	dbSNP
rs1014245049	636	dbSNP
rs1023198708	638	dbSNP
rs1636209	639	dbSNP
rs1636208	640	dbSNP
rs563031773	643	dbSNP
rs1305230305	645	dbSNP
rs1238606268	649	dbSNP
rs940261319	653	dbSNP
rs1392444409	654	dbSNP
rs1017058289	661	dbSNP
rs766208153	662	dbSNP
rs901450120	663	dbSNP
rs753613883	664	dbSNP
rs1303001368	668	dbSNP
rs1307816749	675	dbSNP
rs1703440	680	dbSNP
rs754721700	681	dbSNP
rs530150103	689	dbSNP
rs972236866	693	dbSNP
rs998307009	695	dbSNP
rs1462654137	696	dbSNP
rs1243836328	703	dbSNP
rs918999917	708	dbSNP
rs548532932	709	dbSNP
rs566529319	711	dbSNP
rs1359335488	715	dbSNP
rs527936752	718	dbSNP
rs1313646890	720	dbSNP
rs987152040	723	dbSNP
rs550091247	728	dbSNP
rs1384292609	730	dbSNP
rs866382073	735	dbSNP
rs10557779	738	dbSNP
rs1329335511	738	dbSNP
rs1364737003	738	dbSNP
rs1369088028	738	dbSNP
rs1381265390	738	dbSNP
rs1382388420	738	dbSNP
rs1420147734	738	dbSNP
rs145914884	738	dbSNP
rs397847862	738	dbSNP
rs748968696	738	dbSNP
rs773840244	738	dbSNP
rs779000226	738	dbSNP
rs1177356028	743	dbSNP
rs910506811	747	dbSNP
rs1264201124	748	dbSNP
rs1426942472	748	dbSNP
rs1421530966	749	dbSNP
rs943275411	750	dbSNP
rs1290063281	751	dbSNP
rs552491293	752	dbSNP
rs1426429091	753	dbSNP
rs1166511367	754	dbSNP
rs925796836	755	dbSNP
rs1241418643	756	dbSNP
rs1324314878	757	dbSNP
rs1049918989	758	dbSNP
rs1400239265	760	dbSNP
rs983276378	761	dbSNP
rs747913885	766	dbSNP
rs1301093262	768	dbSNP
rs1053644180	781	dbSNP
rs1167400672	785	dbSNP
rs1374871246	789	dbSNP
rs1394331841	789	dbSNP
rs1314415168	793	dbSNP
rs1000242508	795	dbSNP
rs1480246745	799	dbSNP
rs1032993558	800	dbSNP
rs1272939621	801	dbSNP
rs1014702900	807	dbSNP
rs956250163	814	dbSNP
rs1307276860	816	dbSNP
rs570707341	817	dbSNP
rs1010268134	818	dbSNP
rs191480160	824	dbSNP
rs35317229	824	dbSNP
rs1336810876	826	dbSNP
rs556765657	829	dbSNP
rs1218815241	832	dbSNP
rs1281120113	834	dbSNP
rs1322441478	834	dbSNP
rs1044380424	835	dbSNP
rs1328024693	847	dbSNP
rs1331608712	847	dbSNP
rs1482012494	850	dbSNP
rs971340880	855	dbSNP
rs905831556	857	dbSNP
rs568901231	858	dbSNP
rs1446389698	862	dbSNP
rs374650366	863	dbSNP
rs1186526361	864	dbSNP
rs1418615135	869	dbSNP
rs1017111831	891	dbSNP
rs927116124	892	dbSNP
rs1355533048	896	dbSNP
rs897343393	902	dbSNP
rs1171440650	904	dbSNP
rs1198776201	905	dbSNP
rs1356522718	909	dbSNP
rs1468381934	912	dbSNP
rs951736463	916	dbSNP
rs1322388613	918	dbSNP
rs1260944271	921	dbSNP
rs1336176430	929	dbSNP
rs1224974258	931	dbSNP
rs1383532207	933	dbSNP
rs984964953	939	dbSNP
rs907505923	942	dbSNP
rs1455115449	945	dbSNP
rs1332100295	947	dbSNP
rs1452093118	948	dbSNP
rs1296028166	959	dbSNP
rs1338878319	963	dbSNP
rs940336092	968	dbSNP
rs1026522462	977	dbSNP
rs1040080105	978	dbSNP
rs922838116	979	dbSNP
rs1157230833	980	dbSNP
rs954478228	981	dbSNP
rs1381540910	983	dbSNP
rs1178713414	989	dbSNP
rs987185334	991	dbSNP
rs1017285259	996	dbSNP
rs1211740758	997	dbSNP
rs1442674904	999	dbSNP
rs934252683	1007	dbSNP
rs4646815	1009	dbSNP
rs925849099	1014	dbSNP
rs143759601	1015	dbSNP
rs113008632	1025	dbSNP
rs1380611594	1033	dbSNP
rs917034428	1035	dbSNP
rs950163559	1042	dbSNP
rs868417307	1058	dbSNP
rs1044433589	1059	dbSNP
rs559699841	1064	dbSNP
rs905884679	1065	dbSNP
rs941351913	1073	dbSNP
rs1236568257	1076	dbSNP
rs148167395	1078	dbSNP
rs182806401	1082	dbSNP
rs1010649895	1091	dbSNP
rs572455786	1096	dbSNP
rs1425997213	1097	dbSNP
rs1472910551	1103	dbSNP
rs1241219294	1106	dbSNP
rs1024342018	1115	dbSNP
rs577093649	1116	dbSNP
rs1213218556	1130	dbSNP
rs772872461	1133	dbSNP
rs1286501945	1137	dbSNP
rs1221594689	1138	dbSNP
rs1001452655	1140	dbSNP
rs1292082996	1146	dbSNP
rs757810223	1150	dbSNP
rs1229017920	1152	dbSNP
rs1188066109	1155	dbSNP
rs1029838496	1157	dbSNP
rs1402099892	1162	dbSNP
rs951871913	1164	dbSNP
rs1008671600	1165	dbSNP
rs1479581218	1167	dbSNP
rs760136081	1172	dbSNP
rs1175970728	1173	dbSNP
rs1166276887	1176	dbSNP
rs964405151	1177	dbSNP
rs978408148	1179	dbSNP
rs1184354615	1183	dbSNP
rs1478615719	1184	dbSNP
rs1033384625	1190	dbSNP
rs544357940	1191	dbSNP
rs1015086857	1192	dbSNP
rs1248449413	1194	dbSNP
rs562561250	1207	dbSNP
rs187867243	1214	dbSNP
rs949857368	1219	dbSNP
rs15518	1227	dbSNP
rs76002083	1229	dbSNP
rs941404393	1233	dbSNP
rs1370358433	1234	dbSNP
rs1343958582	1238	dbSNP
rs192294137	1246	dbSNP
rs911504910	1247	dbSNP
rs936151383	1251	dbSNP
rs1353373307	1254	dbSNP
rs115864705	1256	dbSNP
rs1466838680	1264	dbSNP
rs1423965573	1266	dbSNP
rs1175432916	1276	dbSNP
rs1479297200	1283	dbSNP
rs770412283	1285	dbSNP
rs4646816	1286	dbSNP
rs1283512810	1291	dbSNP
rs116249448	1300	dbSNP
rs531927926	1302	dbSNP
rs1051762194	1307	dbSNP
rs907220593	1311	dbSNP
rs183534677	1313	dbSNP
rs1221923303	1316	dbSNP
rs1314257388	1318	dbSNP
rs1007052549	1323	dbSNP
rs1223685488	1330	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.