>TDRKH|NM_001083963|3'UTR
   1 AGTCTGGGCTTCAGTTTGCTCAGCCATCTGCTTTGCTGTGTGAGTGCAGCTATCATCTATCTGTAGCAACAGGAAAGTAA
  81 TGAGGGCGACAGTGGGGCACTTGCTTTGATTCCCTCTTTCCCATGCCCTGTCTTAATATACTTCTCTGCAGCTGCTTTCC
 161 TGCAGCTTAACTTGCTCTCAGATTGAGCACTTTCAAGCTTTTTGTGTATTTCTGTCTTTGGCAGGATTTGGCATAGGAAT
 241 TGGTGCATGGAGGAGAGGAGTGTATGATAAAGGATCCATGCAGTCCTTCCTTTATTACACATATAGTCTGGCTTGCTGTG
 321 GACCAAATTAATATTCTCCTCCCATCAGACTACAAAAAAATTGGACTACCACGCTACAAGTGTGTCTCCCCCATTCCACC
 401 TCCGGATCCCTCCCCAACCCTCCAGTGTTTGAATACTGCTGTGTTACTTCCAGGCCGTTCAACGTCAGGCTCAGTCCCCT
 481 CTACCAGTCATGATTCACATTACTACTAGGCTGTATCCTTTTTGAGGCTGGGAAACAGTCAGGCTTTCGTCATTGGAAGT
 561 GATTCTGCAGACTTCTGACTCACCTTATCAGGTGACTCTGGTTAAGGAAAGCTTTTGAGTGGTGAACTCAAAGACTCCAG
 641 TTGAATCAGGAGGCAAAGGCAAAAATTAGCATAATTATATTTAAAAGCCTCAGGAAGTGGGAAGAGAATACTGCCTCCCA
 721 GCCTCAATTGCTGATATGTTATTGGAGACAGGCTTTTGAAACTGCTCCAGCTATTTCTCTGTAACCTTTAGTTAAAATAT
 801 AAGTAGAAAGGAGACAGGAGGCTCAGGAAATTTTCTAAATTGCTAGTATAATATCTATATGTATACACACATATACACCC
 881 GTGGAGAGAGAGGAAGAGTATACAGTCCTGTTTGAATCATTTGGAGGATTTTTTTGCTGAATAAAGTTCTCAAGAAAATT
 961 TTCTAAAACCAAAAAAAAAAAAAAAA

ID	Duplex structure	Position	Score	MFE
1	miRNA 3' ggGA-AGGAGGAGGGGUCCGGCu 5' || | :| || :|||||||| Target 5' tgCTGTGTTACT-TCCAGGCCGt 3'	437 - 458	155.00	-20.80
2	miRNA 3' ggGAAGGAGGAGGGGUCCGGcu 5' :| ||||:|:|||| ||| Target 5' gaTTCCCTCTTTCCCATGCCct 3'	108 - 129	128.00	-21.80
3	miRNA 3' gggAAG-GAGGAGG-GGUCCGGCu 5' ||| | :: |: |:||||:| Target 5' tgaTTCACATTACTACTAGGCTGt 3'	491 - 514	119.00	-13.70

Mutant ID	Mutant Position	Mutant Source
COSN30466312	6	COSMIC
COSN30126153	74	COSMIC
COSN24389798	87	COSMIC
COSN30168092	108	COSMIC
COSN5354714	144	COSMIC
COSN28881051	150	COSMIC
COSN30118447	163	COSMIC
COSN30119061	175	COSMIC
COSN1089404	281	COSMIC
COSN6002721	453	COSMIC
COSN25791700	457	COSMIC
COSN9363264	519	COSMIC
COSN21730341	918	COSMIC
COSN31522398	928	COSMIC
COSN31582920	956	COSMIC

Mutant ID	Mutant Position	Mutant Source
rs1424825046	2	dbSNP
rs779348669	7	dbSNP
rs1473680169	9	dbSNP
rs368813898	10	dbSNP
rs1181537472	13	dbSNP
rs778263959	22	dbSNP
rs1239292467	25	dbSNP
rs1050182455	28	dbSNP
rs772694780	35	dbSNP
rs755857173	37	dbSNP
rs920322106	40	dbSNP
rs752360217	45	dbSNP
rs1262234101	48	dbSNP
rs201709511	49	dbSNP
rs1036012070	59	dbSNP
rs1455417524	63	dbSNP
rs371359950	65	dbSNP
rs928240873	81	dbSNP
rs544448582	87	dbSNP
rs1290667590	88	dbSNP
rs1397262848	97	dbSNP
rs1284123980	99	dbSNP
rs1347853211	102	dbSNP
rs780396308	114	dbSNP
rs145705926	116	dbSNP
rs1049377849	119	dbSNP
rs866888974	120	dbSNP
rs1372682246	123	dbSNP
rs775780186	125	dbSNP
rs1476358621	128	dbSNP
rs958131089	137	dbSNP
rs1191454746	141	dbSNP
rs561148964	146	dbSNP
rs999558998	151	dbSNP
rs965403924	166	dbSNP
rs1252024899	175	dbSNP
rs1019993623	176	dbSNP
rs1008822809	177	dbSNP
rs922506310	181	dbSNP
rs976999921	188	dbSNP
rs939842966	190	dbSNP
rs907979580	193	dbSNP
rs34048199	195	dbSNP
rs1457464711	202	dbSNP
rs1480026478	204	dbSNP
rs1273358507	220	dbSNP
rs1215234375	233	dbSNP
rs770221678	238	dbSNP
rs1367623383	255	dbSNP
rs889002874	258	dbSNP
rs1288075229	259	dbSNP
rs1050240178	261	dbSNP
rs983560745	262	dbSNP
rs994612404	277	dbSNP
rs952095013	283	dbSNP
rs1320663022	286	dbSNP
rs920627392	293	dbSNP
rs1221584745	297	dbSNP
rs898949089	301	dbSNP
rs990830561	302	dbSNP
rs1337409258	304	dbSNP
rs940391768	305	dbSNP
rs927657015	315	dbSNP
rs959891102	333	dbSNP
rs1389679453	342	dbSNP
rs1399663140	346	dbSNP
rs1423337401	361	dbSNP
rs1326812913	364	dbSNP
rs560457803	372	dbSNP
rs1392703528	373	dbSNP
rs543087622	374	dbSNP
rs1470731141	376	dbSNP
rs1307629841	379	dbSNP
rs746583214	380	dbSNP
rs1021060223	381	dbSNP
rs1417983121	382	dbSNP
rs1246116436	388	dbSNP
rs1253154700	388	dbSNP
rs1010646308	390	dbSNP
rs575682293	391	dbSNP
rs958183632	392	dbSNP
rs746169631	403	dbSNP
rs1623480	404	dbSNP
rs1439399806	408	dbSNP
rs1207691897	409	dbSNP
rs1236842712	413	dbSNP
rs1049864203	415	dbSNP
rs1483516029	424	dbSNP
rs758458119	426	dbSNP
rs1184317110	429	dbSNP
rs996491848	440	dbSNP
rs965809257	441	dbSNP
rs1447699898	443	dbSNP
rs901100390	456	dbSNP
rs1040947017	457	dbSNP
rs1205460072	458	dbSNP
rs939902319	462	dbSNP
rs1028855048	463	dbSNP
rs752703686	464	dbSNP
rs115658720	466	dbSNP
rs566463340	468	dbSNP
rs1362481558	477	dbSNP
rs930752522	478	dbSNP
rs1376248774	483	dbSNP
rs920637172	487	dbSNP
rs1014673719	499	dbSNP
rs991233737	501	dbSNP
rs1443354830	505	dbSNP
rs1217299935	506	dbSNP
rs1277600182	510	dbSNP
rs1323967946	518	dbSNP
rs1004646688	530	dbSNP
rs1246111286	535	dbSNP
rs1463646636	548	dbSNP
rs191907559	549	dbSNP
rs928224289	553	dbSNP
rs186187634	558	dbSNP
rs1476485310	564	dbSNP
rs1171014915	574	dbSNP
rs982407200	579	dbSNP
rs1046085569	584	dbSNP
rs778532720	586	dbSNP
rs570257533	597	dbSNP
rs1387011484	598	dbSNP
rs1401588581	601	dbSNP
rs1021119330	608	dbSNP
rs1387662936	612	dbSNP
rs1327855797	617	dbSNP
rs1433916907	618	dbSNP
rs1273848589	632	dbSNP
rs1157329779	648	dbSNP
rs1345988212	650	dbSNP
rs1225104894	658	dbSNP
rs1266181784	659	dbSNP
rs754807495	664	dbSNP
rs1054037972	669	dbSNP
rs957791379	688	dbSNP
rs1204652366	690	dbSNP
rs1054475	693	dbSNP
rs1448779058	695	dbSNP
rs924114129	697	dbSNP
rs1268425966	699	dbSNP
rs978636463	717	dbSNP
rs1201957128	723	dbSNP
rs6683364	726	dbSNP
rs1472524635	727	dbSNP
rs1159633170	728	dbSNP
rs1403093068	730	dbSNP
rs141109789	730	dbSNP
rs1041097798	734	dbSNP
rs912619505	737	dbSNP
rs985508401	738	dbSNP
rs761880302	747	dbSNP
rs1349627053	752	dbSNP
rs1239730328	758	dbSNP
rs1281204950	759	dbSNP
rs1004165206	771	dbSNP
rs751682709	779	dbSNP
rs1259479496	784	dbSNP
rs1048258909	785	dbSNP
rs764177899	794	dbSNP
rs920689298	799	dbSNP
rs1250130757	804	dbSNP
rs1282415264	810	dbSNP
rs757815895	814	dbSNP
rs973298568	815	dbSNP
rs1366046080	826	dbSNP
rs1471532213	828	dbSNP
rs1345831922	829	dbSNP
rs1054477	835	dbSNP
rs963232812	837	dbSNP
rs1014776029	839	dbSNP
rs763407329	844	dbSNP
rs1385496859	845	dbSNP
rs1005102822	847	dbSNP
rs1054479	849	dbSNP
rs528435462	852	dbSNP
rs147779226	854	dbSNP
rs1011953390	857	dbSNP
rs182551038	858	dbSNP
rs982076202	862	dbSNP
rs1054481	867	dbSNP
rs1338557986	868	dbSNP
rs1242738999	872	dbSNP
rs1328530068	873	dbSNP
rs945634671	874	dbSNP
rs1360233613	878	dbSNP
rs1053414492	879	dbSNP
rs368137347	879	dbSNP
rs760002026	881	dbSNP
rs1376550028	884	dbSNP
rs1176082102	885	dbSNP
rs936920329	888	dbSNP
rs776141312	890	dbSNP
rs770656876	893	dbSNP
rs989621993	908	dbSNP
rs902743662	909	dbSNP
rs1445919496	912	dbSNP
rs58950896	925	dbSNP
rs1168132310	928	dbSNP
rs878882123	929	dbSNP
rs1042585514	936	dbSNP
rs373295432	936	dbSNP
rs563703500	936	dbSNP
rs144226999	945	dbSNP
rs1169387041	950	dbSNP
rs1400010532	951	dbSNP
rs1395437363	953	dbSNP
rs1337279812	954	dbSNP
rs1383711389	960	dbSNP
rs1371110844	963	dbSNP
rs985947078	965	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.