>RPL41|NM_001035267|3'UTR
   1 ACCGCTAGCTTGTTGCACCGTGGAGGCCACAGGAGCAGAAACATGGAATGCCAGACGCTGGGGATGCTGGTACAAGTTGT
  81 GGGACTGCATGCTACTGTCTAGAGCTTGTCTCAATGGATCTAGAACTTCATCGCCCTCTGATCGCCGATCACCTCTGAGA
 161 CCCACCTTGCTCATAAACAAAATGCCCATGTTGGTCCTCTGCCCTGGACCTGTGACATTCTGGACTATTTCTGTGTTTAT
 241 TTGTGGCCGAGTGTAACAACCATATAATAAATCACCTCTTCCGCTGTTTTAGCTGAAGAATTAAATCAAAAAAAAAA

ID	Duplex structure	Position	Score	MFE
1	miRNA 3' gaguCAGGGUC-CGU--UUGGUAUu 5' | || || |:| ||||||| Target 5' ttgtGGCCGAGTGTAACAACCATAt 3'	241 - 265	152.00	-12.40
2	miRNA 3' gagUCAGG-GUC--CGU-UUGGUAUu 5' || || ||| ||| || |||: Target 5' tggAGGCCACAGGAGCAGAAACATGg 3'	21 - 46	113.00	-11.80
3	miRNA 3' gaGUCAGGGUC-----C---GUUUGGUAUu 5' | ||:::|| | :|||:|| | Target 5' cgCTGTTTTAGCTGAAGAATTAAATCAAAa 3'	282 - 311	100.00	-6.40

Mutant ID	Mutant Position	Mutant Source
COSN26571125	20	COSMIC
COSN30124076	47	COSMIC
COSN28687281	55	COSMIC
COSN30509961	66	COSMIC
COSN28510785	134	COSMIC
COSN25044579	144	COSMIC
COSN4703138	296	COSMIC

Mutant ID	Mutant Position	Mutant Source
rs762558153	2	dbSNP
rs1267073419	5	dbSNP
rs1363789835	8	dbSNP
rs1458424195	9	dbSNP
rs1301260872	10	dbSNP
rs767854248	10	dbSNP
rs1366063143	15	dbSNP
rs1265091204	20	dbSNP
rs1236507678	21	dbSNP
rs529277961	26	dbSNP
rs1158304643	34	dbSNP
rs1198695839	35	dbSNP
rs187497064	37	dbSNP
rs907882240	38	dbSNP
rs906718215	44	dbSNP
rs555977573	45	dbSNP
rs1221023921	51	dbSNP
rs1490664916	54	dbSNP
rs1348516660	58	dbSNP
rs1210154393	59	dbSNP
rs1277924942	67	dbSNP
rs999536490	70	dbSNP
rs1031061196	74	dbSNP
rs1280427314	80	dbSNP
rs1448563885	86	dbSNP
rs1193429638	88	dbSNP
rs944677251	95	dbSNP
rs1282757357	96	dbSNP
rs1040476800	107	dbSNP
rs1346077466	111	dbSNP
rs1325426763	112	dbSNP
rs1398800381	113	dbSNP
rs376833166	115	dbSNP
rs1158832127	117	dbSNP
rs574317207	121	dbSNP
rs1050053264	123	dbSNP
rs1198071629	125	dbSNP
rs904348671	127	dbSNP
rs13799	129	dbSNP
rs1191659547	134	dbSNP
rs1446827309	137	dbSNP
rs1435877887	142	dbSNP
rs1031558113	144	dbSNP
rs1029449314	145	dbSNP
rs953949668	147	dbSNP
rs1210923548	148	dbSNP
rs985791743	151	dbSNP
rs1262676937	153	dbSNP
rs1173604004	156	dbSNP
rs573142473	160	dbSNP
rs891479385	162	dbSNP
rs1013904574	171	dbSNP
rs912371469	173	dbSNP
rs1318761532	183	dbSNP
rs943871031	185	dbSNP
rs972584989	193	dbSNP
rs970239081	197	dbSNP
rs1319178732	205	dbSNP
rs2371352	219	dbSNP
rs918328150	221	dbSNP
rs1344831934	225	dbSNP
rs1166712704	232	dbSNP
rs1432913196	233	dbSNP
rs1475389486	239	dbSNP
rs1243163167	240	dbSNP
rs1190917604	241	dbSNP
rs569225203	249	dbSNP
rs556834319	250	dbSNP
rs1371908975	252	dbSNP
rs1242834457	254	dbSNP
rs1204510596	258	dbSNP
rs1314066278	266	dbSNP
rs1270993728	274	dbSNP
rs1214020926	276	dbSNP
rs1233438303	276	dbSNP
rs1048054975	277	dbSNP
rs894805756	279	dbSNP
rs1298171110	281	dbSNP
rs1230411820	282	dbSNP
rs4016501	283	dbSNP
rs948295715	284	dbSNP
rs4016502	287	dbSNP
rs1047099998	291	dbSNP
rs1452887493	295	dbSNP
rs952173579	301	dbSNP
rs1326320648	308	dbSNP
rs1205536593	311	dbSNP
rs1283037722	315	dbSNP
rs752600610	316	dbSNP
rs908107591	318	dbSNP
rs1215248920	319	dbSNP
rs944729696	322	dbSNP
rs538339877	325	dbSNP
rs1184536052	329	dbSNP
rs35934945	335	dbSNP
rs577517731	341	dbSNP
rs976514712	346	dbSNP
rs373838431	349	dbSNP
rs1453318319	350	dbSNP
rs1438451221	357	dbSNP
rs760637102	358	dbSNP
rs1193504710	361	dbSNP
rs867148871	364	dbSNP
rs906684071	366	dbSNP
rs932093125	369	dbSNP
rs999627940	371	dbSNP
rs1380901187	373	dbSNP
rs1031155838	378	dbSNP
rs935790340	379	dbSNP
rs1370600382	384	dbSNP
rs544997843	387	dbSNP
rs1423314121	389	dbSNP
rs1365457795	393	dbSNP
rs1164612935	396	dbSNP
rs559756685	400	dbSNP
rs1053041753	407	dbSNP
rs893882798	414	dbSNP
rs1470577188	417	dbSNP
rs1011412739	419	dbSNP
rs1220286800	421	dbSNP
rs1014158662	425	dbSNP
rs1290866576	427	dbSNP
rs1024422715	428	dbSNP
rs1028961905	431	dbSNP
rs905523075	434	dbSNP
rs1222825042	435	dbSNP
rs1001692193	436	dbSNP
rs1455842731	443	dbSNP
rs953518939	444	dbSNP

- 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.

- 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.