>KLF10|NM_001032282|3'UTR
   1 CAGACCGGAAAGTGAAGAGTCAGAACTAACTTTGGTCTCAGCGGGAGCCAGTGGTGATGTAAAAATGCTTCCACTGCAAG
  81 TCTGTGGCCCCACAACGTGGGCTTAAAGCAGAAGCCCCACAGCCTGGCACGAAGGCCCCGCCTGGGTTAGGTGACTAAAA
 161 GGGCTTCGGCCACAGGCAGGTCACAGAAAGGCAGGTTTCATTTCTTATCACATAAGAGAGATGAGAAAGCTTTTATTCCT
 241 TTGAATATTTTTTGAAGGTTTCAGATGAGGTCAACACAGGTAGCACAGATTTTGAATCTGTGTGCATATTTGTTACTTTA
 321 CTTTTGCTGTTTATACTTGAGACCAACTTTTCAATGTGATTCTTCTAAAGCACTGGTTTCAAGAATATGGAGGCTGGAAG
 401 GAAATAAACATTACGGTACAGACATGGAGATGTAAAATGAGTTTGTATTATTACAAATATTGTCATCTTTTTCTAGAGTT
 481 ATCTTCTTTATTATTCCTAGTCTTTCCAGTCAACATCGTGGATGTAGTGATTAAATATATCTAGAACTATCATTTTTACA
 561 CTATTGTGAATATTTGGAATTGAACGACTGTATATTGCTAAGAGGGCCCAAAGAATTGGAATCCTCCTTAATTTAATTGC
 641 TTTGAAGCATAGCTACAATTTGTTTTTGCATTTTTGTTTTGAAAGTTTAACAAATGACTGTATCTAGGCATTTCATTATG
 721 CTTTGAACTTTAGTTTGCCTGCAGTTTCTTGTGTAGATTTGAAAATTGTATACCAATGTGTTTTCTGTAGACTCTAAGAT
 801 ACACTGCACTTTGTTTAGAAAAAAAACTGAAGATGAAATATATATTGTAAAGAAGGGATATTAAGAATCTTAGATAACTT
 881 CTTGAAAAAGATGGCTTATGTCATCAGTAAAGTACCTTTATGTTATGAGGATATAATGTGTGCTTTATTGAATTAGAAAA
 961 TTAGTGACCATTATTCACAGGTGGACAAATGTTGATGTTGTCCTGTTAATTTATAGGCGTTTTTTGGGGATGTGGAGGTA
1041 GTTGGGTAGAAAAATTATTAGAACATTCACTTTTGTTAACAGTATTTCTCTTTTATTCTGTTATATAGTGGATGATATAC
1121 ACAGTGGCAAAACAAAAGTACATTGCTTAAAATATATAGTGAAAAATGTCACTATATCTTCCCATTTAACATTGTTTTTG
1201 TATATTGGGTGTAGATTTCTGACATCAAAACTTGGACCCTTGGAAAACAAAAGTTTTAATTAAAAAAAATCCTTGTGACT
1281 TACAATTTGCACAATATTTCTTTTGTTGTACTTTATATCTTGTTTACAATAAAGAATTCCCTTTGGTATATGGAAAAAAA
1361 AAAAAAAAAAA

ID	Duplex structure	Position	Score	MFE
1	miRNA 3' gugacguCAGAGUCGGAUCCGu 5' | || :|||||| Target 5' aacaaatGACTGTATCTAGGCa 3'	689 - 710	127.00	-15.11
2	miRNA 3' gugaCGUCAGAGUCGGAUCCGu 5' | || | | ||||:||: Target 5' gcacGAAGGCCCCGCCTGGGTt 3'	127 - 148	126.00	-16.90
3	miRNA 3' guGACGUCAGAGU-CGGAUCCGu 5' || | | |:| ||||| | Target 5' atCTTCTTTATTATTCCTAGTCt 3'	481 - 503	116.00	-6.50

Mutant ID	Mutant Position	Mutant Source
1181757	141	ClinVar
COSN30150449	14	COSMIC
COSN30103496	23	COSMIC
COSN30158948	39	COSMIC
COSN30132230	42	COSMIC
COSN30516222	43	COSMIC
COSN30103063	46	COSMIC
COSN31778708	139	COSMIC
COSN28692661	141	COSMIC
COSN26565442	275	COSMIC
COSN26586988	277	COSMIC
COSN26695644	358	COSMIC
COSN21493019	401	COSMIC
COSN31538760	415	COSMIC
COSN30542455	473	COSMIC
COSN31520218	586	COSMIC
COSN4874262	662	COSMIC
COSN29312227	693	COSMIC
COSN20105759	989	COSMIC
COSN31601095	1261	COSMIC
COSN26565441	1279	COSMIC
rs1050969	630	GWAS

Mutant ID	Mutant Position	Mutant Source
rs772416391	1	dbSNP
rs1363054120	5	dbSNP
rs746104666	6	dbSNP
rs138885279	7	dbSNP
rs201026583	21	dbSNP
rs370999476	25	dbSNP
rs1379414148	28	dbSNP
rs374468113	34	dbSNP
rs779653709	34	dbSNP
rs1310507515	35	dbSNP
rs1052877831	42	dbSNP
rs1249826688	43	dbSNP
rs577208168	50	dbSNP
rs1362646641	52	dbSNP
rs935710808	56	dbSNP
rs558818891	57	dbSNP
rs1023113371	60	dbSNP
rs534246869	72	dbSNP
rs1013083230	76	dbSNP
rs985276127	83	dbSNP
rs566706590	84	dbSNP
rs1470345987	95	dbSNP
rs147192922	96	dbSNP
rs536470594	97	dbSNP
rs1360016102	107	dbSNP
rs893411821	113	dbSNP
rs879064190	114	dbSNP
rs1434367191	118	dbSNP
rs1174442324	122	dbSNP
rs922583457	128	dbSNP
rs1176471481	130	dbSNP
rs977061728	139	dbSNP
rs1376248296	140	dbSNP
rs3191333	141	dbSNP
rs1354896113	142	dbSNP
rs1014855565	149	dbSNP
rs548124839	158	dbSNP
rs1365701823	161	dbSNP
rs75455872	167	dbSNP
rs944798750	168	dbSNP
rs1192169532	170	dbSNP
rs752557515	171	dbSNP
rs1217329655	178	dbSNP
rs1028242356	190	dbSNP
rs532126425	206	dbSNP
rs1261906250	211	dbSNP
rs1050723086	212	dbSNP
rs1001752009	216	dbSNP
rs1438728726	216	dbSNP
rs1220425115	227	dbSNP
rs571311515	229	dbSNP
rs930503239	245	dbSNP
rs1489230263	253	dbSNP
rs764753005	262	dbSNP
rs1199530980	273	dbSNP
rs906020885	277	dbSNP
rs1211118989	282	dbSNP
rs1476840529	284	dbSNP
rs113295876	296	dbSNP
rs1172719813	305	dbSNP
rs1046007480	312	dbSNP
rs1404522857	320	dbSNP
rs1254015465	325	dbSNP
rs1406935701	335	dbSNP
rs1232187012	336	dbSNP
rs1339931835	337	dbSNP
rs767362094	339	dbSNP
rs891484307	343	dbSNP
rs371471779	346	dbSNP
rs935743387	350	dbSNP
rs1339907267	354	dbSNP
rs1288081757	355	dbSNP
rs1313599208	359	dbSNP
rs1222750773	362	dbSNP
rs940576381	365	dbSNP
rs1487002485	374	dbSNP
rs925685204	381	dbSNP
rs774493439	384	dbSNP
rs927662434	388	dbSNP
rs143622457	392	dbSNP
rs1472390097	393	dbSNP
rs537662986	404	dbSNP
rs1415684233	410	dbSNP
rs373863236	414	dbSNP
rs763139201	415	dbSNP
rs1462782112	432	dbSNP
rs1320323059	434	dbSNP
rs1327532983	438	dbSNP
rs907890572	447	dbSNP
rs983378665	448	dbSNP
rs542758749	451	dbSNP
rs952047284	460	dbSNP
rs1027774542	468	dbSNP
rs1422283214	480	dbSNP
rs1188118378	481	dbSNP
rs1284834592	482	dbSNP
rs1350984039	483	dbSNP
rs184619832	485	dbSNP
rs1284283869	486	dbSNP
rs999128646	487	dbSNP
rs1185328107	489	dbSNP
rs970272735	489	dbSNP
rs1239031316	490	dbSNP
rs1444996158	490	dbSNP
rs1024868943	497	dbSNP
rs967607720	502	dbSNP
rs1379950237	505	dbSNP
rs1014525820	517	dbSNP
rs770078734	518	dbSNP
rs1160383751	523	dbSNP
rs1018977745	524	dbSNP
rs1414465949	538	dbSNP
rs892016927	542	dbSNP
rs1031343706	546	dbSNP
rs12547834	549	dbSNP
rs904179156	551	dbSNP
rs1308904741	559	dbSNP
rs1480807511	560	dbSNP
rs889088929	563	dbSNP
rs1049517936	566	dbSNP
rs1279697464	577	dbSNP
rs932370577	580	dbSNP
rs1216687412	585	dbSNP
rs901019802	586	dbSNP
rs1317288459	592	dbSNP
rs1236070821	609	dbSNP
rs781543183	616	dbSNP
rs1184241638	617	dbSNP
rs1364496870	624	dbSNP
rs191662533	626	dbSNP
rs939945033	629	dbSNP
rs1050969	630	dbSNP
rs1470558816	634	dbSNP
rs1036592647	638	dbSNP
rs1398556170	649	dbSNP
rs983997339	651	dbSNP
rs940637305	656	dbSNP
rs188298949	664	dbSNP
rs1046081298	666	dbSNP
rs920571501	675	dbSNP
rs1230478844	681	dbSNP
rs540246852	682	dbSNP
rs980226648	683	dbSNP
rs947731923	685	dbSNP
rs916208552	693	dbSNP
rs970517253	695	dbSNP
rs1167744867	699	dbSNP
rs1024484280	700	dbSNP
rs1366225313	702	dbSNP
rs926170256	704	dbSNP
rs1186373268	710	dbSNP
rs1419343789	715	dbSNP
rs1239764559	718	dbSNP
rs1271129444	725	dbSNP
rs977972640	731	dbSNP
rs1457163405	733	dbSNP
rs747364732	747	dbSNP
rs375649565	752	dbSNP
rs536609520	755	dbSNP
rs1463874154	756	dbSNP
rs1031961822	762	dbSNP
rs1389572271	770	dbSNP
rs1384658189	776	dbSNP
rs1304490681	780	dbSNP
rs1000435798	796	dbSNP
rs1345588827	796	dbSNP
rs904207664	800	dbSNP
rs1028378229	801	dbSNP
rs1354313154	804	dbSNP
rs1019217673	805	dbSNP
rs1009117148	812	dbSNP
rs996618457	819	dbSNP
rs1379469923	827	dbSNP
rs1029380634	833	dbSNP
rs1307366487	836	dbSNP
rs900881424	840	dbSNP
rs1260302433	845	dbSNP
rs1430742955	846	dbSNP
rs1194361450	848	dbSNP
rs1368241350	852	dbSNP
rs1456125896	854	dbSNP
rs994959275	857	dbSNP
rs1372222774	862	dbSNP
rs1418584350	865	dbSNP
rs1326052094	868	dbSNP
rs1040770604	869	dbSNP
rs899228977	872	dbSNP
rs1363991518	873	dbSNP
rs1382701291	876	dbSNP
rs148334775	876	dbSNP
rs1338455026	878	dbSNP
rs376319855	884	dbSNP
rs1048319956	887	dbSNP
rs931197123	895	dbSNP
rs1215991434	897	dbSNP
rs1046300326	899	dbSNP
rs947949868	903	dbSNP
rs920617112	904	dbSNP
rs1355139421	906	dbSNP
rs980474906	909	dbSNP
rs1443138959	912	dbSNP
rs1381711643	917	dbSNP
rs1176398689	943	dbSNP
rs1185756591	948	dbSNP
rs1385508222	959	dbSNP
rs1438802090	968	dbSNP
rs916258804	980	dbSNP
rs1346454968	983	dbSNP
rs866010772	993	dbSNP
rs868528418	994	dbSNP
rs3842195	1001	dbSNP
rs397746174	1001	dbSNP
rs1302172591	1002	dbSNP
rs6935	1018	dbSNP
rs917377243	1019	dbSNP
rs992904354	1021	dbSNP
rs1383817958	1023	dbSNP
rs1239680759	1025	dbSNP
rs1289224828	1026	dbSNP
rs1305043889	1028	dbSNP
rs1318776317	1031	dbSNP
rs977804767	1032	dbSNP
rs1255941326	1040	dbSNP
rs1460338694	1045	dbSNP
rs1205967883	1046	dbSNP
rs1457097095	1048	dbSNP
rs184119705	1053	dbSNP
rs753422024	1058	dbSNP
rs375821965	1062	dbSNP
rs967542872	1070	dbSNP
rs956221197	1081	dbSNP
rs569394051	1088	dbSNP
rs987738200	1090	dbSNP
rs979050781	1093	dbSNP
rs1470882543	1094	dbSNP
rs1337216416	1102	dbSNP
rs953597217	1104	dbSNP
rs1446373961	1105	dbSNP
rs1296643976	1106	dbSNP
rs547521715	1109	dbSNP
rs1027993203	1113	dbSNP
rs996956957	1114	dbSNP
rs963527679	1118	dbSNP
rs1322045911	1119	dbSNP
rs1225871539	1120	dbSNP
rs1264191107	1127	dbSNP
rs1317662565	1134	dbSNP
rs1015430319	1138	dbSNP
rs1434939426	1139	dbSNP
rs965008155	1142	dbSNP
rs557016464	1154	dbSNP
rs1331089278	1156	dbSNP
rs1422714350	1157	dbSNP
rs1408021978	1158	dbSNP
rs1003902695	1174	dbSNP
rs1024733460	1177	dbSNP
rs1443124425	1183	dbSNP
rs1400007097	1187	dbSNP
rs1361930353	1196	dbSNP
rs886958906	1200	dbSNP
rs1343689118	1207	dbSNP
rs1407356500	1208	dbSNP
rs1284512578	1211	dbSNP
rs1317805416	1215	dbSNP
rs1048184440	1222	dbSNP
rs115948454	1262	dbSNP
rs772932960	1270	dbSNP
rs775151449	1270	dbSNP
rs1395456534	1274	dbSNP
rs905068075	1277	dbSNP
rs1289007816	1281	dbSNP
rs1044985458	1283	dbSNP
rs1199444010	1289	dbSNP
rs948763222	1294	dbSNP
rs936344577	1314	dbSNP
rs531311734	1315	dbSNP
rs1188057090	1316	dbSNP
rs1419945975	1317	dbSNP
rs1410804952	1333	dbSNP
rs370479100	1339	dbSNP
rs1193852783	1342	dbSNP
rs1363894893	1349	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.