>CLSTN1|NM_001009566|3'UTR
   1 CCCGTGCCCCCGGCCACCTCGGTTTCTGCTTTCGAAGACTCTGCTGCCATCCGTTCTCCCAGTCCCAAGGGTCCACGATG
  81 TACAAAGTCATTTCGGCCAGTAGGTGTGCAGACCCCTCCCCGCCACGATCGTCGCTGTGCTTGGTGTGTAGGACCCTAGG
 161 CTCCCCGCCCACCCTCTGCCTGGTCGCGCTCTTCAGTCCCACGAGGAGCTGACACGTCCTCTCTGGCCGCCATCCGGCTC
 241 GCACAGGGGCCTCCCAGCGCCTCAGGCCCCGCGTTTGTGTCTGGAGTCTCCCCCCGGGGAGAGGACACTGGCCCCTCGCA
 321 CTCCAGAAAAGCCATGCCAGCTGGGCTCGTTGACAAAGGGTAAAACATGCTCACTCCCACCCGGTAATCATTTTTTTCTT
 401 TTTTTAAAAAAAGTTTTTATTTTTTCCAAACTAGTGCATGTATAAATAATGGCAGGATGGGGGGTACTGTGTAGATGATT
 481 AACTGACTTTTTAATATTTTGTAAATAAATCGGATTCCTTGTGTCCTTTGTGCTAGTGTAACCCGGGACTGGAATGTAAA
 561 GTGAAGTTCGGAGCTCTGAGCACGGGCTCTTCCCGCCGGGTCCTCCCTCCCCAGACCCCAGAGGGAGAGGCCCACCCCGC
 641 CCAGCCCCGCCCCAGCCCCTGCTCAGGTCTGAGTATGGCTGGGAGTCGGGGGCCACAGGCCTCTAGCTGTGCTGCTCAAG
 721 AGACTGGATCAGGGTAGCTACAAGTGGCCGGGCCTTGCCTTTGGGATTCTACCTGTTCCTAATTTGGTGTGGGGTGCGGG
 801 GTCCCTGGCCCCTTTTCCACACTCCTCCTCCGACAGCAGCTCCCTGGGCAGTGGCCTGGTCTCACCGTGTGCAGCCTTGT
 881 GGTTTATGCTTAAATGTACATTTTCCTGCTGGTAAAAGGAGAAACTGAGAGGTGTCCTGCAGACCGGCTGACCACTCCTT
 961 TTGGAGACGGCAGGAGGCCTGAGCGATCCGTACTCAGAACGTCCAGGAGAGACGCATGGCCCGAAGTCAAAGTGCTGGAA
1041 TTTTCCAAAACAGCCTGTTCTCTCCTCTCTCCTCCCCAGAGCACCCCCTGCCATCAGGGGGGTTGAAATCCCTCTCCCCC
1121 AGGAGCCCTGCTGCTTTGCTTGGTGGTAGGGCAGGAGAGCAAACAAACAGTCATGGTCTAAAACCCACATAGCACTTTGC
1201 TCTTAGTTACATGTAAAATTTTAGATTTCTAAAACAGGTGGGCAATCATTTTGAATACTGTTCTGTGACCCTGACTGCTA
1281 GTTCTGAGGACACTGGTGGCTGTGCTATGTGTGGCCATCCTCCATGTCCCGTCCCTGTAGCTGCTCTGTTTAGACAGCGG
1361 ACAGACGCTCACGCCCAGGGGATGTCCTCACGCTGTCGCCGCGCGGTTTCCCTTCGCAGATGTGTATACTCATGATAGGT
1441 CAGAAAGTGTATCCGCTACAATAAAGTTCTGGTTCTAACTAACTCCAAAAAAAAAAAAAAAAAA

ID	Duplex structure	Position	Score	MFE
1	miRNA 3' ugcgUCUCGGGCUUU------CGGGGGUCa 5' :|:| ::|||| ||||||| Target 5' tcagGGGGGTTGAAATCCCTCTCCCCCAGg 3'	1094 - 1123	150.00	-23.90
2	miRNA 3' ugcGUCUCGGGCUUUCGGGGGUCa 5' |:|:| || |:|||:|:|| Target 5' agtCGGGGGCCACAGGCCTCTAGc 3'	684 - 707	137.00	-24.70
3	miRNA 3' ugcgucucGGGCUUUCGGGGGUCa 5' |||| ||||||:| Target 5' --------CCCG--TGCCCCCGGc 3'	1 - 14	136.00	-23.70

Mutant ID	Mutant Position	Mutant Source
COSN26971042	3	COSMIC
COSN26971043	4	COSMIC
COSN26971035	11	COSMIC
COSN13569106	33	COSMIC
COSN31489765	43	COSMIC
COSN31598679	47	COSMIC
COSN30162667	76	COSMIC
COSN507647	77	COSMIC
COSN30108966	83	COSMIC
COSN26971037	112	COSMIC
COSN30103014	117	COSMIC
COSN30454675	120	COSMIC
COSN31498821	144	COSMIC
COSN26677991	170	COSMIC
COSN6954036	256	COSMIC
COSN17182975	271	COSMIC
COSN31531783	272	COSMIC
COSN30176067	919	COSMIC
COSN31534906	1019	COSMIC
COSN20806246	1569	COSMIC
rs14271	1416	GWAS

Mutant ID	Mutant Position	Mutant Source
rs1319059059	1	dbSNP
rs759672760	2	dbSNP
rs200668377	3	dbSNP
rs771099481	4	dbSNP
rs760905356	6	dbSNP
rs1177881293	7	dbSNP
rs773956382	11	dbSNP
rs201581912	12	dbSNP
rs1451472788	13	dbSNP
rs1246279628	15	dbSNP
rs373087974	20	dbSNP
rs556240045	21	dbSNP
rs1256346474	22	dbSNP
rs1212021542	29	dbSNP
rs769162588	33	dbSNP
rs745409451	34	dbSNP
rs1245950489	35	dbSNP
rs532822000	43	dbSNP
rs780882170	43	dbSNP
rs756922857	48	dbSNP
rs963092144	50	dbSNP
rs1033955357	52	dbSNP
rs1002842741	53	dbSNP
rs537961353	58	dbSNP
rs1377745901	60	dbSNP
rs567410594	63	dbSNP
rs1439055393	64	dbSNP
rs1390258190	66	dbSNP
rs1163664307	68	dbSNP
rs1459270852	70	dbSNP
rs117948097	76	dbSNP
rs1003832329	78	dbSNP
rs1381693798	80	dbSNP
rs951279470	82	dbSNP
rs1294750674	87	dbSNP
rs1267647793	89	dbSNP
rs927398463	90	dbSNP
rs1211212534	93	dbSNP
rs1029582642	94	dbSNP
rs536015130	95	dbSNP
rs1050789515	100	dbSNP
rs997996836	103	dbSNP
rs899639754	104	dbSNP
rs1332087329	110	dbSNP
rs879052818	112	dbSNP
rs1382599224	116	dbSNP
rs1297345496	117	dbSNP
rs968670727	117	dbSNP
rs1389092190	118	dbSNP
rs1382064099	120	dbSNP
rs899655590	121	dbSNP
rs1018061123	122	dbSNP
rs935882467	123	dbSNP
rs1200549701	124	dbSNP
rs565867890	126	dbSNP
rs1216315230	127	dbSNP
rs181812755	130	dbSNP
rs1041392917	131	dbSNP
rs945666148	134	dbSNP
rs1344408936	145	dbSNP
rs892762319	155	dbSNP
rs1235778796	163	dbSNP
rs1056626604	166	dbSNP
rs532276918	167	dbSNP
rs981051890	168	dbSNP
rs77950539	170	dbSNP
rs1332129330	172	dbSNP
rs754307668	178	dbSNP
rs778142871	179	dbSNP
rs1460194913	184	dbSNP
rs549502337	186	dbSNP
rs1291518359	187	dbSNP
rs941462059	188	dbSNP
rs1265713124	191	dbSNP
rs909917841	194	dbSNP
rs1354997429	195	dbSNP
rs1281985066	202	dbSNP
rs1279488893	203	dbSNP
rs531480065	203	dbSNP
rs982841968	206	dbSNP
rs60073554	209	dbSNP
rs951353210	212	dbSNP
rs1365771023	215	dbSNP
rs899673144	216	dbSNP
rs1342144802	227	dbSNP
rs1029613957	228	dbSNP
rs149772081	229	dbSNP
rs1340968088	231	dbSNP
rs1000028076	235	dbSNP
rs1463632777	236	dbSNP
rs767817575	240	dbSNP
rs543279645	241	dbSNP
rs1041642088	242	dbSNP
rs1390103094	243	dbSNP
rs1161595437	244	dbSNP
rs1000403944	258	dbSNP
rs892445649	259	dbSNP
rs1472783697	261	dbSNP
rs1188510416	270	dbSNP
rs904276605	271	dbSNP
rs527906257	272	dbSNP
rs1199575331	273	dbSNP
rs1199122911	277	dbSNP
rs560454527	279	dbSNP
rs78105956	288	dbSNP
rs926726389	290	dbSNP
rs1287313884	291	dbSNP
rs981383132	292	dbSNP
rs941525967	295	dbSNP
rs1342298384	296	dbSNP
rs1448598670	296	dbSNP
rs895466499	300	dbSNP
rs113794825	314	dbSNP
rs982971412	315	dbSNP
rs556558334	317	dbSNP
rs1166019826	324	dbSNP
rs1438372901	333	dbSNP
rs1226158495	336	dbSNP
rs112497092	348	dbSNP
rs771174027	349	dbSNP
rs544194852	352	dbSNP
rs905418750	354	dbSNP
rs1451978692	355	dbSNP
rs1291756081	357	dbSNP
rs1237941615	358	dbSNP
rs1352871704	360	dbSNP
rs1309404993	367	dbSNP
rs188784317	369	dbSNP
rs1437440337	374	dbSNP
rs1273897764	377	dbSNP
rs749345073	382	dbSNP
rs1350894972	386	dbSNP
rs1305323294	391	dbSNP
rs1418457734	395	dbSNP
rs111708156	398	dbSNP
rs1360412516	398	dbSNP
rs77314922	399	dbSNP
rs1159736063	400	dbSNP
rs1420980328	404	dbSNP
rs1045237652	405	dbSNP
rs1029249482	406	dbSNP
rs964172066	413	dbSNP
rs976531595	413	dbSNP
rs1018013028	426	dbSNP
rs1330684721	426	dbSNP
rs1321863345	429	dbSNP
rs1248621182	434	dbSNP
rs1431651978	439	dbSNP
rs1371295959	445	dbSNP
rs1286683235	448	dbSNP
rs1168471788	451	dbSNP
rs1000464626	453	dbSNP
rs1309942191	458	dbSNP
rs904337391	465	dbSNP
rs914837423	465	dbSNP
rs573822405	468	dbSNP
rs1285625799	469	dbSNP
rs1398572479	480	dbSNP
rs118038247	481	dbSNP
rs910001624	484	dbSNP
rs1477910476	494	dbSNP
rs1244585528	501	dbSNP
rs1357558908	505	dbSNP
rs892476097	510	dbSNP
rs533993983	511	dbSNP
rs1431762833	512	dbSNP
rs1191720114	521	dbSNP
rs1477382161	522	dbSNP
rs1263553556	523	dbSNP
rs1188275584	525	dbSNP
rs1047578086	526	dbSNP
rs1483086376	533	dbSNP
rs905304782	537	dbSNP
rs1045137426	540	dbSNP
rs1250483062	544	dbSNP
rs1202934447	545	dbSNP
rs1313939779	546	dbSNP
rs941545702	566	dbSNP
rs565887940	569	dbSNP
rs773279202	570	dbSNP
rs910024058	583	dbSNP
rs1168806060	584	dbSNP
rs553638515	584	dbSNP
rs541310463	589	dbSNP
rs746894122	594	dbSNP
rs28492734	595	dbSNP
rs184347342	597	dbSNP
rs1351175834	599	dbSNP
rs1307557784	603	dbSNP
rs968952002	603	dbSNP
rs978507564	606	dbSNP
rs1318140567	611	dbSNP
rs1252298693	612	dbSNP
rs1230117927	613	dbSNP
rs989037332	615	dbSNP
rs1020053809	616	dbSNP
rs1009957369	617	dbSNP
rs1320242509	629	dbSNP
rs968549983	631	dbSNP
rs1312656327	632	dbSNP
rs956296730	634	dbSNP
rs549830821	638	dbSNP
rs1035325125	639	dbSNP
rs959980204	643	dbSNP
rs1177469563	644	dbSNP
rs1414218163	648	dbSNP
rs531318883	649	dbSNP
rs1035599605	652	dbSNP
rs562505473	653	dbSNP
rs1165400857	656	dbSNP
rs1423572930	660	dbSNP
rs1446366540	660	dbSNP
rs1177435382	661	dbSNP
rs1001116316	666	dbSNP
rs1003978298	673	dbSNP
rs1472753194	674	dbSNP
rs7526958	675	dbSNP
rs1045569502	687	dbSNP
rs1045716795	688	dbSNP
rs1005748464	689	dbSNP
rs888616133	691	dbSNP
rs888594411	692	dbSNP
rs1237934223	693	dbSNP
rs1047239504	695	dbSNP
rs549123589	703	dbSNP
rs930058876	707	dbSNP
rs930134539	714	dbSNP
rs1309438131	717	dbSNP
rs922648174	718	dbSNP
rs527351791	722	dbSNP
rs942667433	724	dbSNP
rs910855923	727	dbSNP
rs1269855867	732	dbSNP
rs1358583640	733	dbSNP
rs978922789	736	dbSNP
rs911177786	737	dbSNP
rs1364958855	740	dbSNP
rs1330018640	741	dbSNP
rs560749082	744	dbSNP
rs968637691	746	dbSNP
rs758099177	749	dbSNP
rs371817370	750	dbSNP
rs912980570	758	dbSNP
rs913077250	763	dbSNP
rs1284528705	769	dbSNP
rs988566807	770	dbSNP
rs1303915297	778	dbSNP
rs1351498042	779	dbSNP
rs988672219	785	dbSNP
rs959791021	794	dbSNP
rs1035395182	797	dbSNP
rs1330711966	797	dbSNP
rs1001196341	798	dbSNP
rs1338080087	800	dbSNP
rs1297513663	811	dbSNP
rs1036036268	813	dbSNP
rs758310156	818	dbSNP
rs1170278201	823	dbSNP
rs1023918168	824	dbSNP
rs1465266346	826	dbSNP
rs1377871220	827	dbSNP
rs969801214	831	dbSNP
rs1006229899	832	dbSNP
rs752835523	832	dbSNP
rs1448067856	835	dbSNP
rs888680158	837	dbSNP
rs1023595828	843	dbSNP
rs1323040752	847	dbSNP
rs1025819732	851	dbSNP
rs994301816	856	dbSNP
rs749883230	861	dbSNP
rs545265885	866	dbSNP
rs745670146	867	dbSNP
rs888565458	871	dbSNP
rs901289401	882	dbSNP
rs1410683906	886	dbSNP
rs1041145708	892	dbSNP
rs764754023	901	dbSNP
rs1156533909	908	dbSNP
rs1425018429	912	dbSNP
rs1047120560	924	dbSNP
rs942738362	926	dbSNP
rs994317461	927	dbSNP
rs901315810	928	dbSNP
rs1041702954	930	dbSNP
rs1422001050	931	dbSNP
rs1170381337	934	dbSNP
rs533725338	941	dbSNP
rs1475923289	942	dbSNP
rs1043040809	945	dbSNP
rs1471801361	946	dbSNP
rs1249830444	952	dbSNP
rs761669637	954	dbSNP
rs1205881811	955	dbSNP
rs913115474	968	dbSNP
rs988640375	969	dbSNP
rs1267694361	977	dbSNP
rs938516333	984	dbSNP
rs563016082	985	dbSNP
rs1282366126	987	dbSNP
rs41280774	989	dbSNP
rs1228241069	990	dbSNP
rs1381153551	992	dbSNP
rs1300452329	995	dbSNP
rs1436225984	997	dbSNP
rs969803780	1000	dbSNP
rs1016361649	1001	dbSNP
rs1329060313	1010	dbSNP
rs1410893248	1013	dbSNP
rs984433128	1014	dbSNP
rs953083470	1016	dbSNP
rs1162047906	1022	dbSNP
rs1459181188	1023	dbSNP
rs192396289	1024	dbSNP
rs959875393	1027	dbSNP
rs1025891986	1029	dbSNP
rs1437867278	1029	dbSNP
rs1205411228	1030	dbSNP
rs1163389669	1032	dbSNP
rs561718617	1046	dbSNP
rs201631390	1050	dbSNP
rs144682204	1052	dbSNP
rs1209224694	1064	dbSNP
rs370956160	1066	dbSNP
rs901320497	1068	dbSNP
rs540330989	1069	dbSNP
rs1016585808	1070	dbSNP
rs753288686	1072	dbSNP
rs1279774630	1075	dbSNP
rs984114964	1075	dbSNP
rs1391895604	1087	dbSNP
rs1443916740	1088	dbSNP
rs1321959950	1097	dbSNP
rs760381313	1097	dbSNP
rs573215265	1098	dbSNP
rs1043460067	1099	dbSNP
rs1246009377	1102	dbSNP
rs1165972356	1111	dbSNP
rs754785832	1112	dbSNP
rs1184997963	1114	dbSNP
rs947402713	1116	dbSNP
rs891754450	1118	dbSNP
rs1007462695	1119	dbSNP
rs1266278009	1119	dbSNP
rs371917216	1119	dbSNP
rs890072570	1127	dbSNP
rs1052948751	1134	dbSNP
rs938547424	1144	dbSNP
rs150503011	1148	dbSNP
rs928484021	1149	dbSNP
rs947056075	1149	dbSNP
rs1277368469	1150	dbSNP
rs891440229	1150	dbSNP
rs1052864398	1151	dbSNP
rs1229837927	1151	dbSNP
rs938370878	1152	dbSNP
rs1364915141	1154	dbSNP
rs928369792	1161	dbSNP
rs979991181	1163	dbSNP
rs1346486208	1165	dbSNP
rs1367784110	1168	dbSNP
rs979935875	1169	dbSNP
rs140007416	1170	dbSNP
rs543613651	1170	dbSNP
rs780116290	1170	dbSNP
rs556477279	1173	dbSNP
rs1423362792	1174	dbSNP
rs756634084	1176	dbSNP
rs1025562502	1180	dbSNP
rs908927501	1191	dbSNP
rs1429105717	1196	dbSNP
rs1191490026	1204	dbSNP
rs1485488957	1204	dbSNP
rs538434107	1211	dbSNP
rs984896325	1228	dbSNP
rs1217347373	1231	dbSNP
rs1309879722	1232	dbSNP
rs1177897114	1237	dbSNP
rs1223679311	1238	dbSNP
rs972706473	1245	dbSNP
rs950409934	1247	dbSNP
rs965525781	1249	dbSNP
rs1361834406	1263	dbSNP
rs1190854377	1277	dbSNP
rs761164400	1278	dbSNP
rs1433007054	1279	dbSNP
rs1357433335	1282	dbSNP
rs1020103885	1284	dbSNP
rs1470417286	1295	dbSNP
rs1431224861	1300	dbSNP
rs577903798	1307	dbSNP
rs753248901	1308	dbSNP
rs1168230896	1317	dbSNP
rs768010232	1319	dbSNP
rs1420164333	1325	dbSNP
rs1007084605	1330	dbSNP
rs1206480087	1331	dbSNP
rs759954533	1337	dbSNP
rs1203973311	1344	dbSNP
rs1021900347	1347	dbSNP
rs1250129909	1348	dbSNP
rs1462362952	1352	dbSNP
rs556514271	1355	dbSNP
rs1217220132	1356	dbSNP
rs1313172466	1358	dbSNP
rs1007027077	1359	dbSNP
rs1052807839	1360	dbSNP
rs751897801	1362	dbSNP
rs954305142	1366	dbSNP
rs1021709914	1367	dbSNP
rs576319585	1369	dbSNP
rs1394165305	1370	dbSNP
rs891784239	1372	dbSNP
rs1053020065	1373	dbSNP
rs1002763362	1375	dbSNP
rs1304548214	1380	dbSNP
rs1028668447	1383	dbSNP
rs557869495	1391	dbSNP
rs1445880008	1392	dbSNP
rs1236006723	1394	dbSNP
rs1194818675	1396	dbSNP
rs948599148	1397	dbSNP
rs1479612444	1398	dbSNP
rs907088598	1400	dbSNP
rs374837720	1401	dbSNP
rs1044627081	1402	dbSNP
rs948571362	1403	dbSNP
rs929265596	1404	dbSNP
rs1202752813	1405	dbSNP
rs187828318	1415	dbSNP
rs14271	1416	dbSNP
rs1373865950	1420	dbSNP
rs1299650796	1422	dbSNP
rs1456369585	1423	dbSNP
rs1364918538	1425	dbSNP
rs1164079181	1431	dbSNP
rs1426019295	1431	dbSNP
rs965740041	1432	dbSNP
rs1180718505	1433	dbSNP
rs1419278963	1433	dbSNP
rs1330704443	1437	dbSNP
rs772400148	1437	dbSNP
rs912668770	1438	dbSNP
rs928981885	1448	dbSNP
rs1489947155	1449	dbSNP
rs918946890	1453	dbSNP
rs139670015	1454	dbSNP
rs41280772	1455	dbSNP
rs146095672	1457	dbSNP
rs956307585	1458	dbSNP
rs1336549119	1461	dbSNP
rs1314746948	1466	dbSNP
rs1402897076	1467	dbSNP
rs1344573025	1471	dbSNP
rs1303694703	1480	dbSNP
rs912811973	1481	dbSNP
rs1358129720	1484	dbSNP
rs1044164107	1485	dbSNP
rs142831718	1485	dbSNP
rs529632901	1485	dbSNP
rs1401215583	1486	dbSNP
rs1479661531	1487	dbSNP
rs76391189	1488	dbSNP
rs1200856203	1489	dbSNP
rs775634541	1490	dbSNP
rs1048917590	1491	dbSNP
rs184417664	1495	dbSNP
rs1022156678	1496	dbSNP
rs1469669161	1497	dbSNP
rs1221843578	1499	dbSNP
rs1362179412	1505	dbSNP
rs1322618492	1507	dbSNP
rs919199747	1511	dbSNP
rs1225315132	1512	dbSNP
rs1324649428	1512	dbSNP
rs1190221205	1515	dbSNP
rs1424962450	1520	dbSNP
rs1317490221	1526	dbSNP
rs1011675348	1528	dbSNP
rs1382310495	1530	dbSNP
rs772119200	1533	dbSNP
rs956101145	1534	dbSNP
rs1040674574	1539	dbSNP
rs1468958791	1543	dbSNP
rs1429091457	1546	dbSNP
rs561755558	1556	dbSNP
rs1481602153	1557	dbSNP
rs1466554165	1567	dbSNP
rs1371874330	1569	dbSNP
rs944068442	1571	dbSNP
rs912521239	1572	dbSNP
rs985565907	1572	dbSNP
rs745663402	1573	dbSNP
rs1225138941	1580	dbSNP
rs1263944265	1580	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.

- Genome research, 2016

DNA damage activates TP53-regulated surveillance mechanisms that are crucial in suppressing tumorigenesis. TP53 orchestrates these responses directly by transcriptionally modulating genes, including microRNAs (miRNAs), and by regulating miRNA biogenesis through interacting with the DROSHA complex. However, whether the association between miRNAs and AGO2 is regulated following DNA damage is not yet known. Here, we show that, following DNA damage, TP53 interacts with AGO2 to induce or reduce AGO2's association of a subset of miRNAs, including multiple let-7 family members. Furthermore, we show that specific mutations in TP53 decrease rather than increase the association of let-7 family miRNAs, reducing their activity without preventing TP53 from interacting with AGO2. This is consistent with the oncogenic properties of these mutants. Using AGO2 RIP-seq and PAR-CLIP-seq, we show that the DNA damage-induced increase in binding of let-7 family members to the RISC complex is functional. We unambiguously determine the global miRNA-mRNA interaction networks involved in the DNA damage response, validating them through the identification of miRNA-target chimeras formed by endogenous ligation reactions. We find that the target complementary region of the let-7 seed tends to have highly fixed positions and more variable ones. Additionally, we observe that miRNAs, whose cellular abundance or differential association with AGO2 is regulated by TP53, are involved in an intricate network of regulatory feedback and feedforward circuits. TP53-mediated regulation of AGO2-miRNA interaction represents a new mechanism of miRNA regulation in carcinogenesis.