ID	Duplex structure	Position	Score	MFE
1	miRNA 3' gcUCACACUCUAGUGUGGAGGg 5' :| || ||| :||||| | Target 5' ctGGGGTCAGACAGCACCTACt 3'	631 - 652	128.00	-14.80
2	miRNA 3' gcucacacucuAGUGUGGAGGg 5' |: |||:||| Target 5' caatcccctctTTCCACTTCCa 3'	428 - 449	127.00	-11.70
3	miRNA 3' gcucacacUCU--AGUGUGGAGGg 5' ||| || :||:||| Target 5' tcctccctAGACTTCCTACTTCCt 3'	569 - 592	120.00	-11.76

Mutant ID	Mutant Position	Mutant Source
COSM159561	1	COSMIC
COSN31532716	41	COSMIC
COSN22664817	71	COSMIC
COSN1869417	614	COSMIC
COSN7088581	752	COSMIC
COSN5968418	986	COSMIC
COSN21867848	1001	COSMIC

Mutant ID	Mutant Position	Mutant Source
rs1480658300	3	dbSNP
rs200397152	5	dbSNP
rs1419547215	9	dbSNP
rs767941202	9	dbSNP
rs530053190	10	dbSNP
rs1279826149	12	dbSNP
rs1200212146	17	dbSNP
rs748659610	19	dbSNP
rs1270563248	22	dbSNP
rs1228540019	23	dbSNP
rs1386864190	35	dbSNP
rs1446627515	44	dbSNP
rs1162974298	45	dbSNP
rs6084178	52	dbSNP
rs1368155618	54	dbSNP
rs530655640	55	dbSNP
rs1362173907	58	dbSNP
rs1300031287	63	dbSNP
rs114484391	64	dbSNP
rs1394044563	66	dbSNP
rs554614573	69	dbSNP
rs760277727	71	dbSNP
rs766038083	74	dbSNP
rs985477374	75	dbSNP
rs143915598	81	dbSNP
rs569149623	83	dbSNP
rs1307777983	84	dbSNP
rs6115684	89	dbSNP
rs1342227567	95	dbSNP
rs999460780	105	dbSNP
rs11475330	106	dbSNP
rs397865099	106	dbSNP
rs1238250794	109	dbSNP
rs1187358302	121	dbSNP
rs539324238	124	dbSNP
rs1250215351	126	dbSNP
rs1209918353	132	dbSNP
rs1464800713	150	dbSNP
rs918396160	151	dbSNP
rs1353979474	153	dbSNP
rs1356672011	157	dbSNP
rs1283222649	172	dbSNP
rs6115685	178	dbSNP
rs1367112400	181	dbSNP
rs148640817	185	dbSNP
rs1457000919	187	dbSNP
rs995899556	194	dbSNP
rs1046025991	195	dbSNP
rs1386323946	197	dbSNP
rs1316381243	200	dbSNP
rs373456479	201	dbSNP
rs1407143993	203	dbSNP
rs1414885415	209	dbSNP
rs1162891345	214	dbSNP
rs1029152178	216	dbSNP
rs566505706	217	dbSNP
rs937293942	218	dbSNP
rs1054118658	221	dbSNP
rs1005824594	223	dbSNP
rs1014562856	224	dbSNP
rs1288457415	234	dbSNP
rs1207725916	235	dbSNP
rs1343808549	242	dbSNP
rs962242542	254	dbSNP
rs1020061755	261	dbSNP
rs902652454	263	dbSNP
rs566721271	266	dbSNP
rs1367153570	268	dbSNP
rs928781537	273	dbSNP
rs1350550300	274	dbSNP
rs959126640	277	dbSNP
rs1016873729	278	dbSNP
rs1169678391	282	dbSNP
rs1449227286	286	dbSNP
rs962703518	290	dbSNP
rs1464228538	291	dbSNP
rs972763575	298	dbSNP
rs754896481	302	dbSNP
rs1245658523	305	dbSNP
rs768024849	309	dbSNP
rs750665773	313	dbSNP
rs750767282	314	dbSNP
rs1396597255	315	dbSNP
rs1339813696	317	dbSNP
rs1280399082	318	dbSNP
rs1041714137	320	dbSNP
rs918679071	323	dbSNP
rs191403407	336	dbSNP
rs1352623036	339	dbSNP
rs981294617	339	dbSNP
rs778774852	342	dbSNP
rs1316960125	345	dbSNP
rs935202124	350	dbSNP
rs1040695309	362	dbSNP
rs1257304037	365	dbSNP
rs573733013	385	dbSNP
rs1199320726	391	dbSNP
rs1254700633	401	dbSNP
rs1343623669	404	dbSNP
rs142148313	405	dbSNP
rs556111442	406	dbSNP
rs892781445	410	dbSNP
rs181552243	411	dbSNP
rs1239018577	412	dbSNP
rs901593327	413	dbSNP
rs1311579693	419	dbSNP
rs1276400090	427	dbSNP
rs1221833397	431	dbSNP
rs1331325224	432	dbSNP
rs1289002318	434	dbSNP
rs997710791	436	dbSNP
rs1371419736	440	dbSNP
rs887505131	446	dbSNP
rs1029818769	457	dbSNP
rs1359166431	463	dbSNP
rs889976557	468	dbSNP
rs1476992884	469	dbSNP
rs1007120285	473	dbSNP
rs1213243381	475	dbSNP
rs1005940692	477	dbSNP
rs1014511814	482	dbSNP
rs1416977753	483	dbSNP
rs961693293	485	dbSNP
rs185639098	490	dbSNP
rs375737683	492	dbSNP
rs1235453013	493	dbSNP
rs560741190	494	dbSNP
rs114796491	500	dbSNP
rs1268894857	502	dbSNP
rs1227838486	504	dbSNP
rs1301108680	513	dbSNP
rs992046030	525	dbSNP
rs981961228	532	dbSNP
rs757140810	540	dbSNP
rs927128720	541	dbSNP
rs1437938324	544	dbSNP
rs781088258	551	dbSNP
rs1319358458	558	dbSNP
rs968760693	563	dbSNP
rs1298629319	564	dbSNP
rs1339577662	568	dbSNP
rs1190237218	572	dbSNP
rs914498242	579	dbSNP
rs945988868	580	dbSNP
rs1216481767	581	dbSNP
rs1041398422	582	dbSNP
rs752493472	588	dbSNP
rs977510286	600	dbSNP
rs933068373	604	dbSNP
rs1313422654	608	dbSNP
rs1050619344	611	dbSNP
rs1366630456	616	dbSNP
rs924568476	624	dbSNP
rs889933640	625	dbSNP
rs1312351543	629	dbSNP
rs1380958267	635	dbSNP
rs1392277804	637	dbSNP
rs574565379	639	dbSNP
rs976808305	643	dbSNP
rs755935562	644	dbSNP
rs745699730	652	dbSNP
rs1457130437	654	dbSNP
rs1363307796	656	dbSNP
rs6115686	668	dbSNP
rs1430164359	672	dbSNP
rs898747873	673	dbSNP
rs1190957440	674	dbSNP
rs1434792057	678	dbSNP
rs994412296	682	dbSNP
rs1191809061	695	dbSNP
rs1025585584	698	dbSNP
rs1289842668	704	dbSNP
rs775837869	705	dbSNP
rs1207817878	714	dbSNP
rs201003601	719	dbSNP
rs971826164	728	dbSNP
rs374455869	750	dbSNP
rs550615689	758	dbSNP
rs114513630	760	dbSNP
rs6051416	767	dbSNP
rs1343329192	773	dbSNP
rs958529874	779	dbSNP
rs989982116	780	dbSNP
rs1369744674	783	dbSNP
rs1165903419	784	dbSNP
rs1467562115	785	dbSNP
rs941746326	786	dbSNP
rs1176950537	790	dbSNP
rs1261943732	794	dbSNP
rs1480146319	795	dbSNP
rs1487105770	797	dbSNP
rs1184627082	798	dbSNP
rs190050007	806	dbSNP
rs774253161	808	dbSNP
rs151201399	811	dbSNP
rs977361808	818	dbSNP
rs1257095076	823	dbSNP
rs139699910	824	dbSNP
rs932996005	838	dbSNP
rs549095647	839	dbSNP
rs894694089	845	dbSNP
rs567443662	852	dbSNP
rs1013179048	860	dbSNP
rs1326658460	866	dbSNP
rs1397544199	873	dbSNP
rs910297280	885	dbSNP
rs1021766775	886	dbSNP
rs968876157	887	dbSNP
rs977625141	892	dbSNP
rs16988125	894	dbSNP
rs1161411187	901	dbSNP
rs1038495143	903	dbSNP
rs1368710692	909	dbSNP
rs965514587	916	dbSNP
rs898695378	925	dbSNP
rs1246697772	929	dbSNP
rs994360036	937	dbSNP
rs1460342647	945	dbSNP
rs977133923	952	dbSNP
rs1228452380	953	dbSNP
rs1349574591	954	dbSNP
rs1277402289	984	dbSNP
rs921289234	985	dbSNP
rs1246441891	986	dbSNP
rs1340857734	989	dbSNP
rs1047318935	992	dbSNP
rs931857662	993	dbSNP
rs773851916	1000	dbSNP
rs1322712496	1003	dbSNP
rs1356483459	1008	dbSNP
rs1457831642	1010	dbSNP
rs1034396655	1012	dbSNP
rs778531317	1013	dbSNP
rs986015825	1018	dbSNP
rs761180442	1019	dbSNP
rs1157061760	1023	dbSNP
rs909174549	1026	dbSNP
rs941862563	1027	dbSNP
rs1036184603	1030	dbSNP
rs12479484	1034	dbSNP
rs1250428540	1035	dbSNP
rs766794738	1036	dbSNP
rs1445918995	1049	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.