>KDELR1|NM_006801|3'UTR
   1 CCCCGGTCCTCTCCATCTCTCTCCTCGGCAGCAGCGGGAGGCAGAGGAAGGCGGCAGAAGATGAAGAGCTTTCCCATCCA
  81 GGGGTGACTTTTTTAAGAACCCACCTCTTGTGCTCCCCATCCCGCCTCCTGCCGGGTTTCAGGGGGACAGTGGAGGATCC
 161 AGGTCTTGGGGAGCTCAGGACTTGGGCTGTTTGTAGTTTTTTGCCTTTTAGACAAGAAAAAAAAATCTTTCCACTCTTTA
 241 GTTTTTGATTCTGATGACTCGTTTTTCTTCTACTCTGTGGCCCCAATTTTTATAAAGTGTTTTTGAGTGTCCTATGGGCC
 321 GGGGCAGGGTCCAAGATCTTTTCCCTTCCCCAGGCCCCTCGGCTCCCTCCCAGATCCCACCCCCAGCCCCACTGGTTGCC
 401 AAACACTAAATCTGCCGACACCCATCTGCCCCACCTCCTGCCATGGCCATGAACCGCGACCCCCACTAAATTTCTAGATT
 481 GGGGATAGGGAGAAAGGGAGGCCCAGGAAGGTCTCCCCTGATTTTTTTTCATAGTAATTTTTTTCCCCAGAGTTTGAATT
 561 TTTTGGTCTTCTCCTGGTTTTTTGGCAAATTAGGGGGGCCCGGGGCTCAAGTGCGGGAAGGGGGCTGGCCCGAGGATCCC
 641 ATGGCTCTCACACCATGTTTTTGTACAGAACTGATGGTTGAATCTTTGTTCTCTTGAAATAAACAGAAGAAAATGAAACC
 721 TTTAAAAAAAAAAAAAAAAAA

ID	Duplex structure	Position	Score	MFE
1	miRNA 3' acccUGAGGUA-CGGGGUUc 5' ||||::| ||||||| Target 5' ttctACTCTGTGGCCCCAAt 3'	268 - 287	159.00	-16.40
2	miRNA 3' accCUG-AGGU--ACGGGGUuc 5' ||| ||| ||||||| Target 5' gccGACACCCATCTGCCCCAcc 3'	414 - 435	134.00	-14.70
3	miRNA 3' acccUGAGGUACGGGGUuc 5' || || |||||| Target 5' tcccACCCCCAGCCCCAct 3'	375 - 393	131.00	-13.10

Mutant ID	Mutant Position	Mutant Source
COSN26635187	26	COSMIC
COSN30124524	52	COSMIC
COSN26633375	70	COSMIC
COSN31479986	81	COSMIC
COSN7447500	81	COSMIC
COSN30747997	155	COSMIC
COSN4968104	191	COSMIC
COSN31595700	435	COSMIC
COSN32252181	545	COSMIC
COSN31607485	717	COSMIC

Mutant ID	Mutant Position	Mutant Source
rs762278657	4	dbSNP
rs567654708	5	dbSNP
rs768875633	6	dbSNP
rs1286683545	11	dbSNP
rs370349342	15	dbSNP
rs1235161191	19	dbSNP
rs1348696104	21	dbSNP
rs760822010	22	dbSNP
rs538770451	24	dbSNP
rs1337299674	26	dbSNP
rs867291724	27	dbSNP
rs754805783	32	dbSNP
rs189397701	35	dbSNP
rs772347905	36	dbSNP
rs1398429122	38	dbSNP
rs1192892842	42	dbSNP
rs1383665652	43	dbSNP
rs373903445	46	dbSNP
rs749228576	48	dbSNP
rs1392894239	49	dbSNP
rs370963285	52	dbSNP
rs184944147	53	dbSNP
rs377327443	61	dbSNP
rs202246931	65	dbSNP
rs376883945	65	dbSNP
rs1342043560	75	dbSNP
rs1266493914	87	dbSNP
rs1335082899	91	dbSNP
rs1247662034	97	dbSNP
rs1442763785	100	dbSNP
rs1319929970	106	dbSNP
rs2230412	115	dbSNP
rs2230413	123	dbSNP
rs752865005	124	dbSNP
rs1040324352	128	dbSNP
rs922967723	133	dbSNP
rs551726779	134	dbSNP
rs1365998513	142	dbSNP
rs374386029	146	dbSNP
rs964320303	148	dbSNP
rs1184547687	152	dbSNP
rs1267236167	156	dbSNP
rs984889623	159	dbSNP
rs1456343045	161	dbSNP
rs1175313240	169	dbSNP
rs930398380	172	dbSNP
rs919035655	176	dbSNP
rs1159281039	182	dbSNP
rs1017949454	187	dbSNP
rs1165665445	187	dbSNP
rs1391928077	203	dbSNP
rs1473349473	211	dbSNP
rs1309725898	212	dbSNP
rs1249226683	213	dbSNP
rs1181034154	216	dbSNP
rs11549473	217	dbSNP
rs1343465095	219	dbSNP
rs192910082	220	dbSNP
rs1404081171	222	dbSNP
rs1284248235	225	dbSNP
rs1225428517	226	dbSNP
rs961528817	226	dbSNP
rs1482909569	227	dbSNP
rs979333888	230	dbSNP
rs968325916	244	dbSNP
rs1340093876	247	dbSNP
rs1268496034	253	dbSNP
rs1035869310	256	dbSNP
rs751350753	260	dbSNP
rs981671923	261	dbSNP
rs1487832262	266	dbSNP
rs1271425552	271	dbSNP
rs1020780081	272	dbSNP
rs1190528927	273	dbSNP
rs903683959	275	dbSNP
rs1010766299	282	dbSNP
rs1372024689	286	dbSNP
rs1264911037	288	dbSNP
rs1462033343	292	dbSNP
rs533247441	298	dbSNP
rs143391890	306	dbSNP
rs1363639078	309	dbSNP
rs1423839137	314	dbSNP
rs188500978	320	dbSNP
rs1012017917	321	dbSNP
rs957467303	322	dbSNP
rs541223239	332	dbSNP
rs956088777	334	dbSNP
rs765356708	348	dbSNP
rs1380764366	358	dbSNP
rs1295095751	360	dbSNP
rs1035752581	365	dbSNP
rs1345848467	367	dbSNP
rs1325348846	369	dbSNP
rs1002887446	371	dbSNP
rs998656272	372	dbSNP
rs1385000858	373	dbSNP
rs1389976526	378	dbSNP
rs1267639395	379	dbSNP
rs1040293284	380	dbSNP
rs1428668633	381	dbSNP
rs1007466420	382	dbSNP
rs1458312918	384	dbSNP
rs1382777118	385	dbSNP
rs1409165477	390	dbSNP
rs1443962768	392	dbSNP
rs1157868898	399	dbSNP
rs776593330	416	dbSNP
rs1045043720	417	dbSNP
rs1288577908	422	dbSNP
rs13572	426	dbSNP
rs1006468109	430	dbSNP
rs918975065	432	dbSNP
rs573740197	433	dbSNP
rs1382074442	434	dbSNP
rs1247378243	443	dbSNP
rs1267218448	446	dbSNP
rs1315551430	449	dbSNP
rs1238777228	451	dbSNP
rs377143181	455	dbSNP
rs1047875387	456	dbSNP
rs116458191	458	dbSNP
rs923038402	479	dbSNP
rs148891438	485	dbSNP
rs916181587	486	dbSNP
rs943043557	488	dbSNP
rs575982004	504	dbSNP
rs1417141435	509	dbSNP
rs990162785	510	dbSNP
rs1364092513	515	dbSNP
rs957602653	517	dbSNP
rs1174485488	522	dbSNP
rs1276361784	523	dbSNP
rs1031728672	524	dbSNP
rs1371801114	530	dbSNP
rs879856133	530	dbSNP
rs966142839	530	dbSNP
rs910216657	531	dbSNP
rs1330322651	538	dbSNP
rs1331605828	542	dbSNP
rs184579639	544	dbSNP
rs1260828636	545	dbSNP
rs1437191834	545	dbSNP
rs889036713	545	dbSNP
rs967978880	547	dbSNP
rs1238643621	548	dbSNP
rs545336978	549	dbSNP
rs1235801458	552	dbSNP
rs1479620147	556	dbSNP
rs913749663	556	dbSNP
rs192030448	565	dbSNP
rs897495533	565	dbSNP
rs149228884	576	dbSNP
rs939085015	577	dbSNP
rs927745942	578	dbSNP
rs1352773468	584	dbSNP
rs1461937278	586	dbSNP
rs960499558	594	dbSNP
rs1477223208	595	dbSNP
rs1035784764	597	dbSNP
rs116882936	601	dbSNP
rs1451940889	602	dbSNP
rs1219380620	605	dbSNP
rs1246262025	613	dbSNP
rs970083546	614	dbSNP
rs762893837	615	dbSNP
rs867985676	622	dbSNP
rs1197002695	626	dbSNP
rs1267848691	629	dbSNP
rs888016169	630	dbSNP
rs990814612	631	dbSNP
rs1050671	632	dbSNP
rs1417515413	636	dbSNP
rs566290670	645	dbSNP
rs993635793	651	dbSNP
rs1050682	652	dbSNP
rs1427958173	655	dbSNP
rs901982584	667	dbSNP
rs1372932573	680	dbSNP
rs1423225457	691	dbSNP
rs1040139264	693	dbSNP
rs1366539798	695	dbSNP
rs1436780301	704	dbSNP
rs1276228914	706	dbSNP
rs1359306494	712	dbSNP
rs1213474046	714	dbSNP
rs780853667	714	dbSNP
rs1343944200	716	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.