ID	Duplex structure	Position	Score	MFE
1	miRNA 3' cgccAGGGCGCCGCGGGGCGGa 5' |||: | | ||||||| Target 5' cgccTCCTTCTTC-CCCCGCCg 3'	693 - 713	149.00	-18.50
2	miRNA 3' cgCCAGGGCGC---C--GCGGGGCGGa 5' || | ||| | | ||||||| Target 5' ggGGGCGAGCGCATGACCCCCCCGCCc 3'	209 - 235	146.00	-23.10
3	miRNA 3' cgCCAGGGCG-CCGCGGGGCgga 5' ||| :||: ||||||||| Target 5' ggGGTGTCGTGGGCGCCCCGgac 3'	55 - 77	136.00	-32.80

Mutant ID	Mutant Position	Mutant Source
COSN31492495	39	COSMIC
COSN31932832	59	COSMIC
COSN21429497	71	COSMIC
COSN6667390	80	COSMIC
COSN27209834	177	COSMIC
COSN31524446	385	COSMIC
COSN31565622	386	COSMIC
COSN31543869	403	COSMIC
COSN29725708	459	COSMIC
COSN31517239	512	COSMIC
COSN28716460	514	COSMIC
COSN25214832	521	COSMIC
COSN26568972	548	COSMIC
COSN30539907	578	COSMIC
COSN28658538	647	COSMIC
COSN7355698	672	COSMIC
rs7249	80	GWAS

Mutant ID	Mutant Position	Mutant Source
rs1158816684	1	dbSNP
rs1470981122	3	dbSNP
rs1361682337	7	dbSNP
rs1383543888	11	dbSNP
rs779060071	12	dbSNP
rs1180542852	15	dbSNP
rs769621355	18	dbSNP
rs1244909082	21	dbSNP
rs559347104	23	dbSNP
rs1391029934	24	dbSNP
rs780602435	26	dbSNP
rs1019398113	29	dbSNP
rs1284743855	30	dbSNP
rs1206654215	31	dbSNP
rs1382994984	33	dbSNP
rs966424025	35	dbSNP
rs1259185270	36	dbSNP
rs1007609188	37	dbSNP
rs1378171017	39	dbSNP
rs545983695	44	dbSNP
rs1317797998	46	dbSNP
rs1033149092	47	dbSNP
rs1451043512	48	dbSNP
rs1011063067	50	dbSNP
rs77680610	52	dbSNP
rs1000352178	54	dbSNP
rs1209516304	58	dbSNP
rs1030539204	59	dbSNP
rs1245356399	59	dbSNP
rs1461940547	59	dbSNP
rs1183285417	64	dbSNP
rs532178239	66	dbSNP
rs1241338919	67	dbSNP
rs1017860053	72	dbSNP
rs11550220	73	dbSNP
rs1182662262	74	dbSNP
rs1009114964	75	dbSNP
rs1357477719	77	dbSNP
rs7249	80	dbSNP
rs1041989364	82	dbSNP
rs1406618580	83	dbSNP
rs541443082	84	dbSNP
rs929394045	86	dbSNP
rs1391413189	88	dbSNP
rs527656222	88	dbSNP
rs899242418	93	dbSNP
rs1335618235	99	dbSNP
rs1038189248	101	dbSNP
rs11550221	102	dbSNP
rs1324784435	102	dbSNP
rs1261454563	103	dbSNP
rs1321151468	105	dbSNP
rs991147028	105	dbSNP
rs1196399376	107	dbSNP
rs1249918562	108	dbSNP
rs1417222151	109	dbSNP
rs41352349	109	dbSNP
rs1404459241	110	dbSNP
rs1479964604	111	dbSNP
rs939259303	114	dbSNP
rs1355858041	120	dbSNP
rs1462180478	121	dbSNP
rs927635075	122	dbSNP
rs1393771118	127	dbSNP
rs574511411	128	dbSNP
rs1422866050	133	dbSNP
rs977774432	138	dbSNP
rs1476417366	139	dbSNP
rs1346734411	143	dbSNP
rs966474931	145	dbSNP
rs1198414773	146	dbSNP
rs1309418537	148	dbSNP
rs1205575154	150	dbSNP
rs914992469	155	dbSNP
rs1224858091	157	dbSNP
rs41521444	157	dbSNP
rs1275380571	159	dbSNP
rs1490168985	159	dbSNP
rs1196929512	162	dbSNP
rs1197172647	163	dbSNP
rs3075305	164	dbSNP
rs964881257	164	dbSNP
rs1169372159	165	dbSNP
rs1317806782	166	dbSNP
rs1303255189	167	dbSNP
rs1413014719	167	dbSNP
rs141923000	167	dbSNP
rs1425966013	167	dbSNP
rs71717206	167	dbSNP
rs1292144576	168	dbSNP
rs3075300	169	dbSNP
rs1126915	172	dbSNP
rs1295075034	173	dbSNP
rs1363438360	173	dbSNP
rs1340332111	175	dbSNP
rs1272642213	176	dbSNP
rs2384994	177	dbSNP
rs1358634952	178	dbSNP
rs71309624	178	dbSNP
rs796406160	178	dbSNP
rs1435227228	179	dbSNP
rs1220234342	180	dbSNP
rs1371304160	180	dbSNP
rs1327621321	181	dbSNP
rs1463834583	182	dbSNP
rs1486096669	183	dbSNP
rs143890393	185	dbSNP
rs879939116	185	dbSNP
rs201252044	186	dbSNP
rs1399330646	187	dbSNP
rs1347494526	189	dbSNP
rs1017731753	190	dbSNP
rs761287197	196	dbSNP
rs148144313	197	dbSNP
rs560864628	197	dbSNP
rs1009579070	198	dbSNP
rs1190696228	201	dbSNP
rs954954911	202	dbSNP
rs1255163828	203	dbSNP
rs1226508474	204	dbSNP
rs1286213060	205	dbSNP
rs1317474374	206	dbSNP
rs895446030	209	dbSNP
rs377552155	211	dbSNP
rs1055868866	212	dbSNP
rs1183883613	213	dbSNP
rs1026761608	214	dbSNP
rs1241950952	214	dbSNP
rs541786656	217	dbSNP
rs1457581165	218	dbSNP
rs1011520592	224	dbSNP
rs937084510	225	dbSNP
rs183165834	229	dbSNP
rs1386977807	230	dbSNP
rs1471064350	232	dbSNP
rs899294803	232	dbSNP
rs1382353899	233	dbSNP
rs1037759309	235	dbSNP
rs1207244346	237	dbSNP
rs1281367294	241	dbSNP
rs1373883933	244	dbSNP
rs1223216958	245	dbSNP
rs894127880	250	dbSNP
rs1325484293	251	dbSNP
rs1012916688	264	dbSNP
rs1262068635	268	dbSNP
rs895000944	269	dbSNP
rs1205922829	270	dbSNP
rs909650369	279	dbSNP
rs1048163059	281	dbSNP
rs1177183127	283	dbSNP
rs1348024053	285	dbSNP
rs572706813	286	dbSNP
rs540926782	287	dbSNP
rs1405554510	288	dbSNP
rs1412990045	290	dbSNP
rs1330974177	291	dbSNP
rs976688965	293	dbSNP
rs1355247706	295	dbSNP
rs1441366954	297	dbSNP
rs927887523	299	dbSNP
rs965683726	300	dbSNP
rs1298536820	301	dbSNP
rs945018535	304	dbSNP
rs1342425189	306	dbSNP
rs1444221945	310	dbSNP
rs911859251	311	dbSNP
rs1175402038	315	dbSNP
rs986549082	316	dbSNP
rs914874888	317	dbSNP
rs1435385591	318	dbSNP
rs953387459	323	dbSNP
rs1033075586	324	dbSNP
rs1157071676	328	dbSNP
rs1439394179	332	dbSNP
rs964432518	334	dbSNP
rs1381239741	337	dbSNP
rs1426575009	347	dbSNP
rs1169919302	352	dbSNP
rs1260787662	353	dbSNP
rs978879577	355	dbSNP
rs967529528	356	dbSNP
rs1409400012	357	dbSNP
rs1020877856	359	dbSNP
rs987643837	360	dbSNP
rs1465994472	361	dbSNP
rs8106809	362	dbSNP
rs777829059	366	dbSNP
rs1270369660	367	dbSNP
rs1034061105	372	dbSNP
rs1026564498	373	dbSNP
rs1223962128	375	dbSNP
rs1382415155	376	dbSNP
rs1236066914	377	dbSNP
rs993677197	377	dbSNP
rs200632422	382	dbSNP
rs1424773446	384	dbSNP
rs758172794	385	dbSNP
rs9413	386	dbSNP
rs4393694	387	dbSNP
rs1166791465	388	dbSNP
rs1387218219	388	dbSNP
rs3075299	388	dbSNP
rs74881531	388	dbSNP
rs750430004	388	dbSNP
rs755920352	388	dbSNP
rs779907397	388	dbSNP
rs773233340	389	dbSNP
rs1382949383	392	dbSNP
rs761469291	392	dbSNP
rs1445003796	394	dbSNP
rs1247312684	397	dbSNP
rs1259926623	399	dbSNP
rs1265333427	400	dbSNP
rs576545629	401	dbSNP
rs762658051	406	dbSNP
rs1055394666	408	dbSNP
rs1464598611	409	dbSNP
rs556267060	410	dbSNP
rs1003377537	411	dbSNP
rs1245010306	415	dbSNP
rs906478688	418	dbSNP
rs750466820	420	dbSNP
rs1042314309	422	dbSNP
rs945234812	423	dbSNP
rs1158926514	431	dbSNP
rs1240942657	437	dbSNP
rs1387707689	439	dbSNP
rs1455301525	440	dbSNP
rs1338346450	442	dbSNP
rs1182585999	445	dbSNP
rs1442562540	458	dbSNP
rs1288385544	462	dbSNP
rs1309957966	464	dbSNP
rs1339219879	466	dbSNP
rs1280481657	474	dbSNP
rs780658245	474	dbSNP
rs914927139	474	dbSNP
rs943128152	474	dbSNP
rs1461951569	477	dbSNP
rs1487735977	487	dbSNP
rs1254251034	493	dbSNP
rs1420794024	496	dbSNP
rs1182502710	500	dbSNP
rs1410918436	501	dbSNP
rs1260916171	502	dbSNP
rs1178351504	503	dbSNP
rs1429469037	504	dbSNP
rs1300549200	510	dbSNP
rs910283544	510	dbSNP
rs988082780	512	dbSNP
rs1319687968	518	dbSNP
rs1393613964	519	dbSNP
rs933495438	519	dbSNP
rs1226880146	521	dbSNP
rs1285590060	524	dbSNP
rs896073653	525	dbSNP
rs536344570	526	dbSNP
rs972308089	527	dbSNP
rs1481684430	528	dbSNP
rs1233755768	529	dbSNP
rs1377350554	533	dbSNP
rs1196492783	537	dbSNP
rs41363545	540	dbSNP
rs1201308950	547	dbSNP
rs1429803818	549	dbSNP
rs41495046	550	dbSNP
rs959085254	553	dbSNP
rs1462005910	554	dbSNP
rs1035772289	555	dbSNP
rs1003337591	567	dbSNP
rs906366997	574	dbSNP
rs781502134	576	dbSNP
rs578260519	579	dbSNP
rs15212	587	dbSNP
rs1009497995	589	dbSNP
rs1385820256	590	dbSNP
rs769576919	590	dbSNP
rs1274095361	592	dbSNP
rs1290837904	595	dbSNP
rs776156203	598	dbSNP
rs1224690068	608	dbSNP
rs1339953923	608	dbSNP
rs893713880	608	dbSNP
rs1488012691	609	dbSNP
rs533896386	610	dbSNP
rs373365631	617	dbSNP
rs1166119635	620	dbSNP
rs1001597217	624	dbSNP
rs1428750536	628	dbSNP
rs557699029	633	dbSNP
rs1051525640	635	dbSNP
rs1428358693	638	dbSNP
rs1048132443	644	dbSNP
rs929761539	645	dbSNP
rs1351012437	647	dbSNP
rs896959996	649	dbSNP
rs1427387707	650	dbSNP
rs919447017	654	dbSNP
rs1436161302	660	dbSNP
rs1296933208	661	dbSNP
rs1041279409	665	dbSNP
rs1261891683	670	dbSNP
rs1389540416	671	dbSNP
rs552150750	672	dbSNP
rs1248301384	674	dbSNP
rs532369461	677	dbSNP
rs1219025874	682	dbSNP
rs747499350	685	dbSNP
rs563448649	686	dbSNP
rs1187901737	687	dbSNP
rs756796703	690	dbSNP
rs1445883247	691	dbSNP
rs985417031	693	dbSNP
rs1183695823	695	dbSNP
rs972193385	697	dbSNP
rs1214124168	698	dbSNP
rs1163102320	699	dbSNP
rs192641207	701	dbSNP
rs925976955	702	dbSNP
rs1320090543	704	dbSNP
rs751406416	705	dbSNP
rs1284856995	706	dbSNP
rs978804277	708	dbSNP
rs763749470	709	dbSNP
rs1265801380	711	dbSNP
rs1462390268	711	dbSNP
rs1203673903	713	dbSNP
rs761717454	714	dbSNP
rs981566489	716	dbSNP
rs1410837541	717	dbSNP
rs1473094925	718	dbSNP
rs1158910297	720	dbSNP
rs1020426700	722	dbSNP
rs993419014	723	dbSNP
rs529803290	726	dbSNP
rs1433540874	727	dbSNP
rs1373135313	728	dbSNP
rs758192840	728	dbSNP
rs560924258	735	dbSNP
rs1445691659	738	dbSNP
rs1001783352	739	dbSNP
rs541023467	740	dbSNP
rs1227499169	742	dbSNP
rs41355150	747	dbSNP
rs888806320	747	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.

- Carcinogenesis, 2010

An inflammatory component is present in the microenvironment of most neoplastic tissues, including those not causally related to an obvious inflammatory process. Several microRNAs, and especially miR-155, play an essential role in both the innate and adaptative immune response. Resveratrol (trans-3,4',5-trihydroxystilbene) is a natural antioxidant with anti-inflammatory properties that is currently at the stage of preclinical studies for human cancer prevention. Here, we establish that, in human THP-1 monocytic cells as well as in human blood monocytes, resveratrol upregulates miR-663, a microRNA potentially targeting multiple genes implicated in the immune response. In THP-1 cells, miR-663 decreases endogenous activator protein-1 (AP-1) activity and impairs its upregulation by lipopolysaccharides (LPS), at least in part by directly targeting JunB and JunD transcripts. We further establish that the downregulation of AP-1 activity by resveratrol is miR-663 dependent and that the effects of resveratrol on both AP-1 activity and JunB levels are dose dependent. Finally, we show that resveratrol impairs the upregulation of miR-155 by LPS in a miR-663-dependent manner. Given the role of miR-155 in the innate immune response and the fact that it is upregulated in many cancers, our results suggest that manipulating miR-663 levels may help to optimize the use of resveratrol as both an anti-inflammatory and anticancer agent against malignancies associated with high levels of miR-155.

- 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.

- BMC cancer, 2016

BACKGROUND: MicroRNA-663a expression is downregulated in several tumors. However, its functions and mechanisms in human non-small cell lung (NSCLC) cancer remain obscure. The present study aimed to identify the expression pattern, biological roles and potential mechanisms by which miR-663a dysregulation is associated with NSCLC. METHODS: We examined expression level of miR-663a in 62 cases of NSCLC tissues and 5 NSCLC cell lines by reverse transcription PCR. In vitro, gain-of-function and loss-of-function experiments were performed to examine the impact of miR-663a on proliferation, cell cycle progression and invasion of NSCLC cells. Using fluorescence reporter assays, we also explored the potential targets and possible mechanisms of miR-663a in NSCLC cells. RESULTS: Downregulation of miR-663a was observed in 42 of 62 of lung cancer tissues compared with paired normal tissues (mean cancer/normal value = 0.745) and its downregulation correlated with nodal metastasis. Transfection of miR-663a mimic suppressed cell proliferation, cell cycle progression and invasion, with downregulation of cyclin D1, cyclin E and MMP9 in both H460 and H1299 cell lines. Transfection of miR-663a inhibitor in both H460 and H1299 cell lines exhibited the opposite effects. In addition, we confirmed that miR-663a could inhibit AP-1 activity and AP-1 component JunD was a direct target of miR-663a in lung cancer cells. Transfection of miR-663a mimic downregulated JunD expression. In addition, JunD siRNA treatment abrogated miR-663a inhibitor-induced expression of cyclin D1, cyclin E and MMP9. Above all, both miRNA mimic and inhibitor in two different NSCLC cell lines demonstrated that miR-663a inhibits proliferation and invasion by targeting AP-1 transcription factor JunD. CONCLUSIONS: This study indicates that miR-663a downregulation might be associated with NSCLC progression. MiR-663a suppresses proliferation and invasion by targeting AP-1 component JunD in NSCLC cells.