>DNASE2|NM_001375|3'UTR
   1 CCCTTATGGCCAGGTGCAGTGGCTCACGTATGTAATCCCAGCACTTTGGGAAGCCAAGGAGGGAGGATCACTTGAACTCA
  81 GGAATTCGAGACCAGCCTGGGCTACATAGTGAGACCACATCTCTACTAGAACTTAAAAAAAGTTAGCCAGGCACGGTGAT
 161 AAATGCCTGTAGTCCCAGCCACTGAAGCCAGAGGATCGATTGAACCAGGGAGATCATGGTCACAGTGAACTATGATTACG
 241 CCAACCTGGGTCACATAGCAAGACTCTGTTTCAAAAAAAAAGGGGGGGCGGGGGACGGGTGGGTGCAGTGGCTCACATCT
 321 GTAACCCCAGCACTTTGGGAGGCTGAGATGGGCAGATCACTTGAGGTCAGGAGTTCGAGACCAGCCTGGCCAACATGGTG
 401 AAACCCCATATCCATTAAAAATATTTAAAAATTAGCCAGACATGGTGGCACGCGTCTGTGGTCCTAGCTCCTCGGGAGGC
 481 TGAGGCAGGAGAATCGCTTGAACTCGGGAGGCAGAGGTTGTCATGAGCTGAGCTAACACCACGGCACTTCAGCCTGGGTG
 561 ACAGAATGAGACTCTGTGTCAAAAAAATAAAAAATAAAAAATCTAAGGGCTCAGGAACCAGTTTGGACTTGATTTTGAAT
 641 CCCAGTTCATCCCCTTCCTAGCTGTATGACCTTGATTGTGTGCCTTAACCGCTCTGTGACACAGTCTACCTGTCTGCAAA
 721 ATGGGAAACATAATACCTGCCATCAGGATTGTTGAGGAGTAAATAAATGGAAATTGGTGAAA

ID	Duplex structure	Position	Score	MFE
1	miRNA 3' cuUUAGA---GAUGU----CUUCGGGGUAu 5' |: || | ||| ||| |||||| Target 5' ccAGCCTGGCCAACATGGTGAAACCCCATa 3'	381 - 410	127.00	-15.10
2	miRNA 3' cuUUAGAGAUGUCUUCGGGGUau 5' ||| || | ||:|||| Target 5' taAATGCCT---GTAGTCCCAgc 3'	160 - 179	118.00	-10.60
3	miRNA 3' cuuuagagAUGUCUUCGGG-GUAu 5' |:||| :||:| ||| Target 5' cgggtgggTGCAGTGGCTCACATc 3'	296 - 319	111.00	-11.30

Mutant ID	Mutant Position	Mutant Source
COSN26973793	27	COSMIC
COSN13781668	29	COSMIC
COSN26973795	30	COSMIC
COSN30116047	48	COSMIC
COSN31498678	50	COSMIC
COSN30104257	76	COSMIC
COSN30108794	84	COSMIC
COSN30193777	117	COSMIC
COSN5183599	126	COSMIC
COSN28634264	460	COSMIC
COSN31518161	710	COSMIC
COSN26790900	742	COSMIC

Mutant ID	Mutant Position	Mutant Source
rs1420062223	1	dbSNP
rs1171942859	4	dbSNP
rs759870950	7	dbSNP
rs1247986270	10	dbSNP
rs776917620	12	dbSNP
rs368029639	14	dbSNP
rs1236719583	16	dbSNP
rs933463118	19	dbSNP
rs771385627	20	dbSNP
rs1438757057	25	dbSNP
rs200124589	27	dbSNP
rs775947025	29	dbSNP
rs914552111	30	dbSNP
rs991536297	32	dbSNP
rs768199297	43	dbSNP
rs1239665377	49	dbSNP
rs1375028946	50	dbSNP
rs919347845	53	dbSNP
rs937389483	54	dbSNP
rs1441508740	59	dbSNP
rs928679043	65	dbSNP
rs1325737383	73	dbSNP
rs192025167	74	dbSNP
rs1328811645	80	dbSNP
rs576215922	81	dbSNP
rs1394188971	87	dbSNP
rs944741902	88	dbSNP
rs1160634098	89	dbSNP
rs911860695	93	dbSNP
rs970512070	101	dbSNP
rs79595281	107	dbSNP
rs1157796858	110	dbSNP
rs1198120021	115	dbSNP
rs1256362006	120	dbSNP
rs953620543	123	dbSNP
rs759318810	125	dbSNP
rs538894338	135	dbSNP
rs1196295742	142	dbSNP
rs1450891099	148	dbSNP
rs978909242	155	dbSNP
rs1477187418	161	dbSNP
rs967493166	164	dbSNP
rs1248415677	183	dbSNP
rs1355902536	185	dbSNP
rs963359037	188	dbSNP
rs1016329104	197	dbSNP
rs1401866982	209	dbSNP
rs1413345188	225	dbSNP
rs1295605328	233	dbSNP
rs1356700342	234	dbSNP
rs147116968	239	dbSNP
rs1020722975	240	dbSNP
rs549783671	248	dbSNP
rs186272174	249	dbSNP
rs888795813	253	dbSNP
rs1255643068	259	dbSNP
rs1212794009	268	dbSNP
rs1267384120	268	dbSNP
rs1223330078	272	dbSNP
rs960433311	274	dbSNP
rs537971974	281	dbSNP
rs113410270	282	dbSNP
rs11670107	282	dbSNP
rs1421109595	282	dbSNP
rs1491464664	283	dbSNP
rs1276890091	285	dbSNP
rs556369183	286	dbSNP
rs1002167240	287	dbSNP
rs1287635620	288	dbSNP
rs549599203	288	dbSNP
rs1215265421	289	dbSNP
rs536925734	289	dbSNP
rs905113202	289	dbSNP
rs141495984	290	dbSNP
rs1321653218	295	dbSNP
rs1352896624	296	dbSNP
rs1437660231	297	dbSNP
rs1243795550	300	dbSNP
rs1387125485	300	dbSNP
rs1158993887	312	dbSNP
rs1440797973	317	dbSNP
rs1238135303	319	dbSNP
rs1177089616	325	dbSNP
rs897638025	331	dbSNP
rs1414603496	350	dbSNP
rs1041925124	357	dbSNP
rs1175911701	376	dbSNP
rs1426666157	377	dbSNP
rs947615301	389	dbSNP
rs774253152	390	dbSNP
rs374018333	399	dbSNP
rs1157496241	400	dbSNP
rs1056466392	404	dbSNP
rs1347499267	405	dbSNP
rs1431533884	411	dbSNP
rs1293066601	412	dbSNP
rs1170228290	427	dbSNP
rs1036469212	437	dbSNP
rs937294532	451	dbSNP
rs758290259	452	dbSNP
rs533418406	453	dbSNP
rs369476854	454	dbSNP
rs1317494682	458	dbSNP
rs919076523	461	dbSNP
rs1210707530	467	dbSNP
rs111468604	468	dbSNP
rs1443143318	473	dbSNP
rs926222302	474	dbSNP
rs1237211704	483	dbSNP
rs1469912599	485	dbSNP
rs1175889694	486	dbSNP
rs971950153	490	dbSNP
rs978962619	495	dbSNP
rs963563435	496	dbSNP
rs1217485290	505	dbSNP
rs1463095129	506	dbSNP
rs1347454438	517	dbSNP
rs1326777813	521	dbSNP
rs183425548	523	dbSNP
rs867643049	524	dbSNP
rs913378305	527	dbSNP
rs986019307	534	dbSNP
rs987943432	537	dbSNP
rs529394333	542	dbSNP
rs1029995021	557	dbSNP
rs561850279	578	dbSNP
rs967184425	580	dbSNP
rs980440748	580	dbSNP
rs1256996682	588	dbSNP
rs1435769518	588	dbSNP
rs1202851733	596	dbSNP
rs1020855041	600	dbSNP
rs1235031840	603	dbSNP
rs1470721212	603	dbSNP
rs879797973	604	dbSNP
rs1416369365	607	dbSNP
rs1476207676	609	dbSNP
rs549037267	610	dbSNP
rs897684186	610	dbSNP
rs1408495207	619	dbSNP
rs540682935	623	dbSNP
rs1015162011	627	dbSNP
rs572164665	628	dbSNP
rs1291318598	637	dbSNP
rs890537413	641	dbSNP
rs1233342929	643	dbSNP
rs757107772	650	dbSNP
rs1370830465	652	dbSNP
rs1170070436	656	dbSNP
rs1001787344	657	dbSNP
rs1418523033	660	dbSNP
rs1215895995	661	dbSNP
rs1273293288	664	dbSNP
rs1438706535	666	dbSNP
rs1210662205	671	dbSNP
rs1255994655	673	dbSNP
rs1486972424	686	dbSNP
rs907199383	689	dbSNP
rs759529856	690	dbSNP
rs1182163089	691	dbSNP
rs1474474271	692	dbSNP
rs930036701	695	dbSNP
rs1473742218	696	dbSNP
rs1169821429	700	dbSNP
rs1235612744	704	dbSNP
rs918702596	707	dbSNP
rs1038874881	709	dbSNP
rs1310896964	712	dbSNP
rs1275695105	715	dbSNP
rs932005043	716	dbSNP
rs1297513716	729	dbSNP
rs1207558419	733	dbSNP
rs1432318463	755	dbSNP
rs79893690	782	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.