>RPS14|NM_001025070|3'UTR
   1 ACAAGATTCCTCAAAATATTTTCTGTTAATAAATTGCCTTCATGTAAACTGTTTCAAAAAAAAA

ID	Duplex structure	Position	Score	MFE
1	miRNA 3' ccguauguuagacuGUACAUa 5' |||||| Target 5' taataaattgccttCATGTAa 3'	27 - 47	120.00	-6.10

Mutant ID	Mutant Position	Mutant Source
COSN31611472	39	COSMIC
COSN20488679	61	COSMIC
COSN19626821	64	COSMIC
COSN26859831	84	COSMIC
COSN8492086	171	COSMIC
COSN17598277	205	COSMIC
COSN21346405	701	COSMIC
COSN4917543	1068	COSMIC
COSN4917542	1078	COSMIC
COSN29017255	1112	COSMIC
COSN27916465	1115	COSMIC
COSN24783099	1292	COSMIC
COSN26520621	1328	COSMIC
COSN22798423	1336	COSMIC
COSN24051717	1508	COSMIC
COSN21812915	1550	COSMIC

Mutant ID	Mutant Position	Mutant Source
rs1316182121	7	dbSNP
rs759136657	9	dbSNP
rs537167440	18	dbSNP
rs765964856	19	dbSNP
rs3187814	23	dbSNP
rs1462607115	25	dbSNP
rs1226960371	28	dbSNP
rs762656983	37	dbSNP
rs569735459	38	dbSNP
rs1228882489	39	dbSNP
rs375786077	42	dbSNP
rs1331944371	45	dbSNP
rs865813576	46	dbSNP
rs1394549980	50	dbSNP
rs1236744255	53	dbSNP
rs557990161	57	dbSNP
rs78589669	58	dbSNP
rs376361782	62	dbSNP
rs2070844	64	dbSNP
rs1049336952	65	dbSNP
rs1259477207	66	dbSNP
rs547413476	74	dbSNP
rs774501001	77	dbSNP
rs999894751	83	dbSNP
rs529171012	84	dbSNP
rs898193819	89	dbSNP
rs567349535	90	dbSNP
rs117886463	103	dbSNP
rs1358996012	111	dbSNP
rs1431888333	113	dbSNP
rs1290955979	117	dbSNP
rs1338741107	122	dbSNP
rs756196133	123	dbSNP
rs745911277	126	dbSNP
rs1325755236	129	dbSNP
rs1217455980	130	dbSNP
rs1277795148	131	dbSNP
rs34119373	133	dbSNP
rs373642247	133	dbSNP
rs398102522	133	dbSNP
rs531474297	133	dbSNP
rs1260699987	134	dbSNP
rs530927450	134	dbSNP
rs201554896	135	dbSNP
rs757768541	144	dbSNP
rs751983832	146	dbSNP
rs563395746	147	dbSNP
rs778337430	151	dbSNP
rs1199695910	155	dbSNP
rs1056669405	167	dbSNP
rs1235161722	171	dbSNP
rs1171374803	172	dbSNP
rs545481256	175	dbSNP
rs935190072	181	dbSNP
rs997940378	182	dbSNP
rs923828920	184	dbSNP
rs116575478	192	dbSNP
rs1358949929	193	dbSNP
rs559883668	221	dbSNP
rs141054618	225	dbSNP
rs1444529137	231	dbSNP
rs148157366	232	dbSNP
rs1347511459	238	dbSNP
rs767113436	238	dbSNP
rs910829639	243	dbSNP
rs1332149078	244	dbSNP
rs1351332013	255	dbSNP
rs568807364	259	dbSNP
rs1283708817	261	dbSNP
rs550468441	269	dbSNP
rs1352704207	273	dbSNP
rs1019036565	277	dbSNP
rs1005438319	278	dbSNP
rs1270549372	286	dbSNP
rs768743833	302	dbSNP
rs1028309403	321	dbSNP
rs1449473054	323	dbSNP
rs1197572568	327	dbSNP
rs140602514	329	dbSNP
rs564704432	330	dbSNP
rs1160968139	333	dbSNP
rs1378915843	334	dbSNP
rs1419451021	345	dbSNP
rs115007864	348	dbSNP
rs971462148	351	dbSNP
rs1393177500	355	dbSNP
rs769440564	359	dbSNP
rs1442138281	361	dbSNP
rs557612754	366	dbSNP
rs958852938	368	dbSNP
rs1375924125	370	dbSNP
rs185804184	370	dbSNP
rs1032965412	371	dbSNP
rs1056233811	371	dbSNP
rs1208801725	375	dbSNP
rs1273176132	378	dbSNP
rs935139394	381	dbSNP
rs967032121	390	dbSNP
rs1169520587	394	dbSNP
rs923824147	395	dbSNP
rs1441279588	401	dbSNP
rs1019973074	405	dbSNP
rs997909189	424	dbSNP
rs1253448067	426	dbSNP
rs376782222	428	dbSNP
rs539508153	429	dbSNP
rs1456646705	440	dbSNP
rs1162881602	443	dbSNP
rs1397368733	444	dbSNP
rs900942886	446	dbSNP
rs2545347	455	dbSNP
rs1007759261	457	dbSNP
rs1453208529	459	dbSNP
rs1314615511	464	dbSNP
rs1348121148	483	dbSNP
rs1285107831	485	dbSNP
rs553908685	491	dbSNP
rs1237635675	495	dbSNP
rs889356396	502	dbSNP
rs1355801656	507	dbSNP
rs1340990149	509	dbSNP
rs1196232942	512	dbSNP
rs1049357068	517	dbSNP
rs930891701	519	dbSNP
rs535404536	526	dbSNP
rs1036333926	531	dbSNP
rs919230194	531	dbSNP
rs1187152068	533	dbSNP
rs374675526	537	dbSNP
rs567978689	538	dbSNP
rs1168636510	547	dbSNP
rs1241419293	550	dbSNP
rs1396867705	553	dbSNP
rs1360108364	555	dbSNP
rs1304499382	558	dbSNP
rs991275133	559	dbSNP
rs80135647	564	dbSNP
rs983584621	565	dbSNP
rs1381491513	567	dbSNP
rs950941233	574	dbSNP
rs1277098523	576	dbSNP
rs143823432	578	dbSNP
rs995008798	579	dbSNP
rs1258256380	580	dbSNP
rs925782393	590	dbSNP
rs1200258893	592	dbSNP
rs1472095004	599	dbSNP
rs772273624	600	dbSNP
rs1366249848	604	dbSNP
rs1191772041	608	dbSNP
rs181539285	609	dbSNP
rs1480792265	612	dbSNP
rs1485809914	614	dbSNP
rs1375881627	615	dbSNP
rs1261963170	616	dbSNP
rs1019940525	621	dbSNP
rs796753275	622	dbSNP
rs569705802	624	dbSNP
rs1297181135	631	dbSNP
rs1345644327	633	dbSNP
rs1388037682	641	dbSNP
rs190391347	642	dbSNP
rs1011893923	643	dbSNP
rs896175145	644	dbSNP
rs1056601309	652	dbSNP
rs1356277993	656	dbSNP
rs533445571	658	dbSNP
rs902341793	659	dbSNP
rs1490561023	669	dbSNP
rs527818182	672	dbSNP
rs1265276946	673	dbSNP
rs560108986	701	dbSNP
rs3857421	702	dbSNP
rs1182424598	703	dbSNP
rs900398641	710	dbSNP
rs1038952756	712	dbSNP
rs755532022	714	dbSNP
rs911931410	717	dbSNP
rs898089589	719	dbSNP
rs983940198	725	dbSNP
rs1296519075	744	dbSNP
rs1157790602	746	dbSNP
rs1036301035	761	dbSNP
rs1361650216	763	dbSNP
rs1323275501	764	dbSNP
rs778466059	768	dbSNP
rs547939090	772	dbSNP
rs1291288706	777	dbSNP
rs34778325	777	dbSNP
rs950082764	779	dbSNP
rs1386762303	794	dbSNP
rs1310600060	797	dbSNP
rs79409809	798	dbSNP
rs1379627182	800	dbSNP
rs562319183	803	dbSNP
rs754312655	814	dbSNP
rs576661937	824	dbSNP
rs1285684935	825	dbSNP
rs1322559213	830	dbSNP
rs970233977	835	dbSNP
rs895902767	856	dbSNP
rs1263819769	862	dbSNP
rs116145319	868	dbSNP
rs574374274	875	dbSNP
rs1239980435	878	dbSNP
rs1437690721	884	dbSNP
rs993107271	889	dbSNP
rs576144501	890	dbSNP
rs1034728506	892	dbSNP
rs1162241300	893	dbSNP
rs999600497	902	dbSNP
rs1462022237	905	dbSNP
rs925783248	908	dbSNP
rs1403103677	912	dbSNP
rs902226969	920	dbSNP
rs1022013234	921	dbSNP
rs1230294443	923	dbSNP
rs3900644	927	dbSNP
rs4541646	931	dbSNP
rs1199377797	936	dbSNP
rs750743947	936	dbSNP
rs965078285	938	dbSNP
rs1197926589	945	dbSNP
rs1237897410	963	dbSNP
rs1484098381	965	dbSNP
rs1291885966	966	dbSNP
rs1412659364	974	dbSNP
rs1017953380	977	dbSNP
rs944679595	978	dbSNP
rs890372239	980	dbSNP
rs76920259	981	dbSNP
rs1027798944	982	dbSNP
rs1450677538	983	dbSNP
rs1301415003	985	dbSNP
rs1276382459	987	dbSNP
rs761645467	993	dbSNP
rs2248595	1001	dbSNP
rs1316127627	1004	dbSNP
rs1217986378	1012	dbSNP
rs185540777	1017	dbSNP
rs1313841968	1018	dbSNP
rs1015171023	1019	dbSNP
rs948851681	1028	dbSNP
rs916113400	1032	dbSNP
rs1488451640	1034	dbSNP
rs1014462450	1039	dbSNP
rs1434719911	1042	dbSNP
rs574289915	1046	dbSNP
rs1477193269	1051	dbSNP
rs755286839	1052	dbSNP
rs993074667	1052	dbSNP
rs1172617304	1053	dbSNP
rs1352123344	1054	dbSNP
rs960278945	1055	dbSNP
rs1056213451	1057	dbSNP
rs1032347042	1059	dbSNP
rs1358938643	1061	dbSNP
rs556079092	1062	dbSNP
rs1398999083	1069	dbSNP
rs1167878899	1070	dbSNP
rs1275460791	1072	dbSNP
rs66951851	1072	dbSNP
rs70973580	1072	dbSNP
rs1419729176	1073	dbSNP
rs1190438551	1078	dbSNP
rs1217403217	1087	dbSNP
rs1476885826	1090	dbSNP
rs1354124728	1092	dbSNP
rs1218390107	1097	dbSNP
rs1283481338	1099	dbSNP
rs1248228630	1103	dbSNP
rs1487731794	1103	dbSNP
rs1198974770	1104	dbSNP
rs1194259212	1106	dbSNP
rs904632176	1106	dbSNP
rs751135911	1108	dbSNP
rs1042884400	1109	dbSNP
rs75062706	1109	dbSNP
rs945905867	1110	dbSNP
rs74396409	1112	dbSNP
rs913148948	1112	dbSNP
rs1308337803	1113	dbSNP
rs976625177	1113	dbSNP
rs943941465	1115	dbSNP
rs910860093	1123	dbSNP
rs113793692	1124	dbSNP
rs1210062875	1124	dbSNP
rs1274144681	1124	dbSNP
rs1291480293	1124	dbSNP
rs1306731071	1124	dbSNP
rs373350422	1124	dbSNP
rs547191575	1124	dbSNP
rs555786168	1124	dbSNP
rs569263364	1124	dbSNP
rs758320152	1124	dbSNP
rs770261226	1124	dbSNP
rs1217843785	1125	dbSNP
rs1220060050	1138	dbSNP
rs1252958982	1138	dbSNP
rs1449358264	1138	dbSNP
rs1392898642	1139	dbSNP
rs537734751	1140	dbSNP
rs1304616934	1141	dbSNP
rs1491565714	1141	dbSNP
rs1491468231	1142	dbSNP
rs1375298597	1150	dbSNP
rs1021987289	1152	dbSNP
rs1010644960	1153	dbSNP
rs900343079	1163	dbSNP
rs780672319	1166	dbSNP
rs1017353845	1170	dbSNP
rs1400955643	1171	dbSNP
rs1448811171	1173	dbSNP
rs13161334	1176	dbSNP
rs116087717	1183	dbSNP
rs1354757263	1186	dbSNP
rs1285562952	1194	dbSNP
rs10463296	1195	dbSNP
rs769685067	1197	dbSNP
rs1427057174	1199	dbSNP
rs1174009064	1207	dbSNP
rs566127446	1217	dbSNP
rs1439035794	1223	dbSNP
rs1015055081	1225	dbSNP
rs1236785008	1229	dbSNP
rs1424275180	1232	dbSNP
rs1014431173	1238	dbSNP
rs1188630151	1252	dbSNP
rs13181401	1253	dbSNP
rs1034337885	1254	dbSNP
rs1164305488	1257	dbSNP
rs1424415778	1262	dbSNP
rs13161156	1263	dbSNP
rs556310321	1266	dbSNP
rs915998771	1272	dbSNP
rs562256088	1274	dbSNP
rs1208362180	1275	dbSNP
rs1010326451	1278	dbSNP
rs1314130366	1279	dbSNP
rs778324415	1285	dbSNP
rs368268853	1287	dbSNP
rs938860435	1289	dbSNP
rs532019510	1299	dbSNP
rs1413717367	1300	dbSNP
rs978100212	1303	dbSNP
rs966342248	1306	dbSNP
rs1352188405	1308	dbSNP
rs779008405	1309	dbSNP
rs1256750020	1310	dbSNP
rs943912124	1313	dbSNP
rs911164910	1316	dbSNP
rs1258619649	1324	dbSNP
rs563946250	1325	dbSNP
rs989109729	1328	dbSNP
rs1478828158	1329	dbSNP
rs545748925	1336	dbSNP
rs1445420920	1337	dbSNP
rs1372454301	1339	dbSNP
rs1466435337	1347	dbSNP
rs1376842012	1348	dbSNP
rs13161417	1349	dbSNP
rs972862047	1350	dbSNP
rs780440949	1358	dbSNP
rs539556028	1359	dbSNP
rs561156028	1365	dbSNP
rs1161280556	1369	dbSNP
rs908027056	1387	dbSNP
rs1326360584	1389	dbSNP
rs1234593000	1392	dbSNP
rs1258193039	1397	dbSNP
rs1008711229	1398	dbSNP
rs193256392	1399	dbSNP
rs1026216098	1400	dbSNP
rs1258442302	1407	dbSNP
rs1216352276	1412	dbSNP
rs1487479524	1414	dbSNP
rs1288597610	1415	dbSNP
rs1191615851	1421	dbSNP
rs1240438413	1421	dbSNP
rs753070284	1421	dbSNP
rs993854361	1422	dbSNP
rs1484238430	1429	dbSNP
rs899161445	1432	dbSNP
rs1200899229	1441	dbSNP
rs13161261	1442	dbSNP
rs10463295	1443	dbSNP
rs1001542470	1445	dbSNP
rs894534050	1446	dbSNP
rs1226076414	1449	dbSNP
rs1417404693	1450	dbSNP
rs969082717	1474	dbSNP
rs112783163	1483	dbSNP
rs1387905160	1484	dbSNP
rs13161099	1487	dbSNP
rs891902172	1492	dbSNP
rs924808425	1494	dbSNP
rs1398999928	1495	dbSNP
rs1213904116	1504	dbSNP
rs763759253	1508	dbSNP
rs1488830331	1509	dbSNP
rs1211672628	1510	dbSNP
rs947602021	1511	dbSNP
rs371133298	1516	dbSNP
rs13160685	1518	dbSNP
rs539777224	1519	dbSNP
rs373419440	1522	dbSNP
rs1157882353	1526	dbSNP
rs989080049	1527	dbSNP
rs1050146293	1529	dbSNP
rs1290383967	1533	dbSNP
rs964365776	1534	dbSNP
rs757950961	1535	dbSNP
rs147770582	1542	dbSNP
rs34583186	1555	dbSNP
rs796109530	1555	dbSNP
rs183666345	1560	dbSNP
rs752194564	1561	dbSNP
rs1379558901	1563	dbSNP
rs939756989	1568	dbSNP
rs1306598608	1569	dbSNP
rs765121644	1574	dbSNP
rs1418865695	1578	dbSNP
rs1193300706	1582	dbSNP
rs1271275928	1583	dbSNP
rs954558980	1585	dbSNP
rs1476946057	1586	dbSNP
rs1026602783	1596	dbSNP
rs1456251175	1599	dbSNP
rs1265856896	1600	dbSNP
rs1414100678	1602	dbSNP
rs1425129683	1602	dbSNP
rs992950921	1612	dbSNP
rs1416522201	1625	dbSNP
rs960238410	1625	dbSNP
rs1171985222	1630	dbSNP
rs560983502	1632	dbSNP
rs779728168	1632	dbSNP
rs993331110	1637	dbSNP
rs1380168864	1639	dbSNP
rs963254812	1642	dbSNP
rs1264131190	1648	dbSNP
rs1218754071	1649	dbSNP
rs535935167	1649	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.