>UGT2B4|NM_021139|3'UTR
   1 TTACGTCTGAGGCTGGAAGCTGGGAAACCCAATAAATGAACTCCTTTAGTTTATTACAACAAGAAGACGTTGTGATACAA
  81 GAGATTCCTTTCTTCTTGTGACAAAACATCTTTCAAAACTTACCTTGTCAAGTCAAAATTTGTTTTAGTACCTGTTTAAC
 161 CATTAGAAATATTTCATGTCAAGGAGGAAAACATTAGGGAAAACAAAAATGATATAAAGCCATATGAGGTTATATTGAAA
 241 TGTATTGAGCTTATATTGAAATTTATTGTTCCAATTCACAGGTTACATGAAAAAAAATTTACTAAGCTTAACTACATGTC
 321 ACACATTGTACATGGAAACAAGAACATTAAGAAGTCCACTGACAGTATCAGTACTGTTTTGCAAATACTCAGCATACTTT
 401 GGATCCATTTCATGCAGGATTGTGTTGTTTTAACTGTTGTTGAGGAAGCTAATAAATAATTAAATTGTAAAAAAAAAAAA
 481 AAAAA

ID	Duplex structure	Position	Score	MFE
1	miRNA 3' ucguACA----UGGGUGUCac 5' ||| |::||||| Target 5' ttatTGTTCCAATTCACAGgt 3'	263 - 283	111.00	-8.10
2	miRNA 3' ucgUACA--UGGGUGUCAc 5' | || ||: ||||| Target 5' aagAAGTCCACTGACAGTa 3'	349 - 367	104.00	-6.80
3	miRNA 3' ucguacAUGGGUGU-CAc 5' || |:||| || Target 5' taagctTAACTACATGTc 3'	303 - 320	99.00	-5.10

Mutant ID	Mutant Position	Mutant Source
COSN30100342	4	COSMIC
COSN30105484	5	COSMIC
COSN31554726	8	COSMIC
COSN30110571	16	COSMIC
COSN30183905	23	COSMIC
COSN31499367	24	COSMIC
COSN14121282	38	COSMIC
COSN30101179	41	COSMIC
COSN30456176	43	COSMIC
COSN30121679	44	COSMIC
COSN30738325	69	COSMIC
COSN31501099	69	COSMIC
COSN31582132	73	COSMIC
COSN30130682	83	COSMIC
COSN30455126	83	COSMIC
COSN30108624	90	COSMIC
COSN30477899	110	COSMIC
COSN31506673	114	COSMIC
COSN30133747	118	COSMIC
COSN23016485	122	COSMIC
COSN30179015	124	COSMIC
COSN31534115	125	COSMIC
COSN31556292	131	COSMIC
COSN28760381	151	COSMIC
COSN31611645	189	COSMIC
COSN31549656	204	COSMIC
COSN31598269	219	COSMIC
COSN31605633	237	COSMIC
COSN30135961	267	COSMIC
COSN28013041	290	COSMIC

Mutant ID	Mutant Position	Mutant Source
rs760647912	5	dbSNP
rs773071003	6	dbSNP
rs771821155	7	dbSNP
rs761549102	10	dbSNP
rs904133685	11	dbSNP
rs968143526	15	dbSNP
rs370143836	18	dbSNP
rs1410722086	23	dbSNP
rs768231044	24	dbSNP
rs1460045388	30	dbSNP
rs748960146	32	dbSNP
rs1201306274	37	dbSNP
rs375773104	38	dbSNP
rs769240107	40	dbSNP
rs746357168	43	dbSNP
rs781751752	48	dbSNP
rs751569355	63	dbSNP
rs748186522	68	dbSNP
rs1305505188	74	dbSNP
rs563092551	79	dbSNP
rs1035598068	92	dbSNP
rs1441051843	96	dbSNP
rs1415737819	101	dbSNP
rs1363864628	106	dbSNP
rs778681610	108	dbSNP
rs1241325169	112	dbSNP
rs1280205172	115	dbSNP
rs1351384396	121	dbSNP
rs762512901	123	dbSNP
rs755153405	126	dbSNP
rs1486549719	127	dbSNP
rs969576747	130	dbSNP
rs41298247	132	dbSNP
rs951662136	135	dbSNP
rs1028919761	138	dbSNP
rs753918506	143	dbSNP
rs1397474405	147	dbSNP
rs966353707	149	dbSNP
rs1477368625	160	dbSNP
rs1194840827	161	dbSNP
rs898147687	162	dbSNP
rs1435780654	170	dbSNP
rs1016713751	179	dbSNP
rs1018812686	180	dbSNP
rs1004360903	182	dbSNP
rs1369017850	186	dbSNP
rs1259761750	187	dbSNP
rs1393348925	194	dbSNP
rs367718795	195	dbSNP
rs1188289756	204	dbSNP
rs1329722088	212	dbSNP
rs574577022	215	dbSNP
rs1966151	225	dbSNP
rs1349940472	226	dbSNP
rs750830787	241	dbSNP
rs892573766	248	dbSNP
rs1031022131	250	dbSNP
rs376460975	256	dbSNP
rs1337131229	258	dbSNP
rs1345426367	262	dbSNP
rs767982446	266	dbSNP
rs541206493	268	dbSNP
rs572237033	280	dbSNP
rs558737300	289	dbSNP
rs948371937	293	dbSNP
rs1051752	295	dbSNP
rs1188394282	297	dbSNP
rs190759600	298	dbSNP
rs1208401855	305	dbSNP
rs1463792548	317	dbSNP
rs1056664750	332	dbSNP
rs915240170	336	dbSNP
rs988283663	341	dbSNP
rs1403728518	354	dbSNP
rs1327975870	359	dbSNP
rs879113366	361	dbSNP
rs1373193267	364	dbSNP
rs1301876394	368	dbSNP
rs1441558078	387	dbSNP
rs752157016	392	dbSNP
rs935375861	395	dbSNP
rs928160196	400	dbSNP
rs982657937	412	dbSNP
rs372412473	418	dbSNP
rs1023863317	424	dbSNP
rs1229271012	426	dbSNP
rs930295990	428	dbSNP
rs1355169416	435	dbSNP
rs766225315	446	dbSNP
rs1131878	448	dbSNP
rs75226016	450	dbSNP
rs1174595798	453	dbSNP
rs1274492432	459	dbSNP
rs1468492229	469	dbSNP

- 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.