>M6PR|NM_002355|3'UTR
   1 ATTGCACTTTATATGTCCAGCCTCTTCCTCAGTCCCCCAAACCAAAGCTACACAGCCAGATTTCTCAAGCAGTCTCAACT
  81 CCAGTCCCTCATCTCACCCTTACTATTGCTCTTGCTTTCCAGTTTGCTTTTGATTTGCATCTTCTCACTAGTAAAACTGC
 161 CTTCCCTTTGTTCCTTATTTTCTGTTTTTTCTCTAGAGAGGTACAGTTGTAAGTCAGAGTTAATATAATAGGGCCTGTGA
 241 AAACAGAGGCTTTTGCATTGTCTCTTGACATCAGAAGTTACAATAGGCATATGGGCAAAATGGTGTAGCAGGCTCACTGG
 321 CCGTTTGTTTTTTAAACACATTTTCACAAGTTTTTGAGACACTGGATTTCTTTAATTAAAAAAAAAATGCCAAGAAACAT
 401 TATTTATACAGGGTTGATTGCTTTCATGTTGTTATTCTGTACCCTATAGTAGCCTCCATGAGAATCTGGTATTTCTTGCT
 481 GCTTGGAACTACTTTGCAGTGATTACTTGGTTGCAGTCCAAGTACTCTCGTTTAGTCTGAGCCTGGAGATGTTCTAGACT
 561 TGCTTCTCCCACCTCTGAGATTAGGACAGGAAAAATGTGAAATTTCCCAATTACAGGATTATACGGTACCATCACATCAT
 641 TTGTGGAAATTGGGGTGACTGTATAGCTGGGATTGGGCTAAGGACTGTGGTCTTATCTGTCCACATACAGCCAAAATGCC
 721 TATCCAGAAATCCAGTTCGTTGGAAAGGAAAATTGGTACTCCTGTGCCACAGGGGTTCCAGAAAAGGGAAGTCACTTTAC
 801 CTTGCGGTGGTGGGATCCTGATGTCTTTCATCCATTTGTAGTAAAAGCTGGTAAAGCTTTTCTTACTCCTGGTTCCCTAC
 881 CAGTATTTCTAAACATGTCGCACTTTCTCCACAGGCATGTGGTTTTGACCTTTTTTTCAATCTTCTAGAAAGGGAACGGA
 961 AGCAGAAGTGGGACATCGAGGGCTCTGCTGTCCTCTGCGCTGGGTGTGGAATGCTGCTGCACCTGTCCCTTCTGCTGGCT
1041 CAGGGAAGTGTCTTCTTGCCCACATTTCTGTGGGGAAAGGTTTTTAATCCTCTGATGCTTCCATCTTCCTGTTTAGGCCA
1121 TGTGCCCAGAAACCTGGACTGATCTTTCTTTAATAGTGAACCCCTGGGCCACTGAAGAGTAACATGGCTCCACTGGACAC
1201 AAAAGAGGGATGGAATCAACAGGCAGGGGGCCTTTTATAAGCCTTAGGAAAAGAAAATGAAACTATTTCATCTTTGGACT
1281 TTTCAATACTATTGGAGTGATTTTTTTCTTTCTAAACAGGGAAAATAATGTTACAAAAGCATCTTTTTTGTTATTTGTTT
1361 GCATCCCTCCCCCACACCCTGGTGTTTTAAAATGAAGAAAAAAAACCATCACCTTTTGTACAAAAACTCTTAATGATTAA
1441 AAAACAAACAAAACATAAAAAAAAAAAAAAAAAA

ID	Duplex structure	Position	Score	MFE
1	miRNA 3' cgUUUUCAUUGACG---UCAAAAAc 5' ||| | :| | ||||||| Target 5' ttAAACACATTTTCACAAGTTTTTg 3'	332 - 356	144.00	-7.60
2	miRNA 3' cgUUUUCAUUGACGUCAAAAAc 5' ||||| : | || |||| Target 5' gtAAAAGCTGGTAAAGCTTTTc 3'	841 - 862	124.00	-6.70
3	miRNA 3' cgUUUUCAUUGACGUCAAAAac 5' | |:| | ||::||||| Target 5' ccACAGGCA--TGTGGTTTTga 3'	909 - 928	120.00	-8.00

Mutant ID	Mutant Position	Mutant Source
COSN18714840	24	COSMIC
COSN31533657	28	COSMIC
COSN24399351	30	COSMIC
COSN31501166	33	COSMIC
COSN30123723	64	COSMIC
COSN30488801	82	COSMIC
COSN30184113	89	COSMIC
COSN31582831	103	COSMIC
COSN25556516	121	COSMIC
COSN30106668	132	COSMIC
COSN18714839	170	COSMIC
COSN15131702	220	COSMIC
COSN31483412	250	COSMIC
COSN31530480	370	COSMIC
COSN31554919	377	COSMIC
COSN26596492	421	COSMIC
COSN8586893	899	COSMIC
COSN31564896	1256	COSMIC
COSN26650115	1371	COSMIC
COSN26548371	1413	COSMIC

Mutant ID	Mutant Position	Mutant Source
rs774005170	2	dbSNP
rs1196993695	4	dbSNP
rs754259156	6	dbSNP
rs1268181543	7	dbSNP
rs1211640059	9	dbSNP
rs377063084	11	dbSNP
rs781416108	13	dbSNP
rs1234679473	15	dbSNP
rs773549234	16	dbSNP
rs1355545162	17	dbSNP
rs772087159	18	dbSNP
rs370759645	21	dbSNP
rs985248293	25	dbSNP
rs755158874	28	dbSNP
rs955699549	34	dbSNP
rs1324960410	41	dbSNP
rs762343404	44	dbSNP
rs764054289	44	dbSNP
rs1029823386	49	dbSNP
rs972921458	50	dbSNP
rs1198704838	52	dbSNP
rs1202313477	53	dbSNP
rs961618549	56	dbSNP
rs1425812384	68	dbSNP
rs1162994953	72	dbSNP
rs966401909	82	dbSNP
rs1273115586	84	dbSNP
rs1017231200	93	dbSNP
rs1232841179	94	dbSNP
rs867509292	95	dbSNP
rs1172904952	107	dbSNP
rs1356269662	109	dbSNP
rs1439859444	111	dbSNP
rs1005930828	112	dbSNP
rs1010622512	116	dbSNP
rs1803933	118	dbSNP
rs1379577353	122	dbSNP
rs1416272886	128	dbSNP
rs753633516	141	dbSNP
rs775326685	142	dbSNP
rs1803934	144	dbSNP
rs537006596	150	dbSNP
rs1038844687	154	dbSNP
rs140430754	173	dbSNP
rs772031462	174	dbSNP
rs890318464	179	dbSNP
rs1238434980	184	dbSNP
rs763043445	199	dbSNP
rs1186215507	201	dbSNP
rs929262418	201	dbSNP
rs899123752	206	dbSNP
rs1188374883	207	dbSNP
rs1417386190	208	dbSNP
rs1359652196	209	dbSNP
rs1356725873	211	dbSNP
rs748228346	211	dbSNP
rs1171225578	212	dbSNP
rs1310830040	213	dbSNP
rs1354439518	220	dbSNP
rs1038112408	223	dbSNP
rs1014351991	227	dbSNP
rs796520173	230	dbSNP
rs1213454406	231	dbSNP
rs1359191862	231	dbSNP
rs948803822	231	dbSNP
rs1279998399	234	dbSNP
rs1350674870	235	dbSNP
rs571345715	249	dbSNP
rs770031444	253	dbSNP
rs755222376	254	dbSNP
rs915998587	258	dbSNP
rs1195704028	259	dbSNP
rs1488742593	260	dbSNP
rs1195545028	263	dbSNP
rs551454985	269	dbSNP
rs1249545544	281	dbSNP
rs1475157405	282	dbSNP
rs1175209821	284	dbSNP
rs1056206610	286	dbSNP
rs774585757	292	dbSNP
rs935201658	304	dbSNP
rs1455486327	312	dbSNP
rs1171527575	316	dbSNP
rs1374578776	317	dbSNP
rs938817789	322	dbSNP
rs902406530	323	dbSNP
rs924813727	326	dbSNP
rs1481579268	331	dbSNP
rs1233347744	339	dbSNP
rs1209559598	345	dbSNP
rs1274910925	354	dbSNP
rs1373846886	360	dbSNP
rs1303170696	374	dbSNP
rs752745079	374	dbSNP
rs1345091095	376	dbSNP
rs1282070730	377	dbSNP
rs1354806902	378	dbSNP
rs745364914	379	dbSNP
rs1207242431	380	dbSNP
rs977631648	380	dbSNP
rs143732744	388	dbSNP
rs781608267	388	dbSNP
rs969384487	388	dbSNP
rs1469787912	390	dbSNP
rs1191613488	414	dbSNP
rs1234565436	418	dbSNP
rs1558525	421	dbSNP
rs1160079338	422	dbSNP
rs989572599	425	dbSNP
rs1399699789	430	dbSNP
rs1326002941	434	dbSNP
rs964434680	446	dbSNP
rs1017297144	450	dbSNP
rs1325886938	452	dbSNP
rs1376200303	457	dbSNP
rs1309112381	465	dbSNP
rs1350231096	467	dbSNP
rs1008636698	468	dbSNP
rs35031864	470	dbSNP
rs1275147852	475	dbSNP
rs1467233041	476	dbSNP
rs1213111385	481	dbSNP
rs1414293511	486	dbSNP
rs1373709637	492	dbSNP
rs771366585	494	dbSNP
rs1049949	500	dbSNP
rs1230898212	516	dbSNP
rs756554801	518	dbSNP
rs1175827210	521	dbSNP
rs796220315	525	dbSNP
rs778382478	528	dbSNP
rs890284050	529	dbSNP
rs1156708675	530	dbSNP
rs1420604954	535	dbSNP
rs1251217963	540	dbSNP
rs1187097923	542	dbSNP
rs1335492825	545	dbSNP
rs1484442056	547	dbSNP
rs1258988857	549	dbSNP
rs1210902129	551	dbSNP
rs1485341640	552	dbSNP
rs1258728267	561	dbSNP
rs1339999201	562	dbSNP
rs11544969	572	dbSNP
rs1197444631	575	dbSNP
rs1270652987	581	dbSNP
rs768159745	584	dbSNP
rs1188356397	606	dbSNP
rs1237358109	610	dbSNP
rs1319078481	624	dbSNP
rs752228433	625	dbSNP
rs778326244	627	dbSNP
rs1463995438	629	dbSNP
rs1354052631	635	dbSNP
rs763794596	637	dbSNP
rs1396362438	649	dbSNP
rs1435800956	650	dbSNP
rs1314847049	655	dbSNP
rs1353812715	664	dbSNP
rs1414325951	675	dbSNP
rs1396640714	676	dbSNP
rs1384556034	678	dbSNP
rs1287311733	696	dbSNP
rs1455190017	711	dbSNP
rs1338667027	721	dbSNP
rs1364155241	722	dbSNP
rs1164195592	724	dbSNP
rs753488829	738	dbSNP
rs1209642030	739	dbSNP
rs1474191633	742	dbSNP
rs1429813905	751	dbSNP
rs1419853260	764	dbSNP
rs1455042502	771	dbSNP
rs1188079448	778	dbSNP
rs1439889894	779	dbSNP
rs1373984776	795	dbSNP
rs1427354440	805	dbSNP
rs1259287781	806	dbSNP
rs1387376684	806	dbSNP
rs1380672245	810	dbSNP
rs1206526706	814	dbSNP
rs1487089849	816	dbSNP
rs1269179364	826	dbSNP
rs1305382570	850	dbSNP
rs1345523756	864	dbSNP
rs1232214827	877	dbSNP
rs1261014728	880	dbSNP
rs1486634941	895	dbSNP
rs1202868091	897	dbSNP
rs1359256146	900	dbSNP
rs1260353218	904	dbSNP
rs1469329379	937	dbSNP
rs1195996883	941	dbSNP
rs1393785548	943	dbSNP
rs1454141603	946	dbSNP
rs1160285875	957	dbSNP
rs1166185893	959	dbSNP
rs1451826516	966	dbSNP
rs1475135590	977	dbSNP
rs1395263948	978	dbSNP
rs1298121041	998	dbSNP
rs1420739948	999	dbSNP
rs1026104740	1002	dbSNP
rs1382573946	1024	dbSNP
rs1218485518	1035	dbSNP
rs1307369016	1036	dbSNP
rs1318359273	1037	dbSNP
rs993392379	1041	dbSNP
rs1266965012	1044	dbSNP
rs1334971713	1053	dbSNP
rs1214984051	1057	dbSNP
rs1171142059	1062	dbSNP
rs1195595407	1116	dbSNP
rs1251754820	1121	dbSNP
rs1443070393	1134	dbSNP
rs1242892335	1136	dbSNP
rs1384121271	1149	dbSNP
rs1253021754	1153	dbSNP
rs899088851	1158	dbSNP
rs1418804723	1160	dbSNP
rs1463138909	1164	dbSNP
rs1162858099	1177	dbSNP
rs1392216889	1184	dbSNP
rs1435590719	1191	dbSNP
rs1298565047	1194	dbSNP
rs1389580864	1195	dbSNP
rs8639	1220	dbSNP
rs1287374690	1221	dbSNP
rs1355693889	1224	dbSNP
rs1234659052	1231	dbSNP
rs1270670414	1232	dbSNP
rs1321652027	1243	dbSNP
rs1205793204	1258	dbSNP
rs1037683913	1271	dbSNP
rs1479883622	1278	dbSNP
rs1181901662	1286	dbSNP
rs1459637839	1287	dbSNP
rs1476276032	1307	dbSNP
rs201697448	1308	dbSNP
rs775667584	1308	dbSNP
rs1396620955	1310	dbSNP
rs1171115606	1318	dbSNP
rs1163746255	1320	dbSNP
rs1474816086	1324	dbSNP
rs1307167978	1329	dbSNP
rs750243531	1329	dbSNP
rs1194629366	1330	dbSNP
rs1404099114	1334	dbSNP
rs1428755325	1339	dbSNP
rs1251948627	1341	dbSNP
rs1416176251	1342	dbSNP
rs1193430447	1350	dbSNP
rs1290941688	1353	dbSNP
rs1214611100	1362	dbSNP
rs1377754349	1362	dbSNP
rs1298458195	1371	dbSNP
rs948710072	1373	dbSNP
rs776530188	1375	dbSNP
rs894505369	1392	dbSNP
rs1204906085	1393	dbSNP
rs1210954735	1393	dbSNP
rs1338887209	1394	dbSNP
rs1249701561	1397	dbSNP
rs1486793868	1398	dbSNP
rs1057229420	1402	dbSNP
rs1366236155	1403	dbSNP
rs1475806173	1405	dbSNP
rs1188355833	1406	dbSNP
rs1302887784	1406	dbSNP
rs761699451	1406	dbSNP
rs1438501418	1409	dbSNP
rs1375799228	1412	dbSNP
rs6832	1413	dbSNP
rs1310751373	1416	dbSNP
rs1358209541	1427	dbSNP
rs1430895089	1430	dbSNP
rs924740124	1445	dbSNP
rs1228259020	1453	dbSNP
rs977600350	1453	dbSNP
rs1324196058	1458	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.