ID	Duplex structure	Position	Score	MFE
1	miRNA 3' cgAGCGCGAGU-GCGCAGGGGGUc 5' | | || || | | ||||||| Target 5' tcTAGGGCCCAGCCCCTCCCCCAc 3'	497 - 520	157.00	-21.60
2	miRNA 3' cgaGCGCGAGUGCGC--AGGGGGUc 5' || | | || || ||||||| Target 5' tagCGGGGT-ACCCGGCTCCCCCAg 3'	547 - 570	153.00	-27.70
3	miRNA 3' cgagcgcgaguGCGCAGGGGGUc 5' | | ||||||| Target 5' gaagttggagtCCCATCCCCCAa 3'	625 - 647	144.00	-17.50

Mutant ID	Mutant Position	Mutant Source
COSN20078939	86	COSMIC
COSN31490796	117	COSMIC
COSN2535765	160	COSMIC
COSN26566451	200	COSMIC
COSN2535561	208	COSMIC
COSN31481157	241	COSMIC
COSN20078988	361	COSMIC
COSN32056331	466	COSMIC
COSN1195117	479	COSMIC
COSN8834236	518	COSMIC
COSN30157796	592	COSMIC
COSN32058692	654	COSMIC
COSN27203834	673	COSMIC
COSN26185404	779	COSMIC
COSN24835296	873	COSMIC
COSN31518467	890	COSMIC
COSN31590677	933	COSMIC
COSN24306103	970	COSMIC
COSN28042878	979	COSMIC
COSN17076280	999	COSMIC
COSN31520317	1097	COSMIC

Mutant ID	Mutant Position	Mutant Source
rs1325281692	3	dbSNP
rs1420465230	4	dbSNP
rs1372032256	6	dbSNP
rs1443331152	14	dbSNP
rs1384568095	18	dbSNP
rs1295138241	19	dbSNP
rs965829073	25	dbSNP
rs986148470	25	dbSNP
rs574567497	27	dbSNP
rs925377514	28	dbSNP
rs1250051421	32	dbSNP
rs1205754282	33	dbSNP
rs1053673070	34	dbSNP
rs1343454716	35	dbSNP
rs893740978	35	dbSNP
rs1253043013	36	dbSNP
rs1009605156	37	dbSNP
rs1354134461	38	dbSNP
rs1360532499	39	dbSNP
rs1314980540	40	dbSNP
rs1244497150	41	dbSNP
rs936800819	45	dbSNP
rs1295724945	47	dbSNP
rs1020624648	48	dbSNP
rs200525661	57	dbSNP
rs970835715	62	dbSNP
rs1425075684	65	dbSNP
rs542765427	66	dbSNP
rs949655870	67	dbSNP
rs1046667473	68	dbSNP
rs561321755	69	dbSNP
rs1175580392	70	dbSNP
rs1194014177	71	dbSNP
rs1427952384	72	dbSNP
rs1033414679	76	dbSNP
rs1001884024	77	dbSNP
rs1467347032	80	dbSNP
rs1490570610	86	dbSNP
rs1291597554	88	dbSNP
rs528508387	90	dbSNP
rs1220680579	92	dbSNP
rs540661688	96	dbSNP
rs1252353970	102	dbSNP
rs1324107168	112	dbSNP
rs888201910	112	dbSNP
rs1299703583	113	dbSNP
rs1343055835	116	dbSNP
rs991631564	117	dbSNP
rs1405243630	122	dbSNP
rs1302522239	126	dbSNP
rs909432298	128	dbSNP
rs1301112092	136	dbSNP
rs963666053	138	dbSNP
rs1431346930	143	dbSNP
rs1004006543	147	dbSNP
rs1167187703	151	dbSNP
rs1461556046	168	dbSNP
rs1333344087	171	dbSNP
rs562714140	173	dbSNP
rs919261234	178	dbSNP
rs1178676805	181	dbSNP
rs1480910325	187	dbSNP
rs1268421488	193	dbSNP
rs148193762	201	dbSNP
rs1051834848	204	dbSNP
rs1439883253	212	dbSNP
rs1354944162	216	dbSNP
rs977048602	217	dbSNP
rs910652338	220	dbSNP
rs943157876	221	dbSNP
rs371896718	222	dbSNP
rs1490196422	223	dbSNP
rs953465129	224	dbSNP
rs1223565636	230	dbSNP
rs1053620014	236	dbSNP
rs1191872706	239	dbSNP
rs986104329	242	dbSNP
rs1280924394	245	dbSNP
rs1411434894	250	dbSNP
rs1267908410	253	dbSNP
rs893678414	254	dbSNP
rs925322088	257	dbSNP
rs1179643074	259	dbSNP
rs958113927	262	dbSNP
rs945307763	266	dbSNP
rs1042739448	267	dbSNP
rs1470317190	270	dbSNP
rs1362984350	274	dbSNP
rs906181734	278	dbSNP
rs1160040700	283	dbSNP
rs1003193497	284	dbSNP
rs879156483	287	dbSNP
rs1436625833	289	dbSNP
rs1047062430	290	dbSNP
rs1460429451	292	dbSNP
rs746857392	297	dbSNP
rs894917561	298	dbSNP
rs1278781410	302	dbSNP
rs1236586601	304	dbSNP
rs554489645	306	dbSNP
rs1013000010	308	dbSNP
rs1363352442	310	dbSNP
rs1302579839	315	dbSNP
rs1377472285	320	dbSNP
rs1003944406	327	dbSNP
rs1334775059	331	dbSNP
rs1016440907	334	dbSNP
rs963920465	335	dbSNP
rs1423390201	339	dbSNP
rs1158372814	344	dbSNP
rs1293609280	347	dbSNP
rs1468884244	360	dbSNP
rs772341401	364	dbSNP
rs1392340597	365	dbSNP
rs900980760	373	dbSNP
rs185362222	379	dbSNP
rs1028626782	383	dbSNP
rs1306977279	385	dbSNP
rs768512998	392	dbSNP
rs954663800	400	dbSNP
rs987486256	401	dbSNP
rs865785332	413	dbSNP
rs1203197983	418	dbSNP
rs1361251454	425	dbSNP
rs1315666672	426	dbSNP
rs1242810843	430	dbSNP
rs1245232761	435	dbSNP
rs569360066	446	dbSNP
rs1282542589	449	dbSNP
rs943439157	465	dbSNP
rs1327277799	473	dbSNP
rs989596349	491	dbSNP
rs1399334612	494	dbSNP
rs915078750	496	dbSNP
rs1367913557	498	dbSNP
rs1000108303	501	dbSNP
rs945228648	502	dbSNP
rs1424628375	505	dbSNP
rs1032286979	508	dbSNP
rs1359017292	514	dbSNP
rs958060201	516	dbSNP
rs1190508757	519	dbSNP
rs1222316053	520	dbSNP
rs1292315958	524	dbSNP
rs1267302916	525	dbSNP
rs1042296337	526	dbSNP
rs1357217708	533	dbSNP
rs1274976899	545	dbSNP
rs1216404636	546	dbSNP
rs1340083426	556	dbSNP
rs1269657954	560	dbSNP
rs1479724737	562	dbSNP
rs1193969389	563	dbSNP
rs1404669756	565	dbSNP
rs1237522136	566	dbSNP
rs1364287616	570	dbSNP
rs1173081055	576	dbSNP
rs906457477	580	dbSNP
rs1440020633	582	dbSNP
rs530267540	583	dbSNP
rs1165651067	586	dbSNP
rs1481237927	588	dbSNP
rs988156973	589	dbSNP
rs190570300	607	dbSNP
rs1054723773	609	dbSNP
rs1234540313	611	dbSNP
rs1205204449	615	dbSNP
rs1306843076	634	dbSNP
rs1443626305	636	dbSNP
rs1272427383	637	dbSNP
rs894864958	639	dbSNP
rs1325955962	641	dbSNP
rs982309275	646	dbSNP
rs1365861556	649	dbSNP
rs954997637	652	dbSNP
rs1300255887	653	dbSNP
rs1443651732	653	dbSNP
rs1460062295	653	dbSNP
rs1175187842	654	dbSNP
rs1177538178	654	dbSNP
rs1231054917	654	dbSNP
rs1480295528	654	dbSNP
rs556384866	654	dbSNP
rs878921305	654	dbSNP
rs879094163	654	dbSNP
rs1196865344	663	dbSNP
rs1298068038	673	dbSNP
rs986307260	674	dbSNP
rs1449390339	675	dbSNP
rs1335151770	676	dbSNP
rs1203339705	686	dbSNP
rs926816932	694	dbSNP
rs1382597656	695	dbSNP
rs566196337	698	dbSNP
rs1224665786	699	dbSNP
rs1005251989	701	dbSNP
rs1454128410	702	dbSNP
rs533627149	703	dbSNP
rs1335486378	705	dbSNP
rs1464266006	707	dbSNP
rs1346571641	714	dbSNP
rs1159589190	715	dbSNP
rs1418248446	717	dbSNP
rs1048698279	718	dbSNP
rs1226810706	723	dbSNP
rs558160459	726	dbSNP
rs909533263	727	dbSNP
rs1482429436	734	dbSNP
rs1262666598	737	dbSNP
rs765206512	738	dbSNP
rs1316638688	743	dbSNP
rs1284302355	751	dbSNP
rs1248883296	752	dbSNP
rs1384143120	753	dbSNP
rs570426092	754	dbSNP
rs1313800926	759	dbSNP
rs899318591	763	dbSNP
rs1458160700	768	dbSNP
rs939688612	771	dbSNP
rs777025921	777	dbSNP
rs1241023447	781	dbSNP
rs1358452107	786	dbSNP
rs1165236706	803	dbSNP
rs1425270186	821	dbSNP
rs1026543321	823	dbSNP
rs1186965069	825	dbSNP
rs1238711660	825	dbSNP
rs1422094518	826	dbSNP
rs1264136617	831	dbSNP
rs900930094	832	dbSNP
rs954942972	833	dbSNP
rs998378560	835	dbSNP
rs987434029	839	dbSNP
rs1415551305	840	dbSNP
rs1017607811	851	dbSNP
rs964748689	855	dbSNP
rs537793790	862	dbSNP
rs1291638827	864	dbSNP
rs1241989838	865	dbSNP
rs1308688401	866	dbSNP
rs1295659635	867	dbSNP
rs889641170	872	dbSNP
rs976229277	872	dbSNP
rs1304785832	874	dbSNP
rs1032904525	875	dbSNP
rs1467642178	878	dbSNP
rs915342352	879	dbSNP
rs1174982569	880	dbSNP
rs958007772	881	dbSNP
rs1405764374	884	dbSNP
rs1374926040	889	dbSNP
rs945203389	890	dbSNP
rs1449251068	894	dbSNP
rs1171185523	906	dbSNP
rs747113285	908	dbSNP
rs1261239238	909	dbSNP
rs79996304	912	dbSNP
rs927847185	917	dbSNP
rs1381650332	918	dbSNP
rs1208640298	928	dbSNP
rs1481905308	932	dbSNP
rs1278915364	935	dbSNP
rs1226033599	937	dbSNP
rs970828472	939	dbSNP
rs939279680	946	dbSNP
rs1054999751	949	dbSNP
rs1284766204	961	dbSNP
rs1220367137	968	dbSNP
rs1344700907	971	dbSNP
rs1261224370	976	dbSNP
rs1393106255	979	dbSNP
rs1298840516	981	dbSNP
rs916229792	983	dbSNP
rs1210586388	984	dbSNP
rs548008465	985	dbSNP
rs1038093166	987	dbSNP
rs1480879054	988	dbSNP
rs959554147	990	dbSNP
rs1197162693	994	dbSNP
rs984350357	997	dbSNP
rs1251813603	998	dbSNP
rs1197498517	1000	dbSNP
rs1456026019	1011	dbSNP
rs1264442061	1012	dbSNP
rs896915323	1013	dbSNP
rs1272905176	1014	dbSNP
rs1336307877	1022	dbSNP
rs939635691	1028	dbSNP
rs1263263412	1029	dbSNP
rs1398277436	1034	dbSNP
rs993639773	1037	dbSNP
rs1338777112	1039	dbSNP
rs1470449923	1041	dbSNP
rs1048367436	1049	dbSNP
rs1171216263	1056	dbSNP
rs922301570	1068	dbSNP
rs890659058	1072	dbSNP
rs1178508616	1077	dbSNP
rs1049971502	1078	dbSNP
rs36001900	1078	dbSNP
rs1244482910	1080	dbSNP
rs889587498	1096	dbSNP
rs1009147999	1097	dbSNP
rs773918842	1101	dbSNP
rs1255164630	1110	dbSNP
rs1415341337	1113	dbSNP
rs1206675586	1115	dbSNP
rs935854411	1117	dbSNP
rs1285030307	1121	dbSNP
rs1237954404	1122	dbSNP
rs1178692128	1125	dbSNP
rs773382960	1134	dbSNP
rs1384869109	1142	dbSNP
rs11553124	1147	dbSNP
rs1064133	1148	dbSNP
rs1343868734	1153	dbSNP
rs1453409281	1159	dbSNP
rs1340132460	1160	dbSNP
rs183288956	1164	dbSNP
rs1332365493	1172	dbSNP
rs762940025	1178	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.