ID	Duplex structure	Position	Score	MFE
1	miRNA 3' acggaGGAGGUCCU-AGGUGUGu 5' ||| || | ||||||| Target 5' gaaagCCT-GAGTACTCCACACt 3'	908 - 929	148.00	-14.50
2	miRNA 3' acggaGGAGGUCCUAGGUGUGu 5' :|| :||| | ||||| Target 5' gagggTCTGTAGGTTGCACACt 3'	853 - 874	129.00	-16.10
3	miRNA 3' acGGAGGAGGUCCUAGGUGUGu 5' ::|:||| || |||| Target 5' ttTTTTCTC-----TCAACACc 3'	1173 - 1189	115.00	-7.40

Mutant ID	Mutant Position	Mutant Source
337171	1166	ClinVar
337172	1167	ClinVar
337173	1268	ClinVar
898899	1315	ClinVar
898900	1323	ClinVar
898901	1365	ClinVar
337174	1419	ClinVar
337175	1437	ClinVar
895937	1443	ClinVar
895938	1482	ClinVar
COSN31491713	2	COSMIC
COSN30569488	8	COSMIC
COSN31518289	17	COSMIC
COSN31482386	30	COSMIC
COSN14532144	93	COSMIC
COSN9391534	100	COSMIC
COSN20288801	186	COSMIC
COSN26556738	250	COSMIC
COSN20090570	279	COSMIC
COSN31601278	302	COSMIC
COSN26670157	313	COSMIC
COSN5865552	336	COSMIC
COSN31588545	347	COSMIC
COSN31559515	535	COSMIC
COSN31545991	562	COSMIC
COSN26601554	580	COSMIC
COSN6559526	605	COSMIC
COSN31563363	643	COSMIC
COSN31489295	662	COSMIC
COSN31518105	716	COSMIC
COSN22229193	749	COSMIC
COSN31959778	769	COSMIC
COSN16524245	775	COSMIC
COSN28669283	869	COSMIC
COSN28250198	914	COSMIC
COSN20090571	1017	COSMIC
COSN27886919	1152	COSMIC
COSN31529730	1180	COSMIC
COSN28249874	1182	COSMIC

Mutant ID	Mutant Position	Mutant Source
rs1171039097	1	dbSNP
rs776431969	8	dbSNP
rs1359092024	10	dbSNP
rs1412686279	11	dbSNP
rs1332323028	12	dbSNP
rs372099842	13	dbSNP
rs1448793530	17	dbSNP
rs1315047771	19	dbSNP
rs1338624920	21	dbSNP
rs749458057	23	dbSNP
rs769156900	30	dbSNP
rs774638304	31	dbSNP
rs1342163005	34	dbSNP
rs762233743	37	dbSNP
rs1277360846	39	dbSNP
rs1312288358	50	dbSNP
rs952350922	58	dbSNP
rs1180192001	70	dbSNP
rs1483002521	76	dbSNP
rs1236811167	86	dbSNP
rs1204174398	92	dbSNP
rs1233656160	98	dbSNP
rs1486508152	104	dbSNP
rs984413834	106	dbSNP
rs1484269551	109	dbSNP
rs148739699	112	dbSNP
rs1342436786	114	dbSNP
rs1297358338	120	dbSNP
rs1417541111	123	dbSNP
rs940192158	125	dbSNP
rs1417193735	126	dbSNP
rs1369041877	129	dbSNP
rs1475832951	136	dbSNP
rs1430875852	141	dbSNP
rs1165445622	143	dbSNP
rs530472867	149	dbSNP
rs1163012698	153	dbSNP
rs1423286919	155	dbSNP
rs1407707065	158	dbSNP
rs1414665222	163	dbSNP
rs1188510143	164	dbSNP
rs1476155208	165	dbSNP
rs1249259783	166	dbSNP
rs1480869596	167	dbSNP
rs992982477	167	dbSNP
rs1252678305	168	dbSNP
rs1218975506	174	dbSNP
rs1320547079	177	dbSNP
rs549048191	179	dbSNP
rs917340680	183	dbSNP
rs1235611950	184	dbSNP
rs1349174972	186	dbSNP
rs948859314	192	dbSNP
rs1376036100	195	dbSNP
rs1291961810	201	dbSNP
rs1457616314	206	dbSNP
rs1044866892	220	dbSNP
rs1411469041	222	dbSNP
rs904570942	223	dbSNP
rs1354525598	233	dbSNP
rs1455769270	234	dbSNP
rs1409644134	236	dbSNP
rs1181427467	237	dbSNP
rs1419417499	239	dbSNP
rs1245439519	240	dbSNP
rs935963530	242	dbSNP
rs1337599363	243	dbSNP
rs1053637181	246	dbSNP
rs1487960386	251	dbSNP
rs1273503817	264	dbSNP
rs1215007075	266	dbSNP
rs142372744	277	dbSNP
rs15351	278	dbSNP
rs1268023991	288	dbSNP
rs1009830797	292	dbSNP
rs1319055395	295	dbSNP
rs1299662967	302	dbSNP
rs1386364304	304	dbSNP
rs371796804	305	dbSNP
rs1328239893	308	dbSNP
rs1432962922	311	dbSNP
rs1344621433	312	dbSNP
rs868266117	313	dbSNP
rs562646394	314	dbSNP
rs990394448	317	dbSNP
rs1486164948	320	dbSNP
rs796159921	322	dbSNP
rs534733325	325	dbSNP
rs996646224	332	dbSNP
rs1253219143	341	dbSNP
rs1195159153	343	dbSNP
rs1028075771	354	dbSNP
rs1246905898	357	dbSNP
rs952362235	361	dbSNP
rs983754653	364	dbSNP
rs1254828628	372	dbSNP
rs1166772986	378	dbSNP
rs1232969237	378	dbSNP
rs1390206551	379	dbSNP
rs1226499473	381	dbSNP
rs1431271658	382	dbSNP
rs1015867868	387	dbSNP
rs961626588	388	dbSNP
rs1382644226	390	dbSNP
rs546694561	392	dbSNP
rs571712952	396	dbSNP
rs539230166	398	dbSNP
rs867903069	399	dbSNP
rs1175075474	401	dbSNP
rs1447298989	401	dbSNP
rs6711750	403	dbSNP
rs1193273739	404	dbSNP
rs542611069	406	dbSNP
rs1254658584	407	dbSNP
rs926003757	410	dbSNP
rs936014197	419	dbSNP
rs1282935879	427	dbSNP
rs1429890230	430	dbSNP
rs1203210023	431	dbSNP
rs1298450528	432	dbSNP
rs1367371874	437	dbSNP
rs1271054365	438	dbSNP
rs1229679322	458	dbSNP
rs1053024782	464	dbSNP
rs1232376902	465	dbSNP
rs536237196	467	dbSNP
rs1279873920	471	dbSNP
rs866919338	473	dbSNP
rs1375773820	478	dbSNP
rs1314498025	479	dbSNP
rs1427660599	482	dbSNP
rs1346217852	485	dbSNP
rs1168185796	489	dbSNP
rs1476090835	490	dbSNP
rs1202519257	493	dbSNP
rs1282815268	494	dbSNP
rs913204821	506	dbSNP
rs184837848	508	dbSNP
rs1187391928	509	dbSNP
rs945343846	513	dbSNP
rs1259962509	515	dbSNP
rs572981137	516	dbSNP
rs1446960833	519	dbSNP
rs1482963105	520	dbSNP
rs1041354002	531	dbSNP
rs1197813121	540	dbSNP
rs1354284705	542	dbSNP
rs540302323	544	dbSNP
rs1264952628	549	dbSNP
rs901047641	550	dbSNP
rs144911618	553	dbSNP
rs189711755	557	dbSNP
rs1407740658	563	dbSNP
rs1329069013	564	dbSNP
rs1411323189	566	dbSNP
rs888167879	569	dbSNP
rs545194929	570	dbSNP
rs1394079550	571	dbSNP
rs1180702708	574	dbSNP
rs1466395839	575	dbSNP
rs1233843420	581	dbSNP
rs1174140129	582	dbSNP
rs1382451569	588	dbSNP
rs1267022322	589	dbSNP
rs1214387799	590	dbSNP
rs1400054167	590	dbSNP
rs1337103806	591	dbSNP
rs1321062296	592	dbSNP
rs1226528403	593	dbSNP
rs1391009441	593	dbSNP
rs1438785764	595	dbSNP
rs1279932835	600	dbSNP
rs1302500481	604	dbSNP
rs1328990250	607	dbSNP
rs748649521	610	dbSNP
rs1331864210	614	dbSNP
rs1396076361	617	dbSNP
rs758737664	618	dbSNP
rs560991019	620	dbSNP
rs1278165339	625	dbSNP
rs1014546284	632	dbSNP
rs1024938276	641	dbSNP
rs1477278722	645	dbSNP
rs1377263991	647	dbSNP
rs1194545491	650	dbSNP
rs1469847286	654	dbSNP
rs1350329421	656	dbSNP
rs1206678255	662	dbSNP
rs535170379	672	dbSNP
rs771181010	679	dbSNP
rs1342668115	682	dbSNP
rs1302190722	683	dbSNP
rs970259542	685	dbSNP
rs1465902185	690	dbSNP
rs1867880	693	dbSNP
rs1211243117	694	dbSNP
rs1429503543	697	dbSNP
rs1346298077	701	dbSNP
rs980209264	712	dbSNP
rs1433435376	713	dbSNP
rs1394885634	715	dbSNP
rs1174440135	717	dbSNP
rs1455753618	725	dbSNP
rs528550929	726	dbSNP
rs1185999529	729	dbSNP
rs926054748	742	dbSNP
rs1242607591	744	dbSNP
rs957473607	753	dbSNP
rs1440434587	764	dbSNP
rs1472139632	773	dbSNP
rs191347244	775	dbSNP
rs1211074871	778	dbSNP
rs1349598237	782	dbSNP
rs1390710350	790	dbSNP
rs988841637	792	dbSNP
rs913267650	793	dbSNP
rs1362093910	794	dbSNP
rs1459975102	798	dbSNP
rs1446487539	802	dbSNP
rs1375156011	803	dbSNP
rs1313871355	805	dbSNP
rs1437043321	807	dbSNP
rs1325336696	809	dbSNP
rs1368931892	813	dbSNP
rs1170067959	814	dbSNP
rs944702983	816	dbSNP
rs1388750477	821	dbSNP
rs1474188092	825	dbSNP
rs1188379943	828	dbSNP
rs1256810184	828	dbSNP
rs1486559712	831	dbSNP
rs1249232250	838	dbSNP
rs1050108	845	dbSNP
rs1040972738	847	dbSNP
rs1189695949	848	dbSNP
rs1307513466	857	dbSNP
rs1274512537	858	dbSNP
rs563435482	866	dbSNP
rs922479891	874	dbSNP
rs1229375817	877	dbSNP
rs1290796235	879	dbSNP
rs1294499613	879	dbSNP
rs1333378698	882	dbSNP
rs1233158991	886	dbSNP
rs932486523	887	dbSNP
rs1005336170	890	dbSNP
rs1461045183	890	dbSNP
rs550275542	890	dbSNP
rs888264150	890	dbSNP
rs1417054644	892	dbSNP
rs11537669	901	dbSNP
rs1165619589	903	dbSNP
rs1488483037	905	dbSNP
rs1248174300	914	dbSNP
rs1176207786	915	dbSNP
rs1037185525	918	dbSNP
rs1211335116	922	dbSNP
rs1234315806	924	dbSNP
rs1211262858	926	dbSNP
rs778027496	927	dbSNP
rs1482634166	928	dbSNP
rs745453983	936	dbSNP
rs1024572825	937	dbSNP
rs1327454679	940	dbSNP
rs1306742962	945	dbSNP
rs1474196562	949	dbSNP
rs970689927	950	dbSNP
rs1001721327	958	dbSNP
rs1375788347	958	dbSNP
rs1440227577	969	dbSNP
rs1369199015	975	dbSNP
rs1395355837	978	dbSNP
rs1459501859	979	dbSNP
rs780961774	979	dbSNP
rs1033168197	981	dbSNP
rs1166426235	984	dbSNP
rs957528509	995	dbSNP
rs1361776737	1001	dbSNP
rs1410624452	1022	dbSNP
rs530858793	1031	dbSNP
rs1310265555	1033	dbSNP
rs193153527	1034	dbSNP
rs1409676015	1045	dbSNP
rs1353893910	1046	dbSNP
rs1191402246	1053	dbSNP
rs1414711596	1054	dbSNP
rs1253100585	1058	dbSNP
rs1020750494	1062	dbSNP
rs377450065	1063	dbSNP
rs1260713803	1066	dbSNP
rs1240186938	1068	dbSNP
rs769445498	1069	dbSNP
rs1246324876	1074	dbSNP
rs1301478989	1081	dbSNP
rs528107494	1083	dbSNP
rs371101314	1084	dbSNP
rs1371743567	1087	dbSNP
rs1205363146	1091	dbSNP
rs1382671421	1096	dbSNP
rs976460747	1096	dbSNP
rs922563709	1108	dbSNP
rs1484566600	1115	dbSNP
rs1454093295	1117	dbSNP
rs1346775237	1122	dbSNP
rs1171306013	1123	dbSNP
rs1453427925	1123	dbSNP
rs932581248	1141	dbSNP
rs1194943870	1144	dbSNP
rs985362499	1155	dbSNP
rs370014861	1166	dbSNP
rs909754447	1166	dbSNP
rs1036790776	1167	dbSNP
rs1348859473	1167	dbSNP
rs886056355	1167	dbSNP
rs1305968246	1169	dbSNP
rs896867660	1170	dbSNP
rs1325970199	1172	dbSNP
rs1382731073	1178	dbSNP
rs571321000	1178	dbSNP
rs1363731984	1179	dbSNP
rs1181271111	1180	dbSNP
rs1256752195	1182	dbSNP
rs1425680790	1184	dbSNP
rs1168466588	1185	dbSNP
rs1459993932	1190	dbSNP
rs1372026232	1191	dbSNP
rs1194450449	1192	dbSNP
rs1430810005	1200	dbSNP
rs749255803	1201	dbSNP
rs1437425988	1207	dbSNP
rs1430661455	1210	dbSNP
rs1486229480	1213	dbSNP
rs538854890	1218	dbSNP
rs1282699198	1233	dbSNP
rs1194325563	1234	dbSNP
rs905521973	1235	dbSNP
rs15352	1248	dbSNP
rs1001773700	1252	dbSNP
rs1033223988	1253	dbSNP
rs759788569	1268	dbSNP
rs1465842371	1270	dbSNP
rs1303982107	1275	dbSNP
rs1010329050	1283	dbSNP
rs1020382748	1290	dbSNP
rs1355892117	1295	dbSNP
rs1335730437	1302	dbSNP
rs1063503	1304	dbSNP
rs1389337847	1308	dbSNP
rs551196531	1314	dbSNP
rs867667606	1315	dbSNP
rs149495444	1323	dbSNP
rs1164880630	1327	dbSNP
rs1260077362	1345	dbSNP
rs976174967	1345	dbSNP
rs914377375	1346	dbSNP
rs1179848329	1350	dbSNP
rs1029437962	1351	dbSNP
rs3209936	1357	dbSNP
rs953351844	1365	dbSNP
rs3209940	1367	dbSNP
rs1332821220	1373	dbSNP
rs1276321340	1384	dbSNP
rs985377047	1386	dbSNP
rs909765667	1389	dbSNP
rs1335176210	1393	dbSNP
rs1285740639	1395	dbSNP
rs1236696498	1402	dbSNP
rs1334790056	1418	dbSNP
rs886056356	1419	dbSNP
rs1345531861	1420	dbSNP
rs1448306589	1425	dbSNP
rs1391688425	1430	dbSNP
rs377381751	1437	dbSNP
rs972954833	1440	dbSNP
rs1484208583	1443	dbSNP
rs1157180478	1444	dbSNP
rs1469993083	1452	dbSNP
rs1364569447	1466	dbSNP
rs554866641	1474	dbSNP
rs949866556	1482	dbSNP
rs1252467856	1497	dbSNP
rs1450161562	1499	dbSNP
rs1190813876	1503	dbSNP
rs1468853701	1507	dbSNP
rs1292008040	1509	dbSNP
rs1203132381	1510	dbSNP
rs772325888	1510	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.

- Nature, 2013

Circular RNAs (circRNAs) in animals are an enigmatic class of RNA with unknown function. To explore circRNAs systematically, we sequenced and computationally analysed human, mouse and nematode RNA. We detected thousands of well-expressed, stable circRNAs, often showing tissue/developmental-stage-specific expression. Sequence analysis indicated important regulatory functions for circRNAs. We found that a human circRNA, antisense to the cerebellar degeneration-related protein 1 transcript (CDR1as), is densely bound by microRNA (miRNA) effector complexes and harbours 63 conserved binding sites for the ancient miRNA miR-7. Further analyses indicated that CDR1as functions to bind miR-7 in neuronal tissues. Human CDR1as expression in zebrafish impaired midbrain development, similar to knocking down miR-7, suggesting that CDR1as is a miRNA antagonist with a miRNA-binding capacity ten times higher than any other known transcript. Together, our data provide evidence that circRNAs form a large class of post-transcriptional regulators. Numerous circRNAs form by head-to-tail splicing of exons, suggesting previously unrecognized regulatory potential of coding sequences.

- 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.