>RAI1|NM_030665|3'UTR
   1 TAATCCACCCCAACGGCCGGAGGAGCCGCCGGAGCCCGCCTGCCCGCCCGCCGCCGAAGGAGAGGAGCCGCCTGCGCAGC
  81 CCCCGGGCCTTTGAGCTGCTCCCAGCGCTGGTCCAGAGCCGATCCTTGATCCGGGTCCCGGATCGTGGATCCGGCCGCCT
 161 AGGGCTCAGACTTGCGGCCCCGGGTTGGGAGGAAAACCCGTTCCGGAGCCGCCTGCTCCCGGAACCGGACGGCACAGGGC
 241 GTTCTTGCCCACCCCAGGGGCCAGGCTTGCGGAGGGGGAGCCCGCGGAGCGGCCAGACTCCCCGGGGCGCTCAGCCTCCG
 321 GCGAGGGTGGGAGACGGCTTTGTCCTGGGGACACTTTCCCTCTGGAATCTCAAGACGACGTGGCACACATTCCACGTGGG
 401 TGCTGCCGCCACCCCAGTCGGTCGTGGCGTGCAGCTGGGAGCCCTGGGCTTGGGGGTGGGGGTCGAAACAGTACTGGAAG
 481 AGGCGGAGGGCGGCTCCTAGCTCCGTGGACTAGGCGGGGGAGAAAGGAAGCCTTTCTGAGAGCGGGCTAGGCCGGCACTG
 561 GAGAGGCCGGAGCCTTTGGAACAAACCGTGCGGAACGCGTCCAGGGGCCTTCCCGCCCAGCCTTTGCCAGATCTCTCGTG
 641 CGGTTCGGGCAAAGCCGGGGTAGACCTGGGCTATGCTCAGTTAGGGGTTGCGGGATCCCCGAGTGTGGGCGGGACTGGGA
 721 CACCCTTTGGCCTCTGTTTGTCCCCTTTCCAGTCCTCCACCCCACCCCTGGAGCCCAGCCTGGGAGCGCAAAACCCAAGA
 801 AGCGGCCAGAACGCACCTCCGGCTCCGGCGGACGCGCGACCGTTGTGCACCACCAGGGACCGCCGCGCCTACTCTGCACG
 881 GGAGCAGGGACAGCGCTAGATTTCGTGTACAAAACCTGTGTACCCCTCTATATATATGTTACATAGAATGTATATATGTT
 961 GGGAACATGCTCGCTTCTCCCGTGTGTCGCCGCCGTGCGTCGTGCGCCCGCAACAGAGCCCCAACCGGGCCTTTGCCGGG
1041 TAAGGGGCTACCGCGACGCCACTTGTCCACGCAGCCACCACCGGCCCGGGCCAGTCCCTGCCAGTCCGTCCGCCTGTCCG
1121 TCCGTGTCCTCAGCTCTGTCCACGCTTCGATAGGCCTGACGCAGCCCCCAGCCCAGGGCCGCCCTAGCAACTTCCTGTAC
1201 ATATGACTGTAAAATGGTAAACGTGTGTATTATATCTGGCCTCGTTATATAGTGTATATATATGTATACATATACATATA
1281 TATAATATATATGAAGACTGTAAATGTTAAGACGACTAGTGTTCTTATTAGTATATTGCTTCACACTGAAGATTGTGTGT
1361 ATCGAGCTGTTTCTAAAAGATGTTTATTTTCCTTAAGAGTAAAAAACAGTCATTGCATTCAGAAAAAAAAAAAAAAAAAA
1441 GTCAATAAAGATACAACGATTGTTTTGGAAAAAAAAAA

ID	Duplex structure	Position	Score	MFE
1	miRNA 3' ggGGGUAACGAUGUCGGCGGACa 5' |||:|| | : ||||||||| Target 5' aaCCCGTT-CCGGAGCCGCCTGc 3'	195 - 216	168.00	-27.60
2	miRNA 3' ggGGGUAACG---AUGUCGGCGGACa 5' ||| ||| | |: ||||||| Target 5' gtCCC--TGCCAGTCCGTCCGCCTGt 3'	1094 - 1117	153.00	-21.80
3	miRNA 3' ggggguaacgaugUCGGCGGACa 5' ||||||||| Target 5' gccgaaggagaggAGCCGCCTGc 3'	53 - 75	150.00	-21.30

Mutant ID	Mutant Position	Mutant Source
COSN25990310	20	COSMIC
COSN16130002	53	COSMIC
COSN26441740	133	COSMIC
COSN8832585	420	COSMIC
COSN25269930	545	COSMIC
COSM7717056	772	COSMIC
COSM8960406	782	COSMIC
COSM5784662	800	COSMIC
COSM8908517	800	COSMIC
COSM9809954	805	COSMIC
COSM7192311	810	COSMIC
COSM8495443	810	COSMIC
COSM5548778	830	COSMIC
COSM9004221	834	COSMIC
COSM2740286	839	COSMIC
COSM8959442	863	COSMIC
COSM5516758	866	COSMIC
COSM9004685	867	COSMIC
COSM7440083	881	COSMIC
COSN26572385	951	COSMIC
COSN30673871	983	COSMIC
COSN31579355	999	COSMIC
COSN26554675	1000	COSMIC
COSN26637803	1011	COSMIC
COSN25907822	1028	COSMIC
COSN25807753	1085	COSMIC
COSN31521841	1106	COSMIC
COSN31561698	1111	COSMIC
COSN31779202	1114	COSMIC
COSN31539917	1149	COSMIC
COSN31489782	1161	COSMIC
COSN31535754	1165	COSMIC
COSN31591560	1237	COSMIC
COSN1714750	1262	COSMIC
COSN31556881	1285	COSMIC
COSN31522890	1296	COSMIC
COSN1193686	1315	COSMIC
COSN26161598	1366	COSMIC
COSN24967065	1407	COSMIC
COSN31546478	1414	COSMIC
COSN28852093	1423	COSMIC
COSN31782877	1440	COSMIC

Mutant ID	Mutant Position	Mutant Source
rs1337881858	2	dbSNP
rs1231924384	7	dbSNP
rs1329947776	11	dbSNP
rs1231561691	13	dbSNP
rs767107315	17	dbSNP
rs948181872	18	dbSNP
rs1345987196	19	dbSNP
rs199817588	20	dbSNP
rs1409633308	21	dbSNP
rs1348202138	23	dbSNP
rs752174617	27	dbSNP
rs757738920	28	dbSNP
rs1044595743	30	dbSNP
rs1391448373	33	dbSNP
rs1389467265	36	dbSNP
rs779287545	39	dbSNP
rs1251179379	40	dbSNP
rs1439294802	42	dbSNP
rs1196486103	45	dbSNP
rs1462900119	48	dbSNP
rs1006904320	50	dbSNP
rs1158098230	51	dbSNP
rs1454437658	53	dbSNP
rs905704649	57	dbSNP
rs34693238	59	dbSNP
rs1002752702	63	dbSNP
rs1184323945	68	dbSNP
rs1438463865	74	dbSNP
rs1266686695	78	dbSNP
rs1211924602	85	dbSNP
rs1337532304	86	dbSNP
rs1033476254	87	dbSNP
rs1183994844	90	dbSNP
rs957480581	101	dbSNP
rs1280918514	104	dbSNP
rs1239229894	111	dbSNP
rs1330165878	112	dbSNP
rs989718323	116	dbSNP
rs1418339250	121	dbSNP
rs1156463565	126	dbSNP
rs974162674	126	dbSNP
rs1020780606	133	dbSNP
rs1009937033	135	dbSNP
rs1158937337	136	dbSNP
rs966589252	138	dbSNP
rs982018777	146	dbSNP
rs1021357832	147	dbSNP
rs927904490	154	dbSNP
rs1254157771	157	dbSNP
rs529752687	160	dbSNP
rs543167667	175	dbSNP
rs563265354	176	dbSNP
rs532005208	179	dbSNP
rs1343805506	181	dbSNP
rs1300860145	184	dbSNP
rs974525269	185	dbSNP
rs990502557	188	dbSNP
rs909619102	197	dbSNP
rs1296777841	198	dbSNP
rs941152097	199	dbSNP
rs1428475610	204	dbSNP
rs1346915411	205	dbSNP
rs1432167064	210	dbSNP
rs1037189372	212	dbSNP
rs918779952	214	dbSNP
rs552035217	217	dbSNP
rs565680728	225	dbSNP
rs1401740002	231	dbSNP
rs1172066576	232	dbSNP
rs1390069177	236	dbSNP
rs1455636894	239	dbSNP
rs1051317047	241	dbSNP
rs528269406	242	dbSNP
rs1188019050	243	dbSNP
rs1474686820	245	dbSNP
rs1245263522	249	dbSNP
rs1289688784	250	dbSNP
rs987674251	254	dbSNP
rs1216921244	258	dbSNP
rs1007264819	259	dbSNP
rs1212661127	266	dbSNP
rs548320882	276	dbSNP
rs1273213420	279	dbSNP
rs998996130	280	dbSNP
rs1054502739	282	dbSNP
rs146819296	283	dbSNP
rs1480167711	284	dbSNP
rs973353117	285	dbSNP
rs1175291701	288	dbSNP
rs1446994278	297	dbSNP
rs1353399171	299	dbSNP
rs536718095	309	dbSNP
rs564831128	317	dbSNP
rs1376318825	320	dbSNP
rs948101269	327	dbSNP
rs1045158591	332	dbSNP
rs1444873717	335	dbSNP
rs1187679503	338	dbSNP
rs1472674218	346	dbSNP
rs927118462	354	dbSNP
rs1382840682	356	dbSNP
rs550030101	358	dbSNP
rs1057060212	361	dbSNP
rs768078281	363	dbSNP
rs1250664014	365	dbSNP
rs1171699131	366	dbSNP
rs1354502026	368	dbSNP
rs1273622593	370	dbSNP
rs1227606603	372	dbSNP
rs1460742681	374	dbSNP
rs570044205	378	dbSNP
rs1356304507	387	dbSNP
rs891742479	389	dbSNP
rs1440097356	390	dbSNP
rs1304973329	398	dbSNP
rs34210440	398	dbSNP
rs1010169319	407	dbSNP
rs773215080	414	dbSNP
rs1034867466	417	dbSNP
rs1475765132	418	dbSNP
rs1407021814	428	dbSNP
rs1452184513	430	dbSNP
rs959356179	439	dbSNP
rs1043080002	442	dbSNP
rs539070101	443	dbSNP
rs990881967	444	dbSNP
rs1313260089	445	dbSNP
rs909575721	453	dbSNP
rs962754746	454	dbSNP
rs1275018643	457	dbSNP
rs1306561323	458	dbSNP
rs1328289976	458	dbSNP
rs1215281196	462	dbSNP
rs753973733	470	dbSNP
rs114433624	478	dbSNP
rs1202102158	485	dbSNP
rs1028775446	490	dbSNP
rs954862488	491	dbSNP
rs918352623	493	dbSNP
rs934112631	494	dbSNP
rs1462286678	495	dbSNP
rs1363516603	497	dbSNP
rs1157389348	498	dbSNP
rs1009042385	502	dbSNP
rs1420450741	504	dbSNP
rs1257541477	509	dbSNP
rs1461651465	510	dbSNP
rs572730279	520	dbSNP
rs962241005	521	dbSNP
rs1254801445	523	dbSNP
rs867145257	528	dbSNP
rs1240935164	531	dbSNP
rs773819051	533	dbSNP
rs1464393356	544	dbSNP
rs535015443	547	dbSNP
rs1186616337	548	dbSNP
rs1419352837	551	dbSNP
rs1427261535	554	dbSNP
rs969455855	555	dbSNP
rs1430402832	560	dbSNP
rs943001295	561	dbSNP
rs1308035788	562	dbSNP
rs1054851835	566	dbSNP
rs981257841	567	dbSNP
rs564548872	570	dbSNP
rs1305723868	571	dbSNP
rs1010214320	573	dbSNP
rs938478398	576	dbSNP
rs1041757372	580	dbSNP
rs1287443665	589	dbSNP
rs1455713404	592	dbSNP
rs1345395080	593	dbSNP
rs574953732	598	dbSNP
rs913076820	600	dbSNP
rs1003326716	603	dbSNP
rs543481441	605	dbSNP
rs1043016148	607	dbSNP
rs1427803223	612	dbSNP
rs1034892386	615	dbSNP
rs904177595	616	dbSNP
rs959536482	620	dbSNP
rs1212727012	623	dbSNP
rs995884678	625	dbSNP
rs1012187373	627	dbSNP
rs760727327	630	dbSNP
rs1210348784	632	dbSNP
rs1323951949	636	dbSNP
rs1222706933	638	dbSNP
rs571733121	639	dbSNP
rs890179588	642	dbSNP
rs563270263	643	dbSNP
rs1448382398	647	dbSNP
rs972399205	648	dbSNP
rs1384263130	650	dbSNP
rs374887212	657	dbSNP
rs962189658	660	dbSNP
rs1301522232	662	dbSNP
rs1376924383	667	dbSNP
rs1173676440	669	dbSNP
rs576418511	674	dbSNP
rs757546619	679	dbSNP
rs200249502	687	dbSNP
rs918300252	689	dbSNP
rs955148096	692	dbSNP
rs1256467343	699	dbSNP
rs1480289457	701	dbSNP
rs754026580	707	dbSNP
rs545442390	716	dbSNP
rs911424280	720	dbSNP
rs1201088745	722	dbSNP
rs1338890183	724	dbSNP
rs1250123692	726	dbSNP
rs942928652	732	dbSNP
rs746171281	733	dbSNP
rs980822766	735	dbSNP
rs1293015436	736	dbSNP
rs990396638	742	dbSNP
rs758820067	744	dbSNP
rs542283173	745	dbSNP
rs1282498584	749	dbSNP
rs1446177662	752	dbSNP
rs1385389961	754	dbSNP
rs1323329552	755	dbSNP
rs878885443	757	dbSNP
rs1239008454	760	dbSNP
rs747272504	762	dbSNP
rs1236769344	764	dbSNP
rs1295734344	765	dbSNP
rs140957246	766	dbSNP
rs907287916	768	dbSNP
rs1251747272	769	dbSNP
rs1341401879	772	dbSNP
rs1458422702	774	dbSNP
rs781293447	776	dbSNP
rs1208048968	783	dbSNP
rs748181358	786	dbSNP
rs988223923	787	dbSNP
rs1468780578	788	dbSNP
rs913065572	789	dbSNP
rs1245840528	798	dbSNP
rs1448309151	799	dbSNP
rs938794707	802	dbSNP
rs1375231977	804	dbSNP
rs979073178	805	dbSNP
rs548205719	806	dbSNP
rs1163260866	808	dbSNP
rs1335229794	810	dbSNP
rs1395638243	810	dbSNP
rs1458577310	811	dbSNP
rs1273154916	817	dbSNP
rs1377655706	818	dbSNP
rs1337486327	819	dbSNP
rs1443590914	820	dbSNP
rs1318734505	821	dbSNP
rs1364733984	822	dbSNP
rs1234026818	823	dbSNP
rs1285157716	824	dbSNP
rs1382789630	825	dbSNP
rs759850736	826	dbSNP
rs1320066019	827	dbSNP
rs1346271948	828	dbSNP
rs1242479286	830	dbSNP
rs1413410532	834	dbSNP
rs1056681227	835	dbSNP
rs1333639056	836	dbSNP
rs1272523622	837	dbSNP
rs925915087	838	dbSNP
rs561894887	839	dbSNP
rs1462816066	842	dbSNP
rs764890641	843	dbSNP
rs1265780759	845	dbSNP
rs1157796037	846	dbSNP
rs1464174154	848	dbSNP
rs773083224	849	dbSNP
rs1263219234	854	dbSNP
rs1362317404	856	dbSNP
rs201177542	859	dbSNP
rs1440454368	860	dbSNP
rs1187391865	861	dbSNP
rs73981074	865	dbSNP
rs770892580	866	dbSNP
rs1016817096	868	dbSNP
rs1388437267	871	dbSNP
rs897990782	873	dbSNP
rs898417830	875	dbSNP
rs774129267	878	dbSNP
rs759219352	881	dbSNP
rs767103603	885	dbSNP
rs993830647	886	dbSNP
rs1280976553	887	dbSNP
rs1292556210	889	dbSNP
rs1025349886	892	dbSNP
rs1234845748	895	dbSNP
rs1286214835	905	dbSNP
rs1316195293	908	dbSNP
rs955095973	910	dbSNP
rs752181202	911	dbSNP
rs1481964095	915	dbSNP
rs986592118	916	dbSNP
rs1209529514	917	dbSNP
rs1473274298	921	dbSNP
rs1317327216	922	dbSNP
rs1258756309	923	dbSNP
rs1383046254	924	dbSNP
rs1362743608	925	dbSNP
rs1476464225	927	dbSNP
rs1180728856	931	dbSNP
rs1028304652	936	dbSNP
rs1411648959	937	dbSNP
rs1191848582	938	dbSNP
rs760113790	939	dbSNP
rs1018459821	944	dbSNP
rs1420103488	948	dbSNP
rs1455930845	950	dbSNP
rs964217997	953	dbSNP
rs905423296	955	dbSNP
rs1445692794	962	dbSNP
rs1002883759	972	dbSNP
rs765313154	973	dbSNP
rs914792333	974	dbSNP
rs1034976781	980	dbSNP
rs946334452	983	dbSNP
rs977378594	985	dbSNP
rs1235899774	990	dbSNP
rs1368179860	991	dbSNP
rs1220882784	993	dbSNP
rs1269576902	1000	dbSNP
rs928661403	1006	dbSNP
rs1438712156	1013	dbSNP
rs938699414	1015	dbSNP
rs1298595019	1019	dbSNP
rs1055854858	1020	dbSNP
rs967597350	1021	dbSNP
rs1446674888	1025	dbSNP
rs1436714682	1027	dbSNP
rs894558467	1031	dbSNP
rs530844746	1038	dbSNP
rs925792247	1038	dbSNP
rs1384671063	1049	dbSNP
rs550233963	1058	dbSNP
rs1310767297	1063	dbSNP
rs898408383	1071	dbSNP
rs1212382334	1073	dbSNP
rs1312327888	1075	dbSNP
rs911557134	1083	dbSNP
rs1212673407	1084	dbSNP
rs1341412306	1088	dbSNP
rs1161559411	1089	dbSNP
rs994114365	1094	dbSNP
rs1278556719	1098	dbSNP
rs1232494271	1099	dbSNP
rs1355035009	1100	dbSNP
rs944410584	1101	dbSNP
rs920000802	1104	dbSNP
rs1359749042	1109	dbSNP
rs1410271754	1113	dbSNP
rs1408664247	1114	dbSNP
rs1422314520	1115	dbSNP
rs1171798584	1116	dbSNP
rs1475115260	1120	dbSNP
rs1025297407	1121	dbSNP
rs879207307	1124	dbSNP
rs1008323697	1128	dbSNP
rs1201857628	1135	dbSNP
rs1315370943	1140	dbSNP
rs1381367242	1141	dbSNP
rs1258686329	1142	dbSNP
rs1243179225	1145	dbSNP
rs1332495044	1149	dbSNP
rs1272383861	1150	dbSNP
rs1294906584	1152	dbSNP
rs1230183434	1153	dbSNP
rs1380196888	1159	dbSNP
rs770858828	1161	dbSNP
rs905360229	1162	dbSNP
rs1002455273	1163	dbSNP
rs1403060249	1166	dbSNP
rs1332699555	1171	dbSNP
rs138625473	1184	dbSNP
rs539137740	1186	dbSNP
rs964138980	1191	dbSNP
rs1357676922	1192	dbSNP
rs1423986823	1199	dbSNP
rs766348360	1201	dbSNP
rs1465552170	1202	dbSNP
rs1406841258	1207	dbSNP
rs1313576382	1214	dbSNP
rs148898291	1219	dbSNP
rs1011745684	1223	dbSNP
rs1021776020	1224	dbSNP
rs1212917919	1233	dbSNP
rs1416543885	1233	dbSNP
rs1035304830	1234	dbSNP
rs896473579	1244	dbSNP
rs1286428118	1245	dbSNP
rs751534268	1246	dbSNP
rs1322525063	1247	dbSNP
rs1283890012	1252	dbSNP
rs1020983976	1255	dbSNP
rs967583551	1255	dbSNP
rs1224156596	1256	dbSNP
rs759039705	1256	dbSNP
rs1308607645	1257	dbSNP
rs1310085619	1258	dbSNP
rs1233183429	1262	dbSNP
rs1379303600	1265	dbSNP
rs767025491	1265	dbSNP
rs765758533	1269	dbSNP
rs143628855	1271	dbSNP
rs1295619028	1272	dbSNP
rs1232832359	1273	dbSNP
rs953374040	1275	dbSNP
rs1344223105	1276	dbSNP
rs750881640	1276	dbSNP
rs752344306	1276	dbSNP
rs911840005	1277	dbSNP
rs758837168	1278	dbSNP
rs928901931	1278	dbSNP
rs1481141806	1280	dbSNP
rs959996753	1281	dbSNP
rs1179325283	1283	dbSNP
rs1380314314	1285	dbSNP
rs965666753	1286	dbSNP
rs1423258407	1287	dbSNP
rs971683016	1287	dbSNP
rs758730057	1294	dbSNP
rs1737962	1298	dbSNP
rs550868299	1299	dbSNP
rs1485456923	1301	dbSNP
rs1335263200	1307	dbSNP
rs779177135	1311	dbSNP
rs1305990637	1314	dbSNP
rs991901772	1317	dbSNP
rs915994704	1319	dbSNP
rs747571235	1322	dbSNP
rs930378756	1323	dbSNP
rs1049320806	1325	dbSNP
rs926801708	1325	dbSNP
rs938188040	1327	dbSNP
rs942143277	1327	dbSNP
rs1304124042	1339	dbSNP
rs1387703106	1340	dbSNP
rs1483973497	1354	dbSNP
rs780446053	1354	dbSNP
rs1361616081	1365	dbSNP
rs1287500412	1376	dbSNP
rs1401408178	1382	dbSNP
rs1056711112	1395	dbSNP
rs780654029	1395	dbSNP
rs1432385177	1401	dbSNP
rs896715727	1401	dbSNP
rs1176791185	1404	dbSNP
rs1427858352	1407	dbSNP
rs1259335883	1412	dbSNP
rs1195611852	1414	dbSNP
rs1491527167	1420	dbSNP
rs370601753	1420	dbSNP
rs1210233586	1421	dbSNP
rs1491489489	1421	dbSNP
rs373004318	1421	dbSNP
rs754405451	1421	dbSNP
rs774837774	1421	dbSNP
rs1491285770	1422	dbSNP
rs374829984	1422	dbSNP
rs1172521467	1423	dbSNP
rs1313660650	1423	dbSNP
rs1371303595	1423	dbSNP
rs1403638869	1423	dbSNP
rs1424598478	1423	dbSNP
rs1478057635	1423	dbSNP
rs1491274388	1423	dbSNP
rs1491366426	1423	dbSNP
rs1491442822	1423	dbSNP
rs34061744	1423	dbSNP
rs397718365	1423	dbSNP
rs573904022	1423	dbSNP
rs57663061	1423	dbSNP
rs796900175	1423	dbSNP
rs878861759	1423	dbSNP
rs959750807	1423	dbSNP
rs1326576226	1424	dbSNP
rs1227323539	1426	dbSNP
rs1268981051	1428	dbSNP
rs1009835066	1429	dbSNP
rs1201138647	1432	dbSNP
rs79080059	1438	dbSNP
rs397856773	1439	dbSNP
rs80057141	1440	dbSNP
rs1256770033	1441	dbSNP
rs1224538806	1443	dbSNP
rs1200898920	1444	dbSNP
rs1262689953	1446	dbSNP
rs1321683598	1447	dbSNP
rs1319120456	1453	dbSNP
rs1042357511	1456	dbSNP
rs1231017177	1457	dbSNP
rs1206903047	1458	dbSNP
rs1341921621	1458	dbSNP
rs1390362372	1463	dbSNP
rs1262503462	1468	dbSNP
rs1333357985	1470	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.