>CCNA2|NM_001237|3'UTR
   1 CAATGAAAGACTGCCTTTGTTTTCTAAGATGTAAATCACTCAAAGTATATGGTGTACAGTTTTTAACTTAGGTTTTAATT
  81 TTACAATCATTTCTGAATACAGAAGTTGTGGCCAAGTACAAATTATGGTATCTATTACTTTTTAAATGGTTTTAATTTGT
 161 ATATCTTTTGTATATGTATCTGTCTTAGATATTTGGCTAATTTTAAGTGGTTTTGTTAAAGTATTAATGATGCCAGCTGT
 241 CAGGATAATAAATTGATTTGGAAAACTTTGCAAGTCAAATTTAACTTCTTCAGGATTTTGCTTAGTAAAGAAGTTTACTT
 321 GGTTTACTATATAATGGGAAGTGAAAAGCCTTCCTCTAAAATTAAAGTAGGTTTAGGAAAACAGACCCTCAAATTCTGAC
 401 ATTCATTTTCCTAAGCAACTGGATCAATTTGCTGACTTGGGCATAATCTAATCTAAGCATATCTGAATACAGTATTCAGA
 481 GATAGATACAGTAGAGATTCCCCAGACTTTTTCGCTCTTTGTAAAACCTGTTTGTTTAGGTTTTGCGAGGTAAACTCAAC
 561 AGAGGTTGGGAGTGGAAGAGGGTGGGAAGCTTATATGCAAATTAACAGACGAGAAATGCTCCAGAAGGTTTATTATTTTA
 641 AAGCACATTAAAAACAAAAAACTATTTTTAAAATCCTGCTAGATTTTATAATGGATTTGTGAATAAAAAATACCCAGGGT
 721 TCTCAGAATGGAATAAATATCCCTTTTAATAGTTATATATACAGATATACAACTGTTAGCTTTAATTGGCAGCTCTCTTC
 801 TTTTTTCTTCTTTTCACTGGCTTTTTACTTGGTGCTTTTTCTTGTTTTGCACTGGTGGTCTGTGTTCTGTGAATAAAGCA
 881 AAGTAAGAATTTACTAAGAGTATGTTAAGTTTTGGATTATTGAAATAAGAGGCATTTCTTAGTTTTCCAGTAGGATCTAA
 961 AATGTGTCAGCTATGAGTAAGACTGGCATCCAAGAAGTTTATATTATAGATTTAGGTCCTAATTTTTATAAATCACAAGG
1041 TAAAAAAATCACAGAACAGATGGATCTCTAATGAAAAAGGGATGTCTTTTTGTTTATAGTCATGTGGCAAGATGAGAGTA
1121 AAACCAGAGAGCAAACCTCTATAAGTGTTGAGTATATGTATACATTTGAAATAAACCAGAAATTTGTTACCTTA

ID	Duplex structure	Position	Score	MFE
1	miRNA 3' cgAGGACAGGUUGACCGAg 5' |:|| |:| ||||||| Target 5' tcTTCTTTTC-ACTGGCTt 3'	806 - 823	156.00	-18.20
2	miRNA 3' cgAGGACAGGUUGACCGAg 5' |||| ||||||| | Target 5' ttTCCTAAGCAACTGGATc 3'	407 - 425	129.00	-15.90
3	miRNA 3' cgaggaCAGGUUGACCGag 5' || :|||||| Target 5' ctatgaGTAAGACTGGCat 3'	971 - 989	125.00	-10.90

Mutant ID	Mutant Position	Mutant Source
COSN30531420	23	COSMIC
COSN26969650	38	COSMIC
COSN30488750	51	COSMIC
COSN31590377	121	COSMIC
COSN31542979	132	COSMIC
COSN30504157	144	COSMIC
COSN31540644	222	COSMIC
COSN31552520	232	COSMIC
COSN32063465	514	COSMIC
COSN31558504	630	COSMIC
COSN31582116	644	COSMIC
COSN9587811	678	COSMIC
COSN505717	704	COSMIC
COSN30129112	747	COSMIC
COSN30106020	752	COSMIC
COSN30521335	758	COSMIC
COSN20069249	763	COSMIC
COSM7913092	819	COSMIC
COSM1485636	832	COSMIC
COSN28839051	901	COSMIC
COSN30604626	902	COSMIC
COSN31482235	909	COSMIC
COSN15323853	920	COSMIC
COSN19706406	936	COSMIC
COSN30169559	947	COSMIC
COSN31558722	1026	COSMIC
COSN30144033	1041	COSMIC
COSN31578738	1047	COSMIC
COSN30119732	1049	COSMIC
COSN7728961	1061	COSMIC
COSN31580569	1086	COSMIC
COSN20059256	1159	COSMIC
COSN6794774	1161	COSMIC
COSM8516233	1194	COSMIC

Mutant ID	Mutant Position	Mutant Source
rs1475517613	3	dbSNP
rs760668162	5	dbSNP
rs774377841	11	dbSNP
rs775274179	14	dbSNP
rs767064378	15	dbSNP
rs1157674586	19	dbSNP
rs375866565	20	dbSNP
rs372013591	26	dbSNP
rs1322042871	28	dbSNP
rs770657777	30	dbSNP
rs1212987621	31	dbSNP
rs1003249924	32	dbSNP
rs748917790	34	dbSNP
rs777203965	37	dbSNP
rs769130304	40	dbSNP
rs1404374944	41	dbSNP
rs747533838	42	dbSNP
rs771423852	43	dbSNP
rs780361343	43	dbSNP
rs758540488	45	dbSNP
rs906432889	48	dbSNP
rs1425858778	49	dbSNP
rs764304388	59	dbSNP
rs1390919370	63	dbSNP
rs1289024284	65	dbSNP
rs958560978	84	dbSNP
rs1034618029	86	dbSNP
rs1163401184	88	dbSNP
rs1271103420	88	dbSNP
rs536327566	98	dbSNP
rs1005452542	102	dbSNP
rs1221910910	106	dbSNP
rs1320855957	106	dbSNP
rs952618468	110	dbSNP
rs1479431104	111	dbSNP
rs1025628412	116	dbSNP
rs994172958	117	dbSNP
rs1251831565	125	dbSNP
rs943415890	126	dbSNP
rs1423911272	132	dbSNP
rs1383359991	133	dbSNP
rs1406300621	135	dbSNP
rs1167290993	136	dbSNP
rs149481287	136	dbSNP
rs745359003	137	dbSNP
rs1366933434	138	dbSNP
rs889211779	138	dbSNP
rs527440736	140	dbSNP
rs192441657	146	dbSNP
rs1273163965	150	dbSNP
rs1449801963	152	dbSNP
rs1228700084	153	dbSNP
rs933371141	161	dbSNP
rs924844597	163	dbSNP
rs1191223561	166	dbSNP
rs1453550628	167	dbSNP
rs977693873	169	dbSNP
rs1209418666	170	dbSNP
rs116782449	171	dbSNP
rs1473389691	172	dbSNP
rs769255	174	dbSNP
rs1209380592	182	dbSNP
rs369713475	184	dbSNP
rs1417746024	185	dbSNP
rs1169464752	186	dbSNP
rs770898004	186	dbSNP
rs550113320	187	dbSNP
rs1007408962	189	dbSNP
rs1229829763	197	dbSNP
rs777640763	207	dbSNP
rs3217777	209	dbSNP
rs1312304929	212	dbSNP
rs1358507863	220	dbSNP
rs200394944	222	dbSNP
rs1304431563	223	dbSNP
rs1359596767	224	dbSNP
rs377511727	226	dbSNP
rs1054375770	233	dbSNP
rs936913890	242	dbSNP
rs1033469229	245	dbSNP
rs767948966	247	dbSNP
rs1231480911	252	dbSNP
rs1224784590	258	dbSNP
rs1332519969	269	dbSNP
rs1277211945	273	dbSNP
rs556920628	292	dbSNP
rs1403840450	295	dbSNP
rs1363199644	300	dbSNP
rs902774034	305	dbSNP
rs1309718959	307	dbSNP
rs1041328905	310	dbSNP
rs1430342830	311	dbSNP
rs1189556188	313	dbSNP
rs1392286195	314	dbSNP
rs1452735902	314	dbSNP
rs1025953517	318	dbSNP
rs200022667	319	dbSNP
rs1166011641	321	dbSNP
rs945705128	322	dbSNP
rs527295430	330	dbSNP
rs546148344	332	dbSNP
rs1343268492	347	dbSNP
rs916950609	358	dbSNP
rs1434122991	364	dbSNP
rs992574701	367	dbSNP
rs1479123777	370	dbSNP
rs1366923708	392	dbSNP
rs1438194447	400	dbSNP
rs1273795972	402	dbSNP
rs1345108608	404	dbSNP
rs1221475732	408	dbSNP
rs1282793399	410	dbSNP
rs1378479485	422	dbSNP
rs1209751768	424	dbSNP
rs937116959	432	dbSNP
rs927121985	437	dbSNP
rs772435038	441	dbSNP
rs1467354300	447	dbSNP
rs993344461	448	dbSNP
rs1247405599	449	dbSNP
rs1479035235	450	dbSNP
rs1489869045	452	dbSNP
rs1254101473	456	dbSNP
rs746036642	456	dbSNP
rs899096679	457	dbSNP
rs779163192	460	dbSNP
rs1016012653	461	dbSNP
rs1390551058	463	dbSNP
rs769398720	465	dbSNP
rs889194625	468	dbSNP
rs1346645200	471	dbSNP
rs62322623	472	dbSNP
rs952569255	475	dbSNP
rs1025576034	476	dbSNP
rs972679743	481	dbSNP
rs3217778	483	dbSNP
rs1229534751	484	dbSNP
rs1270492553	484	dbSNP
rs1289681435	485	dbSNP
rs1209517726	487	dbSNP
rs1410359418	488	dbSNP
rs147433128	489	dbSNP
rs1353927262	491	dbSNP
rs181032306	496	dbSNP
rs565160481	498	dbSNP
rs992058989	498	dbSNP
rs1006947002	500	dbSNP
rs937551870	507	dbSNP
rs1416003525	508	dbSNP
rs1471676882	511	dbSNP
rs1162389727	513	dbSNP
rs926344308	513	dbSNP
rs1305702000	514	dbSNP
rs1406679692	514	dbSNP
rs1369396849	516	dbSNP
rs1290730284	520	dbSNP
rs1354057093	521	dbSNP
rs1244558959	524	dbSNP
rs981859348	533	dbSNP
rs1358758740	534	dbSNP
rs1402685132	537	dbSNP
rs549715641	538	dbSNP
rs970462289	538	dbSNP
rs889885241	546	dbSNP
rs1016218849	547	dbSNP
rs1007792750	549	dbSNP
rs559479723	555	dbSNP
rs757451020	556	dbSNP
rs1186592224	559	dbSNP
rs1368812563	561	dbSNP
rs1473612761	562	dbSNP
rs1183059410	565	dbSNP
rs1389065731	569	dbSNP
rs188327001	570	dbSNP
rs1309276620	580	dbSNP
rs1030599684	582	dbSNP
rs1395899987	588	dbSNP
rs1231711241	589	dbSNP
rs577033058	590	dbSNP
rs556706240	594	dbSNP
rs1226523245	596	dbSNP
rs997581463	602	dbSNP
rs542968589	610	dbSNP
rs574202999	611	dbSNP
rs1230702617	618	dbSNP
rs1278210613	619	dbSNP
rs895475006	620	dbSNP
rs1482266846	628	dbSNP
rs1199797226	633	dbSNP
rs1256642872	634	dbSNP
rs1202564653	635	dbSNP
rs1443907225	636	dbSNP
rs1321050554	639	dbSNP
rs1057216060	642	dbSNP
rs554284100	646	dbSNP
rs534409022	656	dbSNP
rs1375416157	659	dbSNP
rs1433417085	660	dbSNP
rs3217779	661	dbSNP
rs1277663007	662	dbSNP
rs928789594	663	dbSNP
rs1433381693	667	dbSNP
rs559089990	668	dbSNP
rs1320264424	670	dbSNP
rs1366215124	670	dbSNP
rs752555122	682	dbSNP
rs1046326969	685	dbSNP
rs949102818	688	dbSNP
rs1361810758	707	dbSNP
rs983937469	720	dbSNP
rs1346985132	721	dbSNP
rs780804921	727	dbSNP
rs377691288	730	dbSNP
rs148015288	733	dbSNP
rs963045445	737	dbSNP
rs1467300501	738	dbSNP
rs200400486	740	dbSNP
rs549907729	742	dbSNP
rs1194023645	743	dbSNP
rs1490039971	746	dbSNP
rs370178349	749	dbSNP
rs953432940	754	dbSNP
rs545304173	755	dbSNP
rs537463367	756	dbSNP
rs755844142	756	dbSNP
rs143489679	757	dbSNP
rs1337621531	759	dbSNP
rs1488785635	760	dbSNP
rs753649535	760	dbSNP
rs767316185	762	dbSNP
rs1387455718	765	dbSNP
rs773876155	767	dbSNP
rs759107049	768	dbSNP
rs770399867	768	dbSNP
rs1267343585	770	dbSNP
rs567664051	770	dbSNP
rs746570518	778	dbSNP
rs1019587190	779	dbSNP
rs547941906	784	dbSNP
rs1056211718	787	dbSNP
rs779606000	788	dbSNP
rs751255089	789	dbSNP
rs772943583	799	dbSNP
rs745543259	803	dbSNP
rs771429379	803	dbSNP
rs769148655	804	dbSNP
rs1387814332	805	dbSNP
rs1471932615	805	dbSNP
rs1396436877	807	dbSNP
rs778497334	807	dbSNP
rs747298248	810	dbSNP
rs757068837	813	dbSNP
rs1401555980	816	dbSNP
rs1413221592	820	dbSNP
rs1170874223	827	dbSNP
rs1051881	828	dbSNP
rs1426544474	831	dbSNP
rs1200989502	834	dbSNP
rs1433318867	835	dbSNP
rs772507554	839	dbSNP
rs746359059	842	dbSNP
rs1349519985	844	dbSNP
rs1458553405	845	dbSNP
rs559300681	847	dbSNP
rs201224124	850	dbSNP
rs1258477522	851	dbSNP
rs757312369	855	dbSNP
rs753609531	860	dbSNP
rs1265029779	861	dbSNP
rs1368783513	862	dbSNP
rs749522181	872	dbSNP
rs532310474	878	dbSNP
rs1287629376	881	dbSNP
rs755932933	891	dbSNP
rs1393661081	900	dbSNP
rs1378025974	901	dbSNP
rs377438764	903	dbSNP
rs1225289035	909	dbSNP
rs777725892	912	dbSNP
rs767321696	913	dbSNP
rs1000941411	914	dbSNP
rs754938060	915	dbSNP
rs1466097549	916	dbSNP
rs1507987	920	dbSNP
rs111499975	921	dbSNP
rs1293364028	929	dbSNP
rs1481771523	929	dbSNP
rs1314080185	938	dbSNP
rs112004858	939	dbSNP
rs1013764329	940	dbSNP
rs1367133051	942	dbSNP
rs986209782	948	dbSNP
rs1167140995	952	dbSNP
rs72915963	964	dbSNP
rs1430291205	966	dbSNP
rs1371097763	969	dbSNP
rs1444229895	970	dbSNP
rs1343436971	981	dbSNP
rs923213947	986	dbSNP
rs975900638	988	dbSNP
rs1358204446	994	dbSNP
rs1316742794	998	dbSNP
rs967227344	1000	dbSNP
rs1406443602	1002	dbSNP
rs1056762425	1003	dbSNP
rs1227036497	1007	dbSNP
rs1020146469	1014	dbSNP
rs1011636955	1022	dbSNP
rs1208635091	1030	dbSNP
rs1001616976	1038	dbSNP
rs1162027628	1040	dbSNP
rs1185762122	1049	dbSNP
rs537870734	1049	dbSNP
rs13117986	1051	dbSNP
rs1249063041	1054	dbSNP
rs13117978	1056	dbSNP
rs907445518	1062	dbSNP
rs1392093817	1066	dbSNP
rs1411625753	1067	dbSNP
rs1173840391	1071	dbSNP
rs1358452988	1075	dbSNP
rs1448520170	1080	dbSNP
rs554122581	1084	dbSNP
rs568877013	1092	dbSNP
rs1239858198	1096	dbSNP
rs540758624	1097	dbSNP
rs1490484041	1099	dbSNP
rs1048170586	1102	dbSNP
rs931078510	1103	dbSNP
rs111281266	1110	dbSNP
rs1363413775	1111	dbSNP
rs1243711851	1114	dbSNP
rs1218034841	1116	dbSNP
rs918393774	1127	dbSNP
rs1278566609	1131	dbSNP
rs1038516018	1136	dbSNP
rs1266567663	1137	dbSNP
rs1464665310	1141	dbSNP
rs572070376	1141	dbSNP
rs369403322	1142	dbSNP
rs756072489	1142	dbSNP
rs1179494441	1143	dbSNP
rs1190644205	1143	dbSNP
rs1477093096	1143	dbSNP
rs752777555	1145	dbSNP
rs1238516431	1147	dbSNP
rs766002721	1150	dbSNP
rs1050085231	1157	dbSNP
rs1252563363	1158	dbSNP
rs1245196827	1160	dbSNP
rs1201303004	1163	dbSNP
rs762488495	1164	dbSNP
rs202018156	1165	dbSNP
rs764937000	1168	dbSNP
rs767646981	1168	dbSNP
rs1282595495	1180	dbSNP
rs923194100	1181	dbSNP
rs1327782621	1186	dbSNP
rs1315031764	1195	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 methods, 2011

Cross-linking and immunoprecipitation (CLIP) is increasingly used to map transcriptome-wide binding sites of RNA-binding proteins. We developed a method for CLIP data analysis, and applied it to compare CLIP with photoactivatable ribonucleoside-enhanced CLIP (PAR-CLIP) and to uncover how differences in cross-linking and ribonuclease digestion affect the identified sites. We found only small differences in accuracies of these methods in identifying binding sites of HuR, which binds low-complexity sequences, and Argonaute 2, which has a complex binding specificity. We found that cross-link-induced mutations led to single-nucleotide resolution for both PAR-CLIP and CLIP. Our results confirm the expectation from original CLIP publications that RNA-binding proteins do not protect their binding sites sufficiently under the denaturing conditions used during the CLIP procedure, and we show that extensive digestion with sequence-specific RNases strongly biases the recovered binding sites. This bias can be substantially reduced by milder nuclease digestion conditions.

- 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.