ID	Duplex structure	Position	Score	MFE
1	miRNA 3' guguGAGUACACCGGGGGUCGu 5' | |:|| |||||||||| Target 5' gggcCACGTG-GGCCCCCAGCc 3'	426 - 446	165.00	-27.60
2	miRNA 3' guGUGAGUACACCG--GGGGUCGu 5' | ||| || ||| ||||||| Target 5' tcCCCTC-TGGGGCGTCCCCAGCc 3'	193 - 215	161.00	-21.90
3	miRNA 3' gugUGAGUACACC--GGGGGUCGu 5' :| || | || |||||||| Target 5' gggGCCCA-GCGGCTCCCCCAGCg 3'	352 - 374	152.00	-22.30

Mutant ID	Mutant Position	Mutant Source
COSN31554956	12	COSMIC
COSN30503270	17	COSMIC
COSN26992393	27	COSMIC
COSN30462050	37	COSMIC
COSN30498155	46	COSMIC
COSN30143517	62	COSMIC
COSN31557064	63	COSMIC
COSN30544218	88	COSMIC
COSN31596269	91	COSMIC
COSN30592867	96	COSMIC
COSN15188182	131	COSMIC
COSN31624103	139	COSMIC
COSN30602079	158	COSMIC
COSM1002950	188	COSMIC
COSN26865063	304	COSMIC
COSN17999429	403	COSMIC
COSN14584244	414	COSMIC

Mutant ID	Mutant Position	Mutant Source
rs1189616057	2	dbSNP
rs747910372	6	dbSNP
rs774398964	7	dbSNP
rs144347019	9	dbSNP
rs749420451	10	dbSNP
rs779936286	13	dbSNP
rs756246131	14	dbSNP
rs368100858	16	dbSNP
rs373918948	17	dbSNP
rs920756294	22	dbSNP
rs1437030103	24	dbSNP
rs757744084	25	dbSNP
rs1292619642	26	dbSNP
rs751820418	27	dbSNP
rs368141828	29	dbSNP
rs764693117	30	dbSNP
rs758764497	32	dbSNP
rs1390116419	34	dbSNP
rs753403508	43	dbSNP
rs765863876	45	dbSNP
rs530607552	46	dbSNP
rs750117113	47	dbSNP
rs1393039303	48	dbSNP
rs767136984	50	dbSNP
rs569863722	55	dbSNP
rs957011514	56	dbSNP
rs1356805453	60	dbSNP
rs1030992822	62	dbSNP
rs1000859844	63	dbSNP
rs551361902	64	dbSNP
rs533229556	73	dbSNP
rs1007108713	75	dbSNP
rs891270464	77	dbSNP
rs1051709615	78	dbSNP
rs929734070	80	dbSNP
rs1374518996	82	dbSNP
rs918372608	85	dbSNP
rs999734570	86	dbSNP
rs1444994843	88	dbSNP
rs1038023137	89	dbSNP
rs1171449549	91	dbSNP
rs559702759	92	dbSNP
rs941036130	96	dbSNP
rs1166016766	98	dbSNP
rs1399473483	105	dbSNP
rs1453358148	109	dbSNP
rs1458018369	110	dbSNP
rs1027803391	111	dbSNP
rs926961193	112	dbSNP
rs3170527	114	dbSNP
rs1402042825	115	dbSNP
rs1257917697	116	dbSNP
rs528499741	118	dbSNP
rs971309456	123	dbSNP
rs561366454	124	dbSNP
rs1261632432	126	dbSNP
rs989082807	131	dbSNP
rs1049411778	136	dbSNP
rs1235235703	139	dbSNP
rs1264124175	144	dbSNP
rs761620713	144	dbSNP
rs773981212	145	dbSNP
rs1000807562	147	dbSNP
rs543149161	150	dbSNP
rs1018247856	151	dbSNP
rs1323232366	151	dbSNP
rs1230292099	153	dbSNP
rs575733551	158	dbSNP
rs775490673	159	dbSNP
rs770030985	160	dbSNP
rs1289022818	162	dbSNP
rs1363657847	163	dbSNP
rs1369096007	164	dbSNP
rs1380231273	164	dbSNP
rs1277017404	166	dbSNP
rs1305579316	167	dbSNP
rs891405474	168	dbSNP
rs1225835811	170	dbSNP
rs1408712156	177	dbSNP
rs1370439979	178	dbSNP
rs745919856	179	dbSNP
rs1355783852	180	dbSNP
rs908057828	181	dbSNP
rs999685073	187	dbSNP
rs1376339864	188	dbSNP
rs781585322	189	dbSNP
rs1433916428	192	dbSNP
rs1427548427	195	dbSNP
rs1029828532	196	dbSNP
rs994767987	200	dbSNP
rs1180048375	205	dbSNP
rs376174636	206	dbSNP
rs916565841	210	dbSNP
rs1207270630	212	dbSNP
rs1482146850	213	dbSNP
rs771238022	215	dbSNP
rs896891461	216	dbSNP
rs1313535157	217	dbSNP
rs1286104438	218	dbSNP
rs1227210109	219	dbSNP
rs747403945	220	dbSNP
rs777943233	221	dbSNP
rs758776393	223	dbSNP
rs558299711	224	dbSNP
rs966488705	226	dbSNP
rs1302569385	227	dbSNP
rs1466898373	228	dbSNP
rs749822416	230	dbSNP
rs1224892246	232	dbSNP
rs767080626	232	dbSNP
rs753213109	234	dbSNP
rs779362582	235	dbSNP
rs563935193	238	dbSNP
rs1412869630	239	dbSNP
rs949938102	240	dbSNP
rs917191535	241	dbSNP
rs1255414379	243	dbSNP
rs1200780783	247	dbSNP
rs778343104	248	dbSNP
rs185184773	249	dbSNP
rs1207777493	252	dbSNP
rs577875277	255	dbSNP
rs767192139	256	dbSNP
rs995548466	257	dbSNP
rs898161876	264	dbSNP
rs1157602299	265	dbSNP
rs761308830	266	dbSNP
rs1312680019	271	dbSNP
rs1396945723	280	dbSNP
rs1385501812	281	dbSNP
rs1318771963	285	dbSNP
rs1321008431	288	dbSNP
rs925821017	290	dbSNP
rs979461843	297	dbSNP
rs4919878	302	dbSNP
rs370350292	303	dbSNP
rs1375097631	304	dbSNP
rs1046624552	307	dbSNP
rs1018223020	308	dbSNP
rs949445571	314	dbSNP
rs748537465	319	dbSNP
rs955632947	320	dbSNP
rs534314034	324	dbSNP
rs1397680954	325	dbSNP
rs994443957	327	dbSNP
rs925321319	332	dbSNP
rs978401294	344	dbSNP
rs573340057	345	dbSNP
rs1465343818	346	dbSNP
rs1412381233	349	dbSNP
rs1017118953	351	dbSNP
rs986632654	352	dbSNP
rs953890529	357	dbSNP
rs1172427515	361	dbSNP
rs555151701	366	dbSNP
rs1337801496	367	dbSNP
rs1005274213	370	dbSNP
rs1003916297	371	dbSNP
rs898124131	373	dbSNP
rs1015286139	374	dbSNP
rs903995553	375	dbSNP
rs1216412063	383	dbSNP
rs905642324	384	dbSNP
rs906565602	388	dbSNP
rs886729383	393	dbSNP
rs1046593224	394	dbSNP
rs866225037	395	dbSNP
rs1476281976	398	dbSNP
rs1257095546	403	dbSNP
rs1200279557	405	dbSNP
rs1475423660	405	dbSNP
rs1482479572	410	dbSNP
rs1420932399	412	dbSNP
rs949775728	415	dbSNP
rs1253658881	416	dbSNP
rs114742743	417	dbSNP
rs895335492	418	dbSNP
rs1413123478	419	dbSNP
rs1333684995	423	dbSNP
rs1053416208	425	dbSNP
rs797018050	426	dbSNP
rs1276350705	429	dbSNP
rs1341948278	432	dbSNP
rs569675451	433	dbSNP
rs1395296168	443	dbSNP
rs755539569	444	dbSNP
rs978159850	450	dbSNP
rs945289569	451	dbSNP
rs551521887	452	dbSNP
rs780054790	454	dbSNP
rs1399673158	455	dbSNP
rs978573750	457	dbSNP
rs539655724	458	dbSNP
rs565935604	459	dbSNP
rs116125090	463	dbSNP
rs955526356	465	dbSNP
rs1029679831	466	dbSNP
rs973353929	467	dbSNP
rs961655537	471	dbSNP
rs539922156	472	dbSNP
rs1359935058	474	dbSNP
rs528487167	479	dbSNP
rs192965845	483	dbSNP
rs1256694098	484	dbSNP
rs549188111	486	dbSNP
rs530999119	487	dbSNP
rs563639427	489	dbSNP
rs545536516	493	dbSNP
rs895291954	494	dbSNP
rs1357830124	498	dbSNP
rs895448425	500	dbSNP
rs577862798	511	dbSNP
rs1052790538	512	dbSNP
rs1450358342	514	dbSNP
rs1243524418	519	dbSNP
rs1055321862	526	dbSNP
rs999144269	528	dbSNP
rs1157011268	529	dbSNP
rs1379931910	530	dbSNP
rs1425599375	531	dbSNP
rs904487754	532	dbSNP
rs903973693	536	dbSNP
rs760553704	538	dbSNP
rs879802573	539	dbSNP
rs912579354	547	dbSNP
rs910397605	548	dbSNP
rs1352517628	551	dbSNP
rs1050939036	556	dbSNP
rs1266673323	557	dbSNP
rs1353669539	558	dbSNP
rs1491206933	558	dbSNP
rs1491218885	559	dbSNP
rs1459326425	565	dbSNP
rs1050247769	568	dbSNP
rs932597607	572	dbSNP
rs921076286	573	dbSNP
rs934092448	575	dbSNP
rs1167237918	586	dbSNP
rs922558584	588	dbSNP
rs559606833	594	dbSNP
rs3179858	598	dbSNP
rs3180572	600	dbSNP
rs962768125	602	dbSNP

- 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.

- Neoplasia (New York, N.Y.), 2016

MicroRNA (miRNA) deregulation in prostate cancer (PCa) contributes to PCa initiation and metastatic progression. To comprehensively define the cancer-associated changes in miRNA targeting and function in commonly studied models of PCa, we performed photoactivatable ribonucleoside-enhanced cross-linking immunoprecipitation of the Argonaute protein in a panel of PCa cell lines modeling different stages of PCa progression. Using this comprehensive catalogue of miRNA targets, we analyzed miRNA targeting on known drivers of PCa and examined tissue-specific and stage-specific pathway targeting by miRNAs. We found that androgen receptor is the most frequently targeted PCa oncogene and that miR-148a targets the largest number of known PCa drivers. Globally, tissue-specific and stage-specific changes in miRNA targeting are driven by homeostatic response to active oncogenic pathways. Our findings indicate that, even in advanced PCa, the miRNA pool adapts to regulate continuing alterations in the cancer genome to balance oncogenic molecular changes. These findings are important because they are the first to globally characterize miRNA changes in PCa and demonstrate how the miRNA target spectrum responds to staged tumorigenesis.