ID	Duplex structure	Position	Score	MFE
1	miRNA 3' guGCAGUCACUGACGCGGGGGa 5' | || | | | |||||||: Target 5' gtCCTCTGAGCCGGCGCCCCTg 3'	367 - 388	144.00	-16.90
2	miRNA 3' gugcagucacugacGCGGGGGa 5' ||||||| Target 5' tcctcccccaccccCGCCCCCa 3'	94 - 115	140.00	-15.20
3	miRNA 3' gugcagucacuGACGCGGGGGa 5' |||:||||:| Target 5' gctggcccctcCTGTGCCCTCt 3'	830 - 851	123.00	-19.00

Mutant ID	Mutant Position	Mutant Source
COSN31554984	38	COSMIC
COSN31540596	74	COSMIC
COSN28675791	108	COSMIC
COSN20290614	132	COSMIC
COSN20303803	133	COSMIC
COSN20093798	146	COSMIC
COSN31487933	179	COSMIC
COSN14930430	318	COSMIC
COSN21409930	458	COSMIC
COSN8611329	531	COSMIC
COSN31553710	551	COSMIC
COSN8611328	629	COSMIC
COSN31489088	630	COSMIC
COSN26596284	661	COSMIC
COSN32055756	767	COSMIC
COSN26258546	773	COSMIC
COSN31530753	821	COSMIC
COSN31591172	865	COSMIC
COSN4623623	957	COSMIC
COSN1252226	995	COSMIC
COSN23798789	1020	COSMIC
COSN31534425	1024	COSMIC
COSN31534508	1032	COSMIC
COSN26639825	1146	COSMIC
COSN31515620	1232	COSMIC
COSN30176274	1258	COSMIC
rs2259797	443	GWAS

Mutant ID	Mutant Position	Mutant Source
rs6010983	1	dbSNP
rs201542437	3	dbSNP
rs773917392	6	dbSNP
rs6010609	9	dbSNP
rs1281639846	10	dbSNP
rs748281787	12	dbSNP
rs942937413	14	dbSNP
rs781456461	15	dbSNP
rs1406283919	16	dbSNP
rs1345591393	18	dbSNP
rs531120927	19	dbSNP
rs1322546025	22	dbSNP
rs755037521	25	dbSNP
rs989498629	26	dbSNP
rs1158967345	27	dbSNP
rs1456466638	29	dbSNP
rs1409732129	30	dbSNP
rs778492578	30	dbSNP
rs545446203	32	dbSNP
rs2150910	33	dbSNP
rs757068345	37	dbSNP
rs753607532	39	dbSNP
rs764058908	40	dbSNP
rs756074326	41	dbSNP
rs752580514	42	dbSNP
rs759016985	43	dbSNP
rs1450112975	44	dbSNP
rs1286545911	46	dbSNP
rs982594384	57	dbSNP
rs1409311141	60	dbSNP
rs1456385925	61	dbSNP
rs1325930488	62	dbSNP
rs970800801	67	dbSNP
rs1023899639	69	dbSNP
rs1206744887	72	dbSNP
rs1483080602	79	dbSNP
rs990586235	89	dbSNP
rs1290663777	92	dbSNP
rs1327254431	95	dbSNP
rs1228030427	101	dbSNP
rs1219781632	102	dbSNP
rs1361068801	103	dbSNP
rs1286354503	104	dbSNP
rs3865523	108	dbSNP
rs1335733391	113	dbSNP
rs1305449741	115	dbSNP
rs1438396175	115	dbSNP
rs375242256	116	dbSNP
rs573805476	118	dbSNP
rs372127609	123	dbSNP
rs1165232866	128	dbSNP
rs1302568036	129	dbSNP
rs1455915804	131	dbSNP
rs1162193256	133	dbSNP
rs533703480	135	dbSNP
rs1172259552	141	dbSNP
rs1411018574	143	dbSNP
rs571028999	146	dbSNP
rs557408344	156	dbSNP
rs1016117373	157	dbSNP
rs1294096520	159	dbSNP
rs1004535028	164	dbSNP
rs1242696249	166	dbSNP
rs1264946766	168	dbSNP
rs1339934506	172	dbSNP
rs886098718	175	dbSNP
rs1272163744	178	dbSNP
rs1482588373	179	dbSNP
rs537480869	180	dbSNP
rs568834328	182	dbSNP
rs1257821477	186	dbSNP
rs1421754476	188	dbSNP
rs1186141738	189	dbSNP
rs1430900987	197	dbSNP
rs1452759917	198	dbSNP
rs1369282890	201	dbSNP
rs548656196	204	dbSNP
rs3908692	207	dbSNP
rs900215097	208	dbSNP
rs1472666486	221	dbSNP
rs1394526343	225	dbSNP
rs1327137856	236	dbSNP
rs1230755315	238	dbSNP
rs1267561853	239	dbSNP
rs1196599713	244	dbSNP
rs1341442216	245	dbSNP
rs1463580369	247	dbSNP
rs1257544393	250	dbSNP
rs567830934	252	dbSNP
rs1199545488	253	dbSNP
rs1261765599	254	dbSNP
rs1450754489	255	dbSNP
rs1290117167	258	dbSNP
rs1210850223	262	dbSNP
rs533626593	263	dbSNP
rs942821002	267	dbSNP
rs1230784122	271	dbSNP
rs879072465	274	dbSNP
rs548032679	278	dbSNP
rs6423444	280	dbSNP
rs1054026094	281	dbSNP
rs200961521	283	dbSNP
rs1234943444	287	dbSNP
rs190188863	288	dbSNP
rs935350839	291	dbSNP
rs1333098741	298	dbSNP
rs923943214	303	dbSNP
rs1324416683	304	dbSNP
rs1206276258	308	dbSNP
rs1464804159	308	dbSNP
rs1192318277	310	dbSNP
rs1381508139	314	dbSNP
rs2738776	318	dbSNP
rs1459027685	320	dbSNP
rs1156957837	321	dbSNP
rs982103140	322	dbSNP
rs1437054724	324	dbSNP
rs1161035849	329	dbSNP
rs949515170	338	dbSNP
rs1307525860	339	dbSNP
rs1330704081	341	dbSNP
rs1457732099	350	dbSNP
rs1428453391	352	dbSNP
rs1173695835	357	dbSNP
rs916647679	364	dbSNP
rs1223199787	365	dbSNP
rs1478705343	367	dbSNP
rs1487832079	382	dbSNP
rs990638541	383	dbSNP
rs1253001790	387	dbSNP
rs1246990226	388	dbSNP
rs867960913	388	dbSNP
rs1473665717	394	dbSNP
rs865976664	398	dbSNP
rs963169048	404	dbSNP
rs1016169573	407	dbSNP
rs1406004230	412	dbSNP
rs983329650	421	dbSNP
rs1348042690	424	dbSNP
rs1308359107	426	dbSNP
rs950623735	426	dbSNP
rs397843628	428	dbSNP
rs1210932436	433	dbSNP
rs1287299224	434	dbSNP
rs1330455223	434	dbSNP
rs1030418434	435	dbSNP
rs531784880	441	dbSNP
rs2259797	443	dbSNP
rs900266457	445	dbSNP
rs1275723435	447	dbSNP
rs1017346193	448	dbSNP
rs1226985795	450	dbSNP
rs1275742080	455	dbSNP
rs397843627	456	dbSNP
rs893968655	458	dbSNP
rs1251343187	459	dbSNP
rs750755386	459	dbSNP
rs1473286813	460	dbSNP
rs140005742	463	dbSNP
rs1423135324	465	dbSNP
rs1405311923	466	dbSNP
rs879230259	467	dbSNP
rs935579808	468	dbSNP
rs1425272224	469	dbSNP
rs902738227	469	dbSNP
rs1046852250	471	dbSNP
rs1377845841	477	dbSNP
rs573893147	479	dbSNP
rs1298956188	482	dbSNP
rs1391583699	483	dbSNP
rs1203447320	484	dbSNP
rs1443157269	492	dbSNP
rs767759209	493	dbSNP
rs1190964679	501	dbSNP
rs879086243	504	dbSNP
rs1465608443	505	dbSNP
rs1482955126	511	dbSNP
rs1189360691	512	dbSNP
rs949396328	523	dbSNP
rs1243141824	524	dbSNP
rs940120459	524	dbSNP
rs1055128354	525	dbSNP
rs560157163	526	dbSNP
rs908513217	527	dbSNP
rs950704625	529	dbSNP
rs1322049991	530	dbSNP
rs987215785	531	dbSNP
rs1367887403	533	dbSNP
rs1226850293	542	dbSNP
rs1444578135	548	dbSNP
rs923188942	554	dbSNP
rs1269925200	559	dbSNP
rs778835418	561	dbSNP
rs1221343372	567	dbSNP
rs1279428814	568	dbSNP
rs1276754250	570	dbSNP
rs1323184707	573	dbSNP
rs1214010002	578	dbSNP
rs1340364899	579	dbSNP
rs976175507	582	dbSNP
rs1463452590	583	dbSNP
rs2315000	584	dbSNP
rs2314999	588	dbSNP
rs540063787	591	dbSNP
rs1170651546	592	dbSNP
rs1424024153	596	dbSNP
rs1457445762	601	dbSNP
rs964394301	605	dbSNP
rs1017398005	606	dbSNP
rs1433768094	608	dbSNP
rs577398556	610	dbSNP
rs1332236948	611	dbSNP
rs957077924	614	dbSNP
rs1032527787	626	dbSNP
rs1323030767	627	dbSNP
rs4063528	632	dbSNP
rs1270051650	633	dbSNP
rs773698578	643	dbSNP
rs1282149904	644	dbSNP
rs1204676844	666	dbSNP
rs1290485404	672	dbSNP
rs1450129285	673	dbSNP
rs1196398440	677	dbSNP
rs1245925762	681	dbSNP
rs999677812	686	dbSNP
rs1327634565	687	dbSNP
rs1456236579	697	dbSNP
rs1163402533	703	dbSNP
rs1392002990	707	dbSNP
rs557479898	710	dbSNP
rs1407694003	725	dbSNP
rs1321936613	726	dbSNP
rs1345313504	729	dbSNP
rs1372070049	761	dbSNP
rs1240226472	763	dbSNP
rs1168835847	764	dbSNP
rs1450548212	765	dbSNP
rs1385020341	766	dbSNP
rs866123462	767	dbSNP
rs1338810697	768	dbSNP
rs3831229	768	dbSNP
rs1258038636	777	dbSNP
rs774704945	777	dbSNP
rs1180415677	782	dbSNP
rs537552719	784	dbSNP
rs1483248521	788	dbSNP
rs1207108003	789	dbSNP
rs1249158549	790	dbSNP
rs1418155040	791	dbSNP
rs1238534200	798	dbSNP
rs1203961331	801	dbSNP
rs1187573502	805	dbSNP
rs1369724235	812	dbSNP
rs1161947636	820	dbSNP
rs571659723	822	dbSNP
rs575211825	826	dbSNP
rs866742551	832	dbSNP
rs1206152189	833	dbSNP
rs146033028	835	dbSNP
rs942127460	836	dbSNP
rs2314998	846	dbSNP
rs1047571512	848	dbSNP
rs11545512	850	dbSNP
rs552491781	852	dbSNP
rs1230259570	854	dbSNP
rs1229773940	858	dbSNP
rs2314997	865	dbSNP
rs929135272	866	dbSNP
rs923207720	873	dbSNP
rs976016018	882	dbSNP
rs1278854382	885	dbSNP
rs11545508	889	dbSNP
rs1182506440	891	dbSNP
rs1385149458	899	dbSNP
rs964769734	915	dbSNP
rs532261113	916	dbSNP
rs1371723800	925	dbSNP
rs1461633114	933	dbSNP
rs1351785936	934	dbSNP
rs1404694910	935	dbSNP
rs1394362606	945	dbSNP
rs4063527	948	dbSNP
rs957130195	949	dbSNP
rs1437222466	952	dbSNP
rs1347716677	953	dbSNP
rs535078420	965	dbSNP
rs1233772173	966	dbSNP
rs1257379544	970	dbSNP
rs1407400338	971	dbSNP
rs1202408599	973	dbSNP
rs4063526	973	dbSNP
rs748529195	1000	dbSNP
rs966896957	1001	dbSNP
rs1191086157	1002	dbSNP
rs1025688278	1008	dbSNP
rs1013839965	1010	dbSNP
rs4063525	1012	dbSNP
rs185474507	1018	dbSNP
rs1177121858	1022	dbSNP
rs1379520652	1023	dbSNP
rs1468445445	1024	dbSNP
rs4063524	1025	dbSNP
rs1471861428	1029	dbSNP
rs149523829	1030	dbSNP
rs1182935957	1032	dbSNP
rs1055060584	1033	dbSNP
rs774961745	1038	dbSNP
rs1006153531	1042	dbSNP
rs1318440216	1042	dbSNP
rs180886995	1044	dbSNP
rs1303137805	1045	dbSNP
rs1490255134	1047	dbSNP
rs1263883843	1050	dbSNP
rs1321548089	1051	dbSNP
rs1047792616	1053	dbSNP
rs1223550440	1067	dbSNP
rs1206334421	1068	dbSNP
rs929163768	1073	dbSNP
rs2314996	1074	dbSNP
rs1269943603	1075	dbSNP
rs4063523	1076	dbSNP
rs1322101974	1077	dbSNP
rs1458879760	1078	dbSNP
rs943315669	1083	dbSNP
rs910451133	1099	dbSNP
rs989839756	1100	dbSNP
rs1331049706	1111	dbSNP
rs935641955	1114	dbSNP
rs1403773474	1117	dbSNP
rs769068334	1118	dbSNP
rs1225971910	1125	dbSNP
rs1305690529	1133	dbSNP
rs977196503	1137	dbSNP
rs1222989870	1139	dbSNP
rs548095149	1140	dbSNP
rs1267799438	1141	dbSNP
rs1489956749	1144	dbSNP
rs1222291869	1152	dbSNP
rs1294919263	1154	dbSNP
rs971515446	1156	dbSNP
rs1439120818	1158	dbSNP
rs1407376352	1162	dbSNP
rs1025149576	1163	dbSNP
rs1158799463	1166	dbSNP
rs749369355	1167	dbSNP
rs959633537	1173	dbSNP
rs761750504	1174	dbSNP
rs1033874182	1177	dbSNP
rs1480134085	1179	dbSNP
rs1265620313	1184	dbSNP
rs534435605	1186	dbSNP
rs1439601442	1187	dbSNP
rs1193127998	1194	dbSNP
rs1006205972	1196	dbSNP
rs887769039	1198	dbSNP
rs1315426381	1211	dbSNP
rs1358013263	1217	dbSNP
rs1245610809	1218	dbSNP
rs571865678	1222	dbSNP
rs1206546708	1223	dbSNP
rs1466217211	1232	dbSNP
rs1026853404	1236	dbSNP
rs1183730067	1238	dbSNP
rs1383298431	1245	dbSNP
rs188985407	1252	dbSNP
rs1168938602	1254	dbSNP
rs1439860601	1255	dbSNP
rs1222437986	1257	dbSNP
rs1309921694	1258	dbSNP
rs1408041113	1262	dbSNP
rs1302688123	1266	dbSNP
rs1169288079	1268	dbSNP
rs1219450033	1269	dbSNP
rs11906631	1271	dbSNP
rs1334123541	1272	dbSNP
rs562806237	1273	dbSNP
rs943167544	1278	dbSNP
rs773074357	1286	dbSNP
rs549376779	1287	dbSNP
rs549674169	1289	dbSNP
rs1313065792	1290	dbSNP
rs1321807965	1293	dbSNP
rs1465660899	1294	dbSNP
rs114015203	1295	dbSNP
rs924304559	1298	dbSNP
rs1189102889	1302	dbSNP
rs1461804255	1305	dbSNP
rs1178244057	1308	dbSNP
rs1059250	1311	dbSNP
rs867032729	1316	dbSNP
rs1173563189	1319	dbSNP
rs949843587	1326	dbSNP
rs1332950017	1327	dbSNP
rs1321781093	1328	dbSNP
rs560677445	1331	dbSNP
rs776704649	1337	dbSNP
rs1429056065	1342	dbSNP
rs577470003	1343	dbSNP
rs1368514731	1348	dbSNP
rs1225615748	1354	dbSNP
rs1261545365	1356	dbSNP
rs1322887921	1357	dbSNP
rs1466083137	1361	dbSNP
rs1209508019	1362	dbSNP
rs992362170	1367	dbSNP
rs959517827	1378	dbSNP
rs1192125765	1381	dbSNP
rs1247085985	1385	dbSNP
rs1478782105	1389	dbSNP
rs1033925031	1394	dbSNP
rs563950721	1398	dbSNP
rs1472625260	1407	dbSNP
rs1210146129	1420	dbSNP
rs543972496	1421	dbSNP
rs1306607085	1423	dbSNP
rs575322883	1424	dbSNP
rs952256653	1426	dbSNP
rs1407199116	1438	dbSNP
rs1226740147	1442	dbSNP
rs1367783640	1443	dbSNP
rs1298725902	1444	dbSNP
rs1395964011	1450	dbSNP
rs770110189	1462	dbSNP
rs1400641594	1465	dbSNP
rs1348389658	1497	dbSNP
rs768087355	1501	dbSNP
rs1304687420	1502	dbSNP
rs116444123	1504	dbSNP
rs1290552501	1508	dbSNP
rs1490772151	1514	dbSNP
rs368196001	1519	dbSNP
rs1166931925	1522	dbSNP
rs375734249	1524	dbSNP
rs572742829	1527	dbSNP
rs993885387	1528	dbSNP
rs1451498849	1538	dbSNP
rs901952342	1539	dbSNP
rs1390563924	1544	dbSNP
rs11545510	1545	dbSNP
rs746501985	1556	dbSNP
rs1186525979	1559	dbSNP
rs1007435253	1563	dbSNP
rs1301686449	1576	dbSNP
rs187425145	1587	dbSNP
rs888950752	1589	dbSNP
rs1258152864	1590	dbSNP
rs1181981071	1591	dbSNP
rs1054252247	1610	dbSNP
rs1000121665	1612	dbSNP
rs903070748	1613	dbSNP
rs1272114001	1615	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.