>PTMA|NM_001099285|3'UTR
   1 ACAGCAAAAAAGGAAAAGTTAAACTAAAAAAAAAAAGGCCGCCGTGACCTATTCACCCTCCACTTCCCGTCTCAGAATCT
  81 AAACGTGGTCACCTTCGAGTAGAGAGGCCCGCCCGCCCACCGTGGGCAGTGCCACCCGCAGATGACACGCGCTCTCCACC
 161 ACCCAACCCAAACCATGAGAATTTGCAACAGGGGAGGAAAAAAGAACCAAAACTTCCAAGGCCCTGCTTTTTTTCTTAAA
 241 AGTACTTTAAAAAGGAAATTTGTTTGTATTTTTTATTTACATTTTATATTTTTGTACATATTGTTAGGGTCAGCCATTTT
 321 TAATGATCTCGGATGACCAAACCAGCCTTCGGAGCGTTCTCTGTCCTACTTCTGACTTTACTTGTGGTGTGACCATGTTC
 401 ATTATAATCTCAAAGGAGAAAAAAAACCTTGTAAAAAAAGCAAAAATGACAACAGAAAAACAATCTTATTCCGAGCATTC
 481 CAGTAACTTTTTTGTGTATGTACTTAGCTGTACTATAAGTAGTTGGTTTGTATGAGATGGTTAAAAAGGCCAAAGATAAA
 561 AGGTTTCTTTTTTTTTCCTTTTTTGTCTATGAAGTTGCTGTTTATTTTTTTTGGCCTGTTTGATGTATGTGTGAAACAAT
 641 GTTGTCCAACAATAAACAGGAATTTTATTTTGCTGAGTTGTTCTAACAAAAAAAAAAAAAAAAAA

ID	Duplex structure	Position	Score	MFE
1	miRNA 3' acgUGCCGUUUUC--UUUGUUAGa 5' |:| ||| || |||||||| Target 5' aaaATGACAACAGAAAAACAATCt 3'	443 - 466	165.00	-11.90
2	miRNA 3' acgugccguuuuCUUUGUUAga 5' |||||||| Target 5' tgatgtatgtgtGAAACAATgt 3'	621 - 642	130.00	-10.60
3	miRNA 3' acgUGCCG--UUUUCUUUGUUAGa 5' || || |||||:|| |:|: Target 5' ---ACAGCAAAAAAGGAAAAGTTa 3'	1 - 21	109.00	-7.30

Mutant ID	Mutant Position	Mutant Source
COSN30177045	13	COSMIC
COSN2531319	37	COSMIC
COSN28739626	42	COSMIC
COSN15661146	56	COSMIC
COSN31597094	61	COSMIC
COSN31489952	70	COSMIC
COSN30541841	106	COSMIC
COSN30117157	113	COSMIC
COSN31536401	116	COSMIC
COSN30120270	136	COSMIC
COSN30529091	186	COSMIC
COSN30177094	198	COSMIC
COSN30177072	207	COSMIC
COSN31596030	248	COSMIC
COSN31558038	258	COSMIC
COSN31491824	293	COSMIC
COSN30131369	297	COSMIC
COSN31479647	326	COSMIC
COSN20993407	336	COSMIC
COSN31498583	343	COSMIC
COSN30191492	348	COSMIC
COSN31538984	351	COSMIC
COSN31614233	352	COSMIC
COSN30449069	366	COSMIC
COSN31575802	372	COSMIC
COSN30170024	375	COSMIC
COSN30463949	383	COSMIC
COSN30166123	412	COSMIC
COSN31529162	425	COSMIC
COSN30494822	427	COSMIC
COSN13977384	428	COSMIC
COSN31527154	440	COSMIC
COSN30526623	447	COSMIC
COSN26465992	448	COSMIC
COSN30488188	466	COSMIC
COSN2382265	473	COSMIC
COSN26669853	484	COSMIC
COSN31579391	494	COSMIC
COSN20681087	508	COSMIC
COSN30497157	517	COSMIC
COSN30453199	532	COSMIC
COSN28886994	544	COSMIC
COSN31492275	549	COSMIC
COSN26990916	556	COSMIC
COSN31548515	556	COSMIC
COSN24397639	565	COSMIC
COSN13977392	568	COSMIC
COSN26990917	572	COSMIC
COSN18726904	577	COSMIC
COSN2534311	577	COSMIC
COSN30525953	578	COSMIC
COSN18726905	579	COSMIC
COSN31524785	592	COSMIC
COSN26990920	613	COSMIC
COSN26990919	615	COSMIC
COSN31568093	618	COSMIC
COSN26676877	630	COSMIC
COSN30490222	634	COSMIC
COSN30528967	675	COSMIC
COSN30173902	676	COSMIC

Mutant ID	Mutant Position	Mutant Source
rs1222878604	1	dbSNP
rs921794203	3	dbSNP
rs1286128329	4	dbSNP
rs1197567819	6	dbSNP
rs1199414248	6	dbSNP
rs1491243450	11	dbSNP
rs753400853	12	dbSNP
rs1487783999	13	dbSNP
rs768026663	14	dbSNP
rs750767589	16	dbSNP
rs1269303790	17	dbSNP
rs760419505	18	dbSNP
rs1054738751	19	dbSNP
rs1208370468	20	dbSNP
rs1239608494	24	dbSNP
rs1293930360	26	dbSNP
rs1369607640	26	dbSNP
rs1429710829	26	dbSNP
rs368863947	26	dbSNP
rs756999912	26	dbSNP
rs766063352	26	dbSNP
rs753427430	27	dbSNP
rs750184715	30	dbSNP
rs754572320	32	dbSNP
rs778264619	34	dbSNP
rs563464274	36	dbSNP
rs758273484	37	dbSNP
rs62197232	39	dbSNP
rs931789374	41	dbSNP
rs758287487	42	dbSNP
rs777564345	44	dbSNP
rs13022221	45	dbSNP
rs1431978194	45	dbSNP
rs1177908478	46	dbSNP
rs1359505446	52	dbSNP
rs1427809644	52	dbSNP
rs1450287590	56	dbSNP
rs1192153372	58	dbSNP
rs1198424169	61	dbSNP
rs1246567780	66	dbSNP
rs13400325	67	dbSNP
rs1479136855	68	dbSNP
rs1041750949	69	dbSNP
rs11266766	70	dbSNP
rs11558923	71	dbSNP
rs1230390514	74	dbSNP
rs1313906697	77	dbSNP
rs1301829024	80	dbSNP
rs1213781417	85	dbSNP
rs896153147	86	dbSNP
rs1003301928	94	dbSNP
rs1389666480	96	dbSNP
rs1302359196	97	dbSNP
rs1464556769	97	dbSNP
rs1014495315	98	dbSNP
rs1056687516	105	dbSNP
rs1045949744	107	dbSNP
rs906066335	109	dbSNP
rs1002087988	111	dbSNP
rs1449736088	112	dbSNP
rs548945335	115	dbSNP
rs1027753837	116	dbSNP
rs1256071818	117	dbSNP
rs1203805154	120	dbSNP
rs932801563	120	dbSNP
rs952195691	122	dbSNP
rs1004885688	123	dbSNP
rs1366216962	124	dbSNP
rs13022261	127	dbSNP
rs1014970982	133	dbSNP
rs567478080	136	dbSNP
rs976023502	138	dbSNP
rs62197233	139	dbSNP
rs757524887	147	dbSNP
rs953256276	149	dbSNP
rs979646609	150	dbSNP
rs1277479483	151	dbSNP
rs975859842	152	dbSNP
rs925064686	153	dbSNP
rs1367537400	155	dbSNP
rs1185051521	156	dbSNP
rs1209560544	158	dbSNP
rs1425174823	167	dbSNP
rs922078928	176	dbSNP
rs1268504808	180	dbSNP
rs1180787095	187	dbSNP
rs1453506410	190	dbSNP
rs1186937726	198	dbSNP
rs3855570	199	dbSNP
rs539522846	203	dbSNP
rs1358546229	204	dbSNP
rs1263439384	205	dbSNP
rs1242941657	207	dbSNP
rs935116188	208	dbSNP
rs1342451991	214	dbSNP
rs1313565923	216	dbSNP
rs1169134174	223	dbSNP
rs746302260	224	dbSNP
rs1052183637	225	dbSNP
rs917612129	227	dbSNP
rs1456341875	228	dbSNP
rs4017855	228	dbSNP
rs558959660	228	dbSNP
rs546739843	229	dbSNP
rs571225495	239	dbSNP
rs112478714	242	dbSNP
rs1162361990	246	dbSNP
rs1391224456	249	dbSNP
rs35194787	249	dbSNP
rs949039468	251	dbSNP
rs1368645116	259	dbSNP
rs4017856	259	dbSNP
rs1157789108	265	dbSNP
rs1471285982	265	dbSNP
rs538669189	266	dbSNP
rs558405680	267	dbSNP
rs576708677	275	dbSNP
rs1182879803	276	dbSNP
rs1450938990	279	dbSNP
rs1442586503	282	dbSNP
rs575637532	282	dbSNP
rs1211367083	283	dbSNP
rs1358763594	287	dbSNP
rs1273987184	289	dbSNP
rs1045983455	293	dbSNP
rs537760044	295	dbSNP
rs1318181644	299	dbSNP
rs1327247842	302	dbSNP
rs1290279890	306	dbSNP
rs1411028348	306	dbSNP
rs1363826683	307	dbSNP
rs13022669	309	dbSNP
rs1322024312	317	dbSNP
rs201291591	317	dbSNP
rs1388829067	318	dbSNP
rs1391008153	323	dbSNP
rs1319550916	325	dbSNP
rs906097546	325	dbSNP
rs181944599	331	dbSNP
rs13022849	332	dbSNP
rs1060635	334	dbSNP
rs1001720763	347	dbSNP
rs1049658179	351	dbSNP
rs1477672273	351	dbSNP
rs887947467	352	dbSNP
rs1244745552	356	dbSNP
rs1005408919	357	dbSNP
rs1247180467	358	dbSNP
rs1015002114	364	dbSNP
rs1208411345	366	dbSNP
rs186289669	373	dbSNP
rs938748360	380	dbSNP
rs1224369702	393	dbSNP
rs1055923400	396	dbSNP
rs1273517959	402	dbSNP
rs894964272	403	dbSNP
rs541095679	405	dbSNP
rs997495771	406	dbSNP
rs1465388965	407	dbSNP
rs1190522789	408	dbSNP
rs1432496741	413	dbSNP
rs1028928039	416	dbSNP
rs1390331343	417	dbSNP
rs1234032040	419	dbSNP
rs1320663807	419	dbSNP
rs1413347047	419	dbSNP
rs746745843	422	dbSNP
rs780099479	424	dbSNP
rs1197364815	426	dbSNP
rs770711299	427	dbSNP
rs953384018	428	dbSNP
rs780315435	429	dbSNP
rs746991146	430	dbSNP
rs553084590	432	dbSNP
rs769741804	432	dbSNP
rs1431486319	433	dbSNP
rs777952470	433	dbSNP
rs749469868	437	dbSNP
rs771204040	438	dbSNP
rs3856532	440	dbSNP
rs774256901	441	dbSNP
rs774573704	445	dbSNP
rs979291369	446	dbSNP
rs1272685086	450	dbSNP
rs748711725	451	dbSNP
rs773718718	454	dbSNP
rs759850417	456	dbSNP
rs772444011	458	dbSNP
rs775951856	461	dbSNP
rs761186811	463	dbSNP
rs371875640	464	dbSNP
rs776394835	467	dbSNP
rs577593108	472	dbSNP
rs764831440	473	dbSNP
rs1411518859	475	dbSNP
rs1301934404	476	dbSNP
rs865776287	477	dbSNP
rs761281623	487	dbSNP
rs1349189726	488	dbSNP
rs545120772	488	dbSNP
rs763506886	488	dbSNP
rs776261091	488	dbSNP
rs563591878	489	dbSNP
rs763948802	491	dbSNP
rs751487975	493	dbSNP
rs1014587787	495	dbSNP
rs761243201	496	dbSNP
rs757095516	497	dbSNP
rs780823188	500	dbSNP
rs749559346	501	dbSNP
rs1289487407	504	dbSNP
rs755107666	508	dbSNP
rs779064314	510	dbSNP
rs764914643	511	dbSNP
rs1448793196	514	dbSNP
rs375182075	516	dbSNP
rs772274590	517	dbSNP
rs1449900758	519	dbSNP
rs773912926	521	dbSNP
rs747494804	523	dbSNP
rs1335599870	524	dbSNP
rs1388214106	524	dbSNP
rs1406585694	526	dbSNP
rs750131903	527	dbSNP
rs771462716	527	dbSNP
rs1323651691	530	dbSNP
rs530674898	531	dbSNP
rs1435043807	535	dbSNP
rs369231484	538	dbSNP
rs1431343886	539	dbSNP
rs542909883	539	dbSNP
rs1229695630	553	dbSNP
rs775067075	556	dbSNP
rs762510360	557	dbSNP
rs763575126	560	dbSNP
rs757150586	564	dbSNP
rs767368552	566	dbSNP
rs1390554544	567	dbSNP
rs953637619	567	dbSNP
rs1189656540	568	dbSNP
rs1235845041	568	dbSNP
rs371651937	568	dbSNP
rs750128516	568	dbSNP
rs758218401	568	dbSNP
rs755235375	569	dbSNP
rs779072251	570	dbSNP
rs1203457785	572	dbSNP
rs748365825	573	dbSNP
rs758597952	577	dbSNP
rs777968490	578	dbSNP
rs766327879	579	dbSNP
rs747548334	581	dbSNP
rs967617922	585	dbSNP
rs1490338087	586	dbSNP
rs780435249	588	dbSNP
rs201368548	590	dbSNP
rs1414814878	593	dbSNP
rs1163284028	595	dbSNP
rs1370990951	600	dbSNP
rs1163770015	601	dbSNP
rs1232309526	605	dbSNP
rs977666615	605	dbSNP
rs927549599	606	dbSNP
rs1476154934	617	dbSNP
rs1179664256	626	dbSNP
rs151332616	635	dbSNP
rs937632347	636	dbSNP
rs1232300378	640	dbSNP
rs928637017	640	dbSNP
rs1475536296	644	dbSNP
rs1251170026	645	dbSNP
rs1180722789	648	dbSNP
rs938717375	656	dbSNP
rs1233861455	662	dbSNP
rs991946232	663	dbSNP
rs1411004995	677	dbSNP
rs1449539208	684	dbSNP
rs1472688424	685	dbSNP
rs1049312415	691	dbSNP
rs554443093	693	dbSNP
rs528310965	697	dbSNP
rs1160904556	700	dbSNP
rs1233370940	701	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.

- Genome biology, 2014

BACKGROUND: Various microRNAs (miRNAs) are up- or downregulated in tumors. However, the repression of cognate miRNA targets responsible for the phenotypic effects of this dysregulation in patients remains largely unexplored. To define miRNA targets and associated pathways, together with their relationship to outcome in breast cancer, we integrated patient-paired miRNA-mRNA expression data with a set of validated miRNA targets and pathway inference. RESULTS: To generate a biochemically-validated set of miRNA-binding sites, we performed argonaute-2 photoactivatable-ribonucleoside-enhanced crosslinking and immunoprecipitation (AGO2-PAR-CLIP) in MCF7 cells. We then defined putative miRNA-target interactions using a computational model, which ranked and selected additional TargetScan-predicted interactions based on features of our AGO2-PAR-CLIP binding-site data. We subselected modeled interactions according to the abundance of their constituent miRNA and mRNA transcripts in tumors, and we took advantage of the variability of miRNA expression within molecular subtypes to detect miRNA repression. Interestingly, our data suggest that miRNA families control subtype-specific pathways; for example, miR-17, miR-19a, miR-25, and miR-200b show high miRNA regulatory activity in the triple-negative, basal-like subtype, whereas miR-22 and miR-24 do so in the HER2 subtype. An independent dataset validated our findings for miR-17 and miR-25, and showed a correlation between the expression levels of miR-182 targets and overall patient survival. Pathway analysis associated miR-17, miR-19a, and miR-200b with leukocyte transendothelial migration. CONCLUSIONS: We combined PAR-CLIP data with patient expression data to predict regulatory miRNAs, revealing potential therapeutic targets and prognostic markers in breast cancer.