>COIL|NM_004645|3'UTR
   1 GTATGACCTCTCCACCTTATAGTTTATGAATGTCTTGTTTGTGAAAGTGACTATAACCCAAACTTTTTTTTTTTTTTAAA
  81 GAGGATTTGGAAGTTGTATGGATTTTTTTGTTATCTTCACTTTACTGCATAGGAAACAATCTACCTCATCATTTAAAATG
 161 ACATGGGTGTCGGTTTTGTAGATCTTTGGTTTTTTTGTCAGGTTTAATTTCAGTTAACAAAATGTAAAACATGACATTCC
 241 CTGCAGATATTGTTGTATACCAGTATGGTTTCTTCTCTTTCTTTAAATGTTTTTGGCCATCAAGTAGCAGTCGTCAGTAG
 321 GAGTTTATAATACCAAGAATGTGCTGCGTATCTTGTCTCAATAAGTTTTAAGTAACATTTAAAAATATTAAAGCATGTTA
 401 TTTGACCTAATTTTTTAGCATTTGAGTTGTTCCATTAAATGGAGCATCTTGTAAATTTCAAGTATTTTATACTTGCAATT
 481 GTTAAGAGTTAACAGGTAGTTGGATTTGTCGCAGACAATGAGTTAAGGAATCCTTTCACGTTTTTCCCAACTTTAAAATT
 561 AAGGATTCTCAGGTCCCTGTGTAGAGCAGTGAAAATAAGATGTGCGTATGTGTGTGTATGCCTGGAGAATTGGTGTTTCA
 641 CTTCAGTGAGAGGATTGGCTGTGAGCTTCAGACCAGGAAATGTGTCATCTTGCCAGGCACCTGGCTGAGTGTGCTGGAGT
 721 GAGGATCTTGAACAGAAACTTCCTTTTCTGTTATTATTCACTACGAAGCTAAAATGGCCAAATATATACCGTGAAAATTG
 801 GTTTCATTTAACAAAAGATCAGATCCCTCCTTCAGCTGTACACATTTTTAAATAAAATCATATTGAACTAAAAAAAAAAA
 881 AAAAAAA

ID	Duplex structure	Position	Score	MFE
1	miRNA 3' acGUGCCGUUUUCUUUGUUAGa 5' :|| ||| |:||||||||| Target 5' ttTACTGCATAGGAAACAATCt 3'	121 - 142	176.00	-18.10
2	miRNA 3' acguGCCGUU--UUCUUUGUUAGa 5' :||| | ||| |:||:|| Target 5' ttttTGGCCATCAAGTAGCAGTCg 3'	290 - 313	128.00	-10.70
3	miRNA 3' acGUG-CCGUU-UUC--UUUGUUAGa 5' |:| | ||| :|| ||: |||| Target 5' gtCGCAGACAATGAGTTAAGGAATCc 3'	508 - 533	110.00	-6.90

Mutant ID	Mutant Position	Mutant Source
COSN27399494	63	COSMIC
COSN1198942	64	COSMIC
COSN26538201	77	COSMIC
COSN7440581	78	COSMIC
COSN30514551	83	COSMIC
COSN30140822	87	COSMIC
COSN1198941	151	COSMIC
COSN31558878	312	COSMIC
COSN25563492	503	COSMIC
COSN23846691	650	COSMIC

Mutant ID	Mutant Position	Mutant Source
rs377687480	2	dbSNP
rs761872987	3	dbSNP
rs762485796	3	dbSNP
rs1381879699	7	dbSNP
rs183772985	8	dbSNP
rs768322523	12	dbSNP
rs191880365	15	dbSNP
rs536527958	20	dbSNP
rs1429765030	32	dbSNP
rs960640604	32	dbSNP
rs1234634289	37	dbSNP
rs771761268	39	dbSNP
rs200015896	40	dbSNP
rs961077656	41	dbSNP
rs772684443	43	dbSNP
rs2332857	44	dbSNP
rs371312180	49	dbSNP
rs2332858	51	dbSNP
rs1258176939	53	dbSNP
rs1005506508	54	dbSNP
rs2332859	59	dbSNP
rs2332860	60	dbSNP
rs966450667	64	dbSNP
rs568626909	67	dbSNP
rs866625853	72	dbSNP
rs905673010	77	dbSNP
rs1294307761	78	dbSNP
rs1313984330	78	dbSNP
rs3056865	78	dbSNP
rs878862719	78	dbSNP
rs1311063814	81	dbSNP
rs1416073035	86	dbSNP
rs1331705724	89	dbSNP
rs2332861	98	dbSNP
rs1284372833	106	dbSNP
rs11541636	110	dbSNP
rs1225339696	110	dbSNP
rs866280648	115	dbSNP
rs1022825207	117	dbSNP
rs1010741081	122	dbSNP
rs889730386	126	dbSNP
rs1053202418	130	dbSNP
rs2332862	140	dbSNP
rs538813966	143	dbSNP
rs1415233785	145	dbSNP
rs1028229927	148	dbSNP
rs1280928618	155	dbSNP
rs775195400	157	dbSNP
rs1198801133	163	dbSNP
rs904564875	167	dbSNP
rs2332863	171	dbSNP
rs1301271870	172	dbSNP
rs1231431226	173	dbSNP
rs943665504	176	dbSNP
rs1174716132	178	dbSNP
rs546641880	180	dbSNP
rs528608684	184	dbSNP
rs1433330262	189	dbSNP
rs2332864	190	dbSNP
rs1400812524	191	dbSNP
rs1161380309	194	dbSNP
rs1399458882	196	dbSNP
rs869291409	197	dbSNP
rs1445758468	199	dbSNP
rs1042237	210	dbSNP
rs1051855502	217	dbSNP
rs552777898	218	dbSNP
rs1005385958	219	dbSNP
rs1230906970	223	dbSNP
rs561110336	224	dbSNP
rs2332865	227	dbSNP
rs868609175	230	dbSNP
rs2332866	248	dbSNP
rs1255365564	259	dbSNP
rs1042238	272	dbSNP
rs1042239	275	dbSNP
rs72842329	278	dbSNP
rs1457534323	279	dbSNP
rs11541637	281	dbSNP
rs2332867	286	dbSNP
rs1042240	289	dbSNP
rs1042241	292	dbSNP
rs1194508242	294	dbSNP
rs1255220885	295	dbSNP
rs1431821855	297	dbSNP
rs922319327	299	dbSNP
rs917571425	302	dbSNP
rs1374188673	303	dbSNP
rs530834293	312	dbSNP
rs1049260814	313	dbSNP
rs930796752	324	dbSNP
rs916861255	327	dbSNP
rs1397669734	332	dbSNP
rs1255886733	334	dbSNP
rs1326189768	335	dbSNP
rs1396350330	342	dbSNP
rs1055800802	343	dbSNP
rs1300474580	345	dbSNP
rs1179703821	346	dbSNP
rs778334417	347	dbSNP
rs117110855	348	dbSNP
rs1317388016	351	dbSNP
rs1217399745	352	dbSNP
rs866509947	355	dbSNP
rs1275316101	361	dbSNP
rs144891760	367	dbSNP
rs977776075	368	dbSNP
rs1467055954	370	dbSNP
rs1263031181	383	dbSNP
rs966899400	388	dbSNP
rs1192133979	389	dbSNP
rs1233850804	395	dbSNP
rs1336609804	396	dbSNP
rs1477225126	397	dbSNP
rs1165149389	404	dbSNP
rs1802588	418	dbSNP
rs1456184021	426	dbSNP
rs565126566	430	dbSNP
rs1385403436	431	dbSNP
rs748704570	442	dbSNP
rs1296288366	446	dbSNP
rs1290693012	455	dbSNP
rs1433051310	460	dbSNP
rs540319456	462	dbSNP
rs572925074	471	dbSNP
rs1463497357	476	dbSNP
rs554244722	478	dbSNP
rs1215027703	487	dbSNP
rs745357336	494	dbSNP
rs904511409	495	dbSNP
rs1019398224	510	dbSNP
rs1051973068	511	dbSNP
rs1364109974	515	dbSNP
rs777583986	518	dbSNP
rs1156735025	525	dbSNP
rs184600765	528	dbSNP
rs1415462852	537	dbSNP
rs919464893	539	dbSNP
rs886550260	540	dbSNP
rs1395612367	547	dbSNP
rs1308008831	550	dbSNP
rs1036721802	556	dbSNP
rs193173687	557	dbSNP
rs1049124654	562	dbSNP
rs1285906560	565	dbSNP
rs994854302	568	dbSNP
rs895319304	573	dbSNP
rs8599	574	dbSNP
rs1482001164	579	dbSNP
rs939631293	588	dbSNP
rs188181598	594	dbSNP
rs909635102	597	dbSNP
rs1214182420	601	dbSNP
rs983765859	604	dbSNP
rs752037367	605	dbSNP
rs1263450088	606	dbSNP
rs1379611557	610	dbSNP
rs915823776	614	dbSNP
rs151097637	622	dbSNP
rs1308276942	623	dbSNP
rs1298051338	624	dbSNP
rs1226505267	630	dbSNP
rs1379462460	630	dbSNP
rs1445017005	650	dbSNP
rs1364486430	652	dbSNP
rs1372195121	657	dbSNP
rs1237077991	658	dbSNP
rs945010347	665	dbSNP
rs914881570	677	dbSNP
rs1309900229	680	dbSNP
rs1208876709	684	dbSNP
rs571503854	688	dbSNP
rs1251514540	697	dbSNP
rs1389295984	700	dbSNP
rs1031540054	704	dbSNP
rs1237282476	715	dbSNP
rs1454568182	716	dbSNP
rs999109798	745	dbSNP
rs1423027583	748	dbSNP
rs765204180	754	dbSNP
rs1293294692	763	dbSNP
rs1432651618	764	dbSNP
rs1171299411	765	dbSNP
rs553186385	770	dbSNP
rs989247762	779	dbSNP
rs867076244	781	dbSNP
rs953738013	785	dbSNP
rs144424393	791	dbSNP
rs889146969	797	dbSNP
rs1273559331	810	dbSNP
rs368156860	810	dbSNP
rs1367589447	813	dbSNP
rs1218125326	814	dbSNP
rs976606850	816	dbSNP
rs1278203665	820	dbSNP
rs112223706	821	dbSNP
rs758882903	823	dbSNP
rs1455520891	827	dbSNP
rs1196313564	834	dbSNP
rs965715289	838	dbSNP
rs1015493992	842	dbSNP
rs1005323493	847	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.