ID	Duplex structure	Position	Score	MFE
1	miRNA 3' cgUCG-GUCGA-GAUG--GGGGCGGu 5' :|| ||||| | :| ||||||| Target 5' ctGGCTCAGCTCCCGCGGCCCCGCCc 3'	586 - 611	158.00	-25.80
2	miRNA 3' cgUCGGUCGAGA------UGGGGGCGGu 5' |||| |||| |:|||||| Target 5' caAGCCCCCTCTTCTCTCCCTCCCGCCc 3'	559 - 586	142.00	-23.80
3	miRNA 3' cgUCGGUCGAGA--UGGGGGCGGu 5' ||| || ||| |:|:|:||| Target 5' atAGCGAGATCTAAATCTCTGCCa 3'	249 - 272	138.00	-23.20

Mutant ID	Mutant Position	Mutant Source
COSN30103723	3	COSMIC
COSN31573549	4	COSMIC
COSN26981267	6	COSMIC
COSN30107427	20	COSMIC
COSN31522949	20	COSMIC
COSN19668592	24	COSMIC
COSN30188156	26	COSMIC
COSN29661453	37	COSMIC
COSN2532129	38	COSMIC
COSN31556837	108	COSMIC
COSN31587766	126	COSMIC
COSN30119348	128	COSMIC
COSN30162295	129	COSMIC
COSN30540037	180	COSMIC
COSN31490169	186	COSMIC
COSN22651174	328	COSMIC
COSN30161851	461	COSMIC
COSN20042664	462	COSMIC
COSN15904812	488	COSMIC
COSN30749700	489	COSMIC
COSN32071620	568	COSMIC
COSN21900085	582	COSMIC
COSN30749145	583	COSMIC
COSN32071700	602	COSMIC
COSN29024686	603	COSMIC
COSN32071335	613	COSMIC
COSN32069628	620	COSMIC
COSN31537411	720	COSMIC
COSN31601006	729	COSMIC

Mutant ID	Mutant Position	Mutant Source
rs766514395	3	dbSNP
rs373531467	4	dbSNP
rs1207035169	7	dbSNP
rs1245473082	11	dbSNP
rs750674142	18	dbSNP
rs376723443	19	dbSNP
rs762122897	21	dbSNP
rs774500044	24	dbSNP
rs777193847	35	dbSNP
rs369293348	37	dbSNP
rs887002938	39	dbSNP
rs1244572971	40	dbSNP
rs761283656	41	dbSNP
rs775818254	43	dbSNP
rs771631974	47	dbSNP
rs1448503443	48	dbSNP
rs762981895	48	dbSNP
rs768870967	48	dbSNP
rs769600035	48	dbSNP
rs775569966	48	dbSNP
rs1344314387	49	dbSNP
rs1348203307	50	dbSNP
rs1225324505	58	dbSNP
rs1353208728	59	dbSNP
rs1232096264	65	dbSNP
rs1278328397	68	dbSNP
rs1046956461	70	dbSNP
rs1351321295	74	dbSNP
rs995326659	77	dbSNP
rs1237359499	79	dbSNP
rs1384427097	85	dbSNP
rs542558687	86	dbSNP
rs1451556417	87	dbSNP
rs898282332	93	dbSNP
rs1259816878	94	dbSNP
rs1484842669	99	dbSNP
rs1332625097	102	dbSNP
rs573855333	103	dbSNP
rs1476346075	104	dbSNP
rs1166032581	106	dbSNP
rs1409396257	109	dbSNP
rs1414782319	110	dbSNP
rs1177990159	111	dbSNP
rs1039471623	112	dbSNP
rs942407857	121	dbSNP
rs1298270172	122	dbSNP
rs890806964	124	dbSNP
rs557212204	126	dbSNP
rs1387221421	127	dbSNP
rs1184435955	128	dbSNP
rs373157908	129	dbSNP
rs924175927	137	dbSNP
rs141757137	141	dbSNP
rs1448745056	142	dbSNP
rs1447468029	143	dbSNP
rs557466259	147	dbSNP
rs990922083	156	dbSNP
rs1195226473	158	dbSNP
rs534653817	158	dbSNP
rs1393111675	160	dbSNP
rs1237947004	162	dbSNP
rs961040728	163	dbSNP
rs1360972039	167	dbSNP
rs780402105	171	dbSNP
rs1398405486	178	dbSNP
rs1035039670	179	dbSNP
rs1326326049	179	dbSNP
rs893858425	180	dbSNP
rs565316158	181	dbSNP
rs1306071472	183	dbSNP
rs999638997	186	dbSNP
rs1234028646	188	dbSNP
rs1244719603	191	dbSNP
rs1232254048	196	dbSNP
rs1353133320	197	dbSNP
rs1376548074	198	dbSNP
rs1025559789	200	dbSNP
rs1283696766	201	dbSNP
rs995378857	210	dbSNP
rs1215547314	217	dbSNP
rs1251076112	220	dbSNP
rs1453500792	223	dbSNP
rs1179056468	227	dbSNP
rs1365161342	228	dbSNP
rs1468318447	230	dbSNP
rs898336335	237	dbSNP
rs1390902038	252	dbSNP
rs1462576511	253	dbSNP
rs555997081	254	dbSNP
rs535788720	255	dbSNP
rs1433290019	256	dbSNP
rs1440570705	258	dbSNP
rs1310511029	261	dbSNP
rs1346208975	264	dbSNP
rs181761973	265	dbSNP
rs1018088834	269	dbSNP
rs201433687	270	dbSNP
rs1418479076	271	dbSNP
rs1357073129	272	dbSNP
rs1367456141	272	dbSNP
rs1164304787	274	dbSNP
rs1006655846	279	dbSNP
rs890848235	281	dbSNP
rs1188544530	282	dbSNP
rs1252487576	283	dbSNP
rs1475612795	284	dbSNP
rs1262293655	285	dbSNP
rs1475881088	286	dbSNP
rs1050804927	287	dbSNP
rs1328360317	287	dbSNP
rs1340763872	287	dbSNP
rs1356371184	287	dbSNP
rs1416295407	287	dbSNP
rs35757137	287	dbSNP
rs397796586	287	dbSNP
rs1214279843	288	dbSNP
rs138633372	294	dbSNP
rs1291807936	295	dbSNP
rs1334067112	295	dbSNP
rs902805064	302	dbSNP
rs1253022886	306	dbSNP
rs1337129725	308	dbSNP
rs1195045131	312	dbSNP
rs1043953586	313	dbSNP
rs1185115053	319	dbSNP
rs1256269052	320	dbSNP
rs1041105839	321	dbSNP
rs1475157256	324	dbSNP
rs946930285	325	dbSNP
rs533246756	326	dbSNP
rs916754712	328	dbSNP
rs991366225	332	dbSNP
rs1438112176	333	dbSNP
rs1402616812	334	dbSNP
rs1383590964	339	dbSNP
rs1330159468	341	dbSNP
rs1311131322	344	dbSNP
rs189845233	346	dbSNP
rs983506069	346	dbSNP
rs1226394936	347	dbSNP
rs1163218594	349	dbSNP
rs1349591451	354	dbSNP
rs1208349540	356	dbSNP
rs1394957394	359	dbSNP
rs911821821	361	dbSNP
rs950693571	362	dbSNP
rs1012599758	365	dbSNP
rs1488293082	365	dbSNP
rs1050645830	366	dbSNP
rs1264411774	367	dbSNP
rs1192917109	368	dbSNP
rs1436985637	369	dbSNP
rs1027620620	370	dbSNP
rs1435702463	372	dbSNP
rs973996583	373	dbSNP
rs547581070	379	dbSNP
rs773993674	383	dbSNP
rs962593650	384	dbSNP
rs1441626184	385	dbSNP
rs779363674	387	dbSNP
rs1475378224	388	dbSNP
rs1007115954	389	dbSNP
rs890906187	395	dbSNP
rs920311815	395	dbSNP
rs15383	397	dbSNP
rs1317166999	407	dbSNP
rs1217282730	408	dbSNP
rs1258506529	410	dbSNP
rs1218415821	415	dbSNP
rs1437236237	416	dbSNP
rs973116072	419	dbSNP
rs940470579	422	dbSNP
rs1254183922	423	dbSNP
rs1248288558	424	dbSNP
rs1192180454	425	dbSNP
rs766149298	426	dbSNP
rs1289102523	427	dbSNP
rs999184611	430	dbSNP
rs370894402	436	dbSNP
rs762929023	451	dbSNP
rs368278157	455	dbSNP
rs561965000	455	dbSNP
rs1396637447	456	dbSNP
rs1316935796	459	dbSNP
rs1438377977	459	dbSNP
rs35768476	460	dbSNP
rs75985763	460	dbSNP
rs1217215218	461	dbSNP
rs1325030407	467	dbSNP
rs1326146757	469	dbSNP
rs1011125742	472	dbSNP
rs375598365	472	dbSNP
rs1233402163	475	dbSNP
rs1274304654	476	dbSNP
rs1470259704	480	dbSNP
rs1284456211	483	dbSNP
rs1179104874	490	dbSNP
rs1481072526	490	dbSNP
rs1386775382	497	dbSNP
rs1055328346	503	dbSNP
rs773052511	506	dbSNP
rs1221367016	513	dbSNP
rs1359461412	515	dbSNP
rs542876916	516	dbSNP
rs1212694281	521	dbSNP
rs1279205275	524	dbSNP
rs991366238	526	dbSNP
rs1048279799	531	dbSNP
rs1444117642	533	dbSNP
rs1361212248	534	dbSNP
rs529239803	534	dbSNP
rs1296052235	537	dbSNP
rs1372189696	541	dbSNP
rs1414844500	548	dbSNP
rs1270744016	549	dbSNP
rs1432596382	560	dbSNP
rs563452736	563	dbSNP
rs1302764584	565	dbSNP
rs1425552649	566	dbSNP
rs1367459034	567	dbSNP
rs1289803563	568	dbSNP
rs1308378107	568	dbSNP
rs1207100621	569	dbSNP
rs1231344653	574	dbSNP
rs752899836	577	dbSNP
rs144697112	578	dbSNP
rs1409851646	579	dbSNP
rs755865840	582	dbSNP
rs1188843369	583	dbSNP
rs748141502	586	dbSNP
rs1353531313	590	dbSNP
rs1268698371	593	dbSNP
rs911116467	594	dbSNP
rs1490420160	597	dbSNP
rs541993293	599	dbSNP
rs955379789	600	dbSNP
rs1029455702	601	dbSNP
rs564168292	602	dbSNP
rs999238560	604	dbSNP
rs748187164	605	dbSNP
rs758511852	607	dbSNP
rs750536697	608	dbSNP
rs185368013	611	dbSNP
rs1405739020	612	dbSNP
rs1385942254	614	dbSNP
rs1158110050	615	dbSNP
rs1347649001	616	dbSNP
rs1296720472	617	dbSNP
rs142423316	618	dbSNP
rs555102950	619	dbSNP
rs1173149803	620	dbSNP
rs1389392843	620	dbSNP
rs1435113569	621	dbSNP
rs1468702361	624	dbSNP
rs1428978694	629	dbSNP
rs1177627638	630	dbSNP
rs1003759875	640	dbSNP
rs1433503888	645	dbSNP
rs906704499	648	dbSNP
rs1433583239	650	dbSNP
rs1268773165	654	dbSNP
rs1268978552	662	dbSNP
rs760897427	663	dbSNP
rs1480016575	665	dbSNP
rs1346055495	671	dbSNP
rs1232965080	672	dbSNP
rs1200389556	678	dbSNP
rs1285129545	681	dbSNP
rs1321369094	681	dbSNP
rs1189933817	682	dbSNP
rs1262228609	684	dbSNP
rs1223879165	687	dbSNP
rs57918812	690	dbSNP
rs1247343100	693	dbSNP
rs1305129720	693	dbSNP
rs879929660	695	dbSNP
rs767842048	696	dbSNP
rs1299998429	698	dbSNP
rs745860323	699	dbSNP
rs780848156	699	dbSNP
rs902634358	699	dbSNP
rs1398457563	700	dbSNP
rs1451031443	701	dbSNP
rs1319084631	702	dbSNP
rs376474045	704	dbSNP
rs1442073277	706	dbSNP
rs770820682	706	dbSNP
rs1471156023	707	dbSNP
rs1240926777	720	dbSNP
rs920660443	725	dbSNP
rs1376316532	726	dbSNP
rs866509806	728	dbSNP
rs1222166424	729	dbSNP
rs1267371259	737	dbSNP
rs1468896584	738	dbSNP
rs1019592618	739	dbSNP
rs943341138	744	dbSNP
rs1450670693	747	dbSNP
rs1406457700	751	dbSNP
rs1008235038	752	dbSNP
rs1365216509	756	dbSNP
rs1468114558	759	dbSNP
rs1157839624	761	dbSNP
rs911179075	762	dbSNP
rs576374342	767	dbSNP
rs955284069	768	dbSNP
rs922440673	773	dbSNP
rs1388957952	774	dbSNP
rs543928151	775	dbSNP
rs1386573162	781	dbSNP
rs776763108	783	dbSNP
rs1337773747	787	dbSNP
rs1440080823	788	dbSNP
rs1287852340	789	dbSNP
rs966456308	789	dbSNP
rs977869722	789	dbSNP
rs868654870	791	dbSNP
rs768861049	792	dbSNP
rs931922819	793	dbSNP
rs1010569319	794	dbSNP
rs1435762120	795	dbSNP
rs1180824253	796	dbSNP
rs959301205	796	dbSNP
rs1491489963	797	dbSNP
rs1190618272	800	dbSNP
rs898982661	804	dbSNP
rs1378007462	805	dbSNP
rs1457673808	806	dbSNP
rs1037539320	808	dbSNP
rs940408427	810	dbSNP
rs1257247323	816	dbSNP
rs906763687	820	dbSNP
rs62107577	823	dbSNP
rs556327996	824	dbSNP
rs1026510158	835	dbSNP
rs993654791	835	dbSNP
rs981717857	836	dbSNP
rs1339855430	837	dbSNP
rs1262995460	845	dbSNP
rs1218061992	850	dbSNP
rs771014326	851	dbSNP
rs949092660	852	dbSNP
rs747288961	854	dbSNP
rs943425301	864	dbSNP
rs1248371800	866	dbSNP
rs889121231	869	dbSNP
rs1486346804	870	dbSNP
rs1208124148	871	dbSNP
rs1254657218	872	dbSNP
rs372415969	878	dbSNP
rs916259892	880	dbSNP
rs1194339812	883	dbSNP
rs933918519	887	dbSNP
rs189359496	888	dbSNP
rs1394032574	889	dbSNP
rs1301211849	890	dbSNP
rs528107957	890	dbSNP
rs747994346	890	dbSNP
rs1401406272	891	dbSNP
rs1386925309	892	dbSNP
rs1297658189	893	dbSNP
rs570958113	893	dbSNP
rs547839359	894	dbSNP
rs1303621023	895	dbSNP
rs915037354	895	dbSNP
rs989198181	895	dbSNP
rs959126389	896	dbSNP
rs1033784069	897	dbSNP
rs534052028	900	dbSNP
rs1444823685	901	dbSNP
rs113170492	906	dbSNP
rs1264483943	906	dbSNP
rs1455799975	906	dbSNP
rs398059536	906	dbSNP
rs879249125	906	dbSNP
rs1367499717	907	dbSNP
rs1185030355	913	dbSNP
rs1422423925	914	dbSNP
rs368944741	915	dbSNP
rs1377081432	916	dbSNP
rs1264384539	923	dbSNP
rs1290513815	927	dbSNP
rs1386382692	928	dbSNP
rs1434065883	930	dbSNP
rs1326382514	932	dbSNP
rs1372724763	934	dbSNP
rs1217179516	935	dbSNP
rs1194940506	937	dbSNP
rs1316921446	941	dbSNP
rs568429029	944	dbSNP
rs1270524210	951	dbSNP
rs1283908658	954	dbSNP
rs1224853766	955	dbSNP
rs1357190907	957	dbSNP
rs1189623676	958	dbSNP
rs1265061502	959	dbSNP
rs1242957614	960	dbSNP
rs1419695427	960	dbSNP
rs1161443646	961	dbSNP
rs1327973997	962	dbSNP
rs1278626285	963	dbSNP
rs1409625402	965	dbSNP
rs1456705817	965	dbSNP
rs1428066684	966	dbSNP
rs548324400	966	dbSNP
rs1396335002	967	dbSNP
rs1434036527	968	dbSNP
rs551871526	968	dbSNP
rs60365888	968	dbSNP
rs1491303870	969	dbSNP
rs73920661	969	dbSNP
rs1219848285	970	dbSNP
rs1323836622	970	dbSNP
rs1265057122	971	dbSNP
rs1399272284	976	dbSNP
rs1184438128	978	dbSNP
rs1481107622	978	dbSNP
rs1199712372	980	dbSNP
rs1249789720	980	dbSNP
rs1403341530	980	dbSNP
rs67354590	980	dbSNP
rs67603778	980	dbSNP
rs74266717	980	dbSNP
rs796881092	980	dbSNP
rs903056222	980	dbSNP
rs1338379030	981	dbSNP
rs1463252893	982	dbSNP
rs1304922672	983	dbSNP
rs1026557846	986	dbSNP
rs1405428110	986	dbSNP
rs1294388903	990	dbSNP
rs1414898107	990	dbSNP
rs754947108	991	dbSNP
rs1226938092	994	dbSNP
rs1161093931	1003	dbSNP
rs1312549411	1009	dbSNP
rs1463206269	1009	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.

- 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.