ID	Duplex structure	Position	Score	MFE
1	miRNA 3' uaUUUACUG-------UGGAGGAACACUu 5' |:||||| |||| ||||||| Target 5' ccAGATGACACTTAAGACCTACTTGTGAt 3'	35 - 63	168.00	-19.40
2	miRNA 3' uauUUACUG----UGGAGGAACACUu 5' | |||: ||||:||| | | Target 5' cctATTGATTTGGACCTTCTTCTTAa 3'	86 - 111	101.00	-7.83

Mutant ID	Mutant Position	Mutant Source
COSN30153809	1	COSMIC
COSN30184991	11	COSMIC
COSN1296851	18	COSMIC
COSN5271427	33	COSMIC
COSN2027996	107	COSMIC
COSN6830304	246	COSMIC
COSN6830303	258	COSMIC
COSN31571123	388	COSMIC

Mutant ID	Mutant Position	Mutant Source
rs757463458	4	dbSNP
rs754196035	5	dbSNP
rs780452617	6	dbSNP
rs755740515	10	dbSNP
rs762889419	11	dbSNP
rs1305964176	13	dbSNP
rs750130162	18	dbSNP
rs530765321	21	dbSNP
rs767107544	22	dbSNP
rs773551284	22	dbSNP
rs548381262	23	dbSNP
rs751045563	27	dbSNP
rs764059798	28	dbSNP
rs763054300	29	dbSNP
rs144617064	33	dbSNP
rs769765202	35	dbSNP
rs759277422	37	dbSNP
rs1016468430	38	dbSNP
rs1352359300	39	dbSNP
rs1327633071	41	dbSNP
rs773431723	44	dbSNP
rs772193750	45	dbSNP
rs370969641	47	dbSNP
rs951022036	50	dbSNP
rs1270965986	53	dbSNP
rs1467988914	55	dbSNP
rs1216347771	61	dbSNP
rs1345211376	63	dbSNP
rs35627846	71	dbSNP
rs1484636241	74	dbSNP
rs1025720826	76	dbSNP
rs1304136333	78	dbSNP
rs1414156646	80	dbSNP
rs993850254	83	dbSNP
rs140856391	87	dbSNP
rs143647638	96	dbSNP
rs34768896	111	dbSNP
rs909200437	112	dbSNP
rs983878379	117	dbSNP
rs1006676323	120	dbSNP
rs1428787899	123	dbSNP
rs532439920	134	dbSNP
rs1288353991	146	dbSNP
rs1036153256	148	dbSNP
rs1235304650	151	dbSNP
rs1291234773	153	dbSNP
rs1050353342	169	dbSNP
rs188042991	179	dbSNP
rs756430165	180	dbSNP
rs913159764	182	dbSNP
rs746783402	183	dbSNP
rs1480238570	184	dbSNP
rs938686266	191	dbSNP
rs1199916612	192	dbSNP
rs1478917102	200	dbSNP
rs183121157	204	dbSNP
rs1185300782	206	dbSNP
rs928689313	208	dbSNP
rs575332403	210	dbSNP
rs200953297	219	dbSNP
rs758423264	221	dbSNP
rs1159493289	228	dbSNP
rs1011830154	229	dbSNP
rs1399393182	240	dbSNP
rs555469288	241	dbSNP
rs1031988470	245	dbSNP
rs80193495	246	dbSNP
rs1311333154	247	dbSNP
rs1355048316	250	dbSNP
rs909355361	252	dbSNP
rs985006371	255	dbSNP
rs902191032	256	dbSNP
rs573325069	258	dbSNP
rs1223098479	261	dbSNP
rs1284273413	265	dbSNP
rs997259669	266	dbSNP
rs553555975	267	dbSNP
rs1221273208	275	dbSNP
rs900336500	278	dbSNP
rs1026587619	280	dbSNP
rs1371683018	282	dbSNP
rs1182986854	288	dbSNP
rs972356854	294	dbSNP
rs1469072188	299	dbSNP
rs1178524510	300	dbSNP
rs1396176120	304	dbSNP
rs1171844931	306	dbSNP
rs1436714462	306	dbSNP
rs965031953	309	dbSNP
rs1330664806	314	dbSNP
rs1410690575	314	dbSNP
rs139037922	320	dbSNP
rs1047651846	321	dbSNP
rs1304136969	329	dbSNP
rs752514157	330	dbSNP
rs765222535	334	dbSNP
rs754441468	337	dbSNP
rs1469444434	338	dbSNP
rs768511855	349	dbSNP
rs1006624988	350	dbSNP
rs889571428	351	dbSNP
rs1178560007	359	dbSNP
rs143519900	360	dbSNP
rs1021847530	362	dbSNP
rs1275588933	366	dbSNP
rs1011427084	368	dbSNP
rs891667193	377	dbSNP
rs1052974966	379	dbSNP
rs1254254127	381	dbSNP
rs1802628	385	dbSNP
rs938635376	391	dbSNP
rs1455914107	392	dbSNP
rs765007383	396	dbSNP
rs1377092246	402	dbSNP
rs957580305	403	dbSNP
rs571135468	412	dbSNP
rs1326326160	417	dbSNP
rs746576910	417	dbSNP
rs1032312675	420	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.