>UGDH|NM_001184700|3'UTR
   1 AGATTGCCATTTTTATTTGTGATTTTTTTTTTTTTTTTTTGGTACTTCAGGATAGCAAATATCTATCTGCTATTAAATGG
  81 TAAATGAACCAAGTGTTTTTTTTTGTTTTTTTTTTGAGACAGAGTCTCACTGTTGCCCAGGCTGGAGTGCAGTGGTGCAA
 161 TCTCGGCTCACTGCAAGCTCTGCTTCCCAGGTTCACGCCATTCTCCTGGCTCAGCCTCCCAAGTAGCTGGGACTACAGGC
 241 ACCCGCCACAGTGCCTGGCTAATTTTTTGTATTTTTAGTAGAGACAGGGTTTCACCATGTGAGCCAGGATGGTCTCAATC
 321 TCCTGACCTTGTGAACCACCCGTCTCGGCCTCCCAAAGTGCTGGGATTACAGGTGTGAGCCACCACGCCTGGCCCATGAA
 401 CCAAGTGTTTTTAAGGAAACAAAACTATTTTTTTAATCATCAGATTTATACTAGCTATATGGATATTAGCATATCTGGTA
 481 ATTATGAATCTAGAATTTTTTTACATATTTTTATAATACTGTTAGCTCAGTTATTGGATGAGTGAAAGATAATCATGTTG
 561 GTTTTAATAGTGTCAATTTTTGTAAAATAAAAATTAAACTTCAAACTCTTTACTTTATAAATTGTCCATAGGCCACACTT
 641 TAATATCACATTATAAAGGGAAGGACAGTCTTCATTCCTCCTGGTTATTGGTTTGTTTGTCATTAAAGATATATTTTGAA
 721 TCCATGAAATTGCTATGCTAAACAGCCTTTACATGTATGGTCTGGTTAAAGTTCCTTTGTTCCTTTTGTTTTAATAAAAT
 801 GTGTCACTGATTTTTTAGCTCAAAATCATCACTGTTAATTTCCAGTCACCCCAAATATGGTTAAAAGATTTTTTTTTTAA
 881 TCATGAAGAGAAAATTAGTAGCATTTCTTTCTCTCCCCATTATTTATTGGTTTTCCTCACTAATCTTTTTTTTTTTAGTC
 961 CAAAAGCCAAAAATATTTATCTTGGTTTTACATTTTAATTTCCATTCTTAATTGTAATTTTTTTCTTTAAATAAGGAAAC
1041 CAATATAATCTCATGTATAAAAACTTAAATATTTTACAAGTTACATATAGCATCATTCTAAAATAAGAATTTTTTTTGTT
1121 TTCTGTCTGCTTTTTTCTTATGTCTCTTGTTGAGTTTTATATTTTCAGTGGTTATTTTTGCTTGTGTTAGATCATTATTA
1201 AAATATATCCAATGTCCCTTTGATACTTGTGCTCTGCTGAGAATGTACAGTTTGCATTAAACATCCCAGGTCTCATCCTT
1281 CAGGAATTTTGCAGTTCAATGAGAAGAGGGAGACAAATATAAAGATGAGGACAGAAGCATCTCTACAGATGAAAATTACA
1361 TAAATAAAACATTCTCCATCAACAACTAAAAAAAAAAAAAAAAAAA

ID	Duplex structure	Position	Score	MFE
1	miRNA 3' ggacaggUAGGCGGAC-ACGGGUCu 5' :||: ||| ||||||| Target 5' agacagaGTCTCACTGTTGCCCAGg 3'	117 - 141	153.00	-19.30
2	miRNA 3' ggacagGUAGGCG--GACACGGGUCu 5' || |||| | |||||::| Target 5' tacaggCACCCGCCACAGTGCCTGGc 3'	234 - 259	132.00	-21.60
3	miRNA 3' ggACAGGUAGGC---GGACACGGGUCu 5' ||||| |::| |:|||||:| | Target 5' aaTGTCCCTTTGATACTTGTGCTCTGc 3'	1211 - 1237	130.00	-20.60

Mutant ID	Mutant Position	Mutant Source
COSN26584180	15	COSMIC
COSN20099966	23	COSMIC
COSN29051066	23	COSMIC
COSN30156189	51	COSMIC
COSN30558399	95	COSMIC
COSN30570231	95	COSMIC
COSN30648583	96	COSMIC
COSN14111246	104	COSMIC
COSN14111243	105	COSMIC
COSN20099963	105	COSMIC
COSN14111241	106	COSMIC
COSN8490715	118	COSMIC
COSN30143959	161	COSMIC
COSN1296865	214	COSMIC
COSN20099958	946	COSMIC
COSN6830315	1144	COSMIC

Mutant ID	Mutant Position	Mutant Source
rs1180965913	3	dbSNP
rs774232472	4	dbSNP
rs768851040	6	dbSNP
rs1251984053	14	dbSNP
rs780662298	15	dbSNP
rs770254620	18	dbSNP
rs746196826	19	dbSNP
rs1254167605	21	dbSNP
rs968229282	22	dbSNP
rs1487332458	24	dbSNP
rs1283838509	25	dbSNP
rs1215747324	26	dbSNP
rs781707095	27	dbSNP
rs756902603	28	dbSNP
rs1226395614	32	dbSNP
rs77838464	37	dbSNP
rs202227157	39	dbSNP
rs1235593127	41	dbSNP
rs200660972	41	dbSNP
rs56814765	41	dbSNP
rs60656244	41	dbSNP
rs747530231	41	dbSNP
rs750682668	41	dbSNP
rs757453539	41	dbSNP
rs761117281	41	dbSNP
rs777047292	41	dbSNP
rs796374269	41	dbSNP
rs796764519	41	dbSNP
rs878908036	41	dbSNP
rs879029271	41	dbSNP
rs879085598	41	dbSNP
rs1271823919	42	dbSNP
rs1293501722	42	dbSNP
rs1491349512	42	dbSNP
rs1239976242	43	dbSNP
rs1318828816	44	dbSNP
rs751292134	47	dbSNP
rs1416127760	50	dbSNP
rs1021582678	58	dbSNP
rs1286042029	73	dbSNP
rs1445355997	78	dbSNP
rs1231734839	79	dbSNP
rs1009738946	80	dbSNP
rs1476060326	83	dbSNP
rs1334415236	87	dbSNP
rs1162572684	89	dbSNP
rs372155217	90	dbSNP
rs911671935	94	dbSNP
rs375681686	95	dbSNP
rs559757240	96	dbSNP
rs74462207	104	dbSNP
rs1291880165	105	dbSNP
rs1313097994	105	dbSNP
rs1398866320	105	dbSNP
rs370656620	105	dbSNP
rs1218149361	106	dbSNP
rs397761986	106	dbSNP
rs398083020	107	dbSNP
rs1263029993	114	dbSNP
rs1432060980	115	dbSNP
rs1486803142	116	dbSNP
rs58175625	116	dbSNP
rs1347355404	117	dbSNP
rs577021038	119	dbSNP
rs1255172456	125	dbSNP
rs1419462411	129	dbSNP
rs931850463	131	dbSNP
rs1049471606	135	dbSNP
rs995703876	136	dbSNP
rs1376875376	139	dbSNP
rs1416704688	141	dbSNP
rs1165107562	142	dbSNP
rs756509423	143	dbSNP
rs1475912172	148	dbSNP
rs543016246	158	dbSNP
rs543695037	160	dbSNP
rs138137686	164	dbSNP
rs978094764	165	dbSNP
rs539247532	167	dbSNP
rs113565511	169	dbSNP
rs536209475	171	dbSNP
rs1350188621	174	dbSNP
rs1208921357	181	dbSNP
rs970769221	189	dbSNP
rs866935209	192	dbSNP
rs1468258276	196	dbSNP
rs774224917	203	dbSNP
rs937983361	205	dbSNP
rs1274046121	206	dbSNP
rs1439063488	208	dbSNP
rs1235314195	209	dbSNP
rs58958665	214	dbSNP
rs1174899310	221	dbSNP
rs1354817692	223	dbSNP
rs979541040	225	dbSNP
rs992301675	228	dbSNP
rs1300318323	231	dbSNP
rs1012800741	233	dbSNP
rs961179816	241	dbSNP
rs1294904360	242	dbSNP
rs959574210	244	dbSNP
rs113746940	245	dbSNP
rs914031358	246	dbSNP
rs139160141	251	dbSNP
rs1308348144	253	dbSNP
rs1229315214	257	dbSNP
rs1440630733	264	dbSNP
rs1395596048	269	dbSNP
rs1326202018	271	dbSNP
rs966236814	289	dbSNP
rs1019139894	295	dbSNP
rs1462660488	305	dbSNP
rs1466742924	311	dbSNP
rs1007787655	327	dbSNP
rs953734087	328	dbSNP
rs146689241	330	dbSNP
rs189575810	341	dbSNP
rs534375273	342	dbSNP
rs1036843999	345	dbSNP
rs890183216	346	dbSNP
rs1453592630	347	dbSNP
rs550036670	361	dbSNP
rs761878107	372	dbSNP
rs931770762	373	dbSNP
rs746663330	377	dbSNP
rs1276554720	379	dbSNP
rs777230044	386	dbSNP
rs1054063099	387	dbSNP
rs1044117607	388	dbSNP
rs536467992	392	dbSNP
rs567524250	394	dbSNP
rs946796428	402	dbSNP
rs913986496	408	dbSNP
rs936590442	410	dbSNP
rs758070221	411	dbSNP
rs1301895166	414	dbSNP
rs1486563262	428	dbSNP
rs1234143833	435	dbSNP
rs1372223992	438	dbSNP
rs1262097710	442	dbSNP
rs1477697308	448	dbSNP
rs1306049709	449	dbSNP
rs978040875	450	dbSNP
rs1388205863	454	dbSNP
rs988212555	456	dbSNP
rs142543281	478	dbSNP
rs1297169891	485	dbSNP
rs912099643	492	dbSNP
rs1296574539	495	dbSNP
rs1340167799	501	dbSNP
rs917966991	502	dbSNP
rs745613346	508	dbSNP
rs1376740772	516	dbSNP
rs148153514	521	dbSNP
rs752959753	530	dbSNP
rs1213909804	531	dbSNP
rs1284829227	535	dbSNP
rs1171718385	541	dbSNP
rs776603078	544	dbSNP
rs1433991096	547	dbSNP
rs1027145781	554	dbSNP
rs1239542057	557	dbSNP
rs115329965	567	dbSNP
rs1181776571	569	dbSNP
rs1409437341	583	dbSNP
rs1456491159	584	dbSNP
rs1156978981	606	dbSNP
rs1360005813	618	dbSNP
rs1195252419	624	dbSNP
rs1435528777	626	dbSNP
rs961600552	627	dbSNP
rs11544853	647	dbSNP
rs1315009803	647	dbSNP
rs552249257	649	dbSNP
rs532495796	663	dbSNP
rs1004521538	666	dbSNP
rs1046573	677	dbSNP
rs1481669694	683	dbSNP
rs1051907675	687	dbSNP
rs555032653	691	dbSNP
rs1348019156	695	dbSNP
rs1212495283	713	dbSNP
rs1276135908	720	dbSNP
rs1441040821	738	dbSNP
rs74535222	743	dbSNP
rs1233938724	753	dbSNP
rs1034888219	754	dbSNP
rs900280924	755	dbSNP
rs1379697560	757	dbSNP
rs796576230	762	dbSNP
rs1053610554	765	dbSNP
rs905125273	776	dbSNP
rs1282989564	777	dbSNP
rs1400419398	779	dbSNP
rs1413669937	784	dbSNP
rs1043701683	791	dbSNP
rs936527449	792	dbSNP
rs569187280	801	dbSNP
rs946692893	805	dbSNP
rs1444432995	817	dbSNP
rs1330600543	825	dbSNP
rs574953532	827	dbSNP
rs1305872961	831	dbSNP
rs1052469069	855	dbSNP
rs1391561417	858	dbSNP
rs371670655	859	dbSNP
rs1351839632	867	dbSNP
rs570636726	869	dbSNP
rs1303162394	879	dbSNP
rs879734036	879	dbSNP
rs1238161442	881	dbSNP
rs777135902	886	dbSNP
rs550898179	890	dbSNP
rs912026682	898	dbSNP
rs949347656	901	dbSNP
rs1451370023	905	dbSNP
rs367874306	916	dbSNP
rs186287281	922	dbSNP
rs3172642	926	dbSNP
rs959471445	927	dbSNP
rs1473679274	935	dbSNP
rs920858270	940	dbSNP
rs1255560870	946	dbSNP
rs558615963	949	dbSNP
rs1330032903	957	dbSNP
rs35551098	957	dbSNP
rs78496970	957	dbSNP
rs879186142	957	dbSNP
rs199867019	958	dbSNP
rs920026585	973	dbSNP
rs1271579407	977	dbSNP
rs1320430233	987	dbSNP
rs538723626	1000	dbSNP
rs1187298763	1010	dbSNP
rs1217260391	1021	dbSNP
rs1257946212	1030	dbSNP
rs973709971	1035	dbSNP
rs1212177211	1057	dbSNP
rs962675622	1076	dbSNP
rs974243182	1077	dbSNP
rs1194100332	1079	dbSNP
rs1265692847	1084	dbSNP
rs1486323759	1089	dbSNP
rs1476698325	1093	dbSNP
rs1260234465	1109	dbSNP
rs1203845646	1111	dbSNP
rs1015309696	1118	dbSNP
rs11544852	1118	dbSNP
rs1161394889	1118	dbSNP
rs1389314548	1118	dbSNP
rs1400839326	1118	dbSNP
rs1261647422	1123	dbSNP
rs961548919	1125	dbSNP
rs1330756593	1129	dbSNP
rs1015818602	1132	dbSNP
rs987049704	1133	dbSNP
rs955643452	1134	dbSNP
rs1398520616	1137	dbSNP
rs1277908632	1138	dbSNP
rs1356539425	1140	dbSNP
rs11931052	1149	dbSNP
rs960453719	1159	dbSNP
rs1288396480	1162	dbSNP
rs996270162	1165	dbSNP
rs1487400344	1171	dbSNP
rs1413630495	1193	dbSNP
rs1193252289	1199	dbSNP
rs1355472198	1212	dbSNP
rs900226665	1214	dbSNP
rs1336113027	1215	dbSNP
rs34844833	1219	dbSNP
rs1185311948	1223	dbSNP
rs1380414931	1232	dbSNP
rs1034825924	1239	dbSNP
rs1470172163	1244	dbSNP
rs181729245	1247	dbSNP
rs1450	1249	dbSNP
rs1000621202	1267	dbSNP
rs902359077	1271	dbSNP
rs969276440	1272	dbSNP
rs143808039	1274	dbSNP
rs1313121592	1276	dbSNP
rs1403289587	1281	dbSNP
rs1398220291	1296	dbSNP
rs547660133	1299	dbSNP
rs896421895	1300	dbSNP
rs1340450605	1302	dbSNP
rs1055113905	1307	dbSNP
rs1164402301	1308	dbSNP
rs1311498747	1310	dbSNP
rs1475584701	1319	dbSNP
rs892457784	1343	dbSNP
rs1281384508	1345	dbSNP
rs1484108836	1346	dbSNP
rs1052393869	1348	dbSNP
rs1255359370	1360	dbSNP
rs1008896823	1378	dbSNP
rs1370220445	1388	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.

- Genome biology, 2013

BACKGROUND: In recent years, a variety of small RNAs derived from other RNAs with well-known functions such as tRNAs and snoRNAs, have been identified. The functional relevance of these RNAs is largely unknown. To gain insight into the complexity of snoRNA processing and the functional relevance of snoRNA-derived small RNAs, we sequence long and short RNAs, small RNAs that co-precipitate with the Argonaute 2 protein and RNA fragments obtained in photoreactive nucleotide-enhanced crosslinking and immunoprecipitation (PAR-CLIP) of core snoRNA-associated proteins. RESULTS: Analysis of these data sets reveals that many loci in the human genome reproducibly give rise to C/D box-like snoRNAs, whose expression and evolutionary conservation are typically less pronounced relative to the snoRNAs that are currently cataloged. We further find that virtually all C/D box snoRNAs are specifically processed inside the regions of terminal complementarity, retaining in the mature form only 4-5 nucleotides upstream of the C box and 2-5 nucleotides downstream of the D box. Sequencing of the total and Argonaute 2-associated populations of small RNAs reveals that despite their cellular abundance, C/D box-derived small RNAs are not efficiently incorporated into the Ago2 protein. CONCLUSIONS: We conclude that the human genome encodes a large number of snoRNAs that are processed along the canonical pathway and expressed at relatively low levels. Generation of snoRNA-derived processing products with alternative, particularly miRNA-like, functions appears to be uncommon.

- Neoplasia (New York, N.Y.), 2016

MicroRNA (miRNA) deregulation in prostate cancer (PCa) contributes to PCa initiation and metastatic progression. To comprehensively define the cancer-associated changes in miRNA targeting and function in commonly studied models of PCa, we performed photoactivatable ribonucleoside-enhanced cross-linking immunoprecipitation of the Argonaute protein in a panel of PCa cell lines modeling different stages of PCa progression. Using this comprehensive catalogue of miRNA targets, we analyzed miRNA targeting on known drivers of PCa and examined tissue-specific and stage-specific pathway targeting by miRNAs. We found that androgen receptor is the most frequently targeted PCa oncogene and that miR-148a targets the largest number of known PCa drivers. Globally, tissue-specific and stage-specific changes in miRNA targeting are driven by homeostatic response to active oncogenic pathways. Our findings indicate that, even in advanced PCa, the miRNA pool adapts to regulate continuing alterations in the cancer genome to balance oncogenic molecular changes. These findings are important because they are the first to globally characterize miRNA changes in PCa and demonstrate how the miRNA target spectrum responds to staged tumorigenesis.