>ZNF394|NM_032164|3'UTR
   1 TCCCAGCACTTTGGGAGGCCAAGGCAGGCAGATCATTTGAGATCAGGAGTTTGAAACCAGCCTGGCCAACATGGTAAAAT
  81 CCTGTCTCTACTAAAAATACAAAAATGAGCCGGGCATGGTGGTGCATGCCTGTAAGCCCAGCTATTCGGGAGGCTGAGGT
 161 AGGAGAATCACTTGAACCCAGGAGGCGGAAGTTGCAGTGAGCTGAGATCATGCCACTGCACTCCAGCCTGGGCAACAGAG
 241 CGAGACTCCATCTCAAAAAAGAAATAAAGTGCTGTCATTTTGATATGTTTCTATGTGAAAAAAAAAAAAAAAAAAAAAAA
 321 AAA

ID	Duplex structure	Position	Score	MFE
1	miRNA 3' cggUUCCCUUACCGUCCCUUUa 5' :||| | |||||| |:| Target 5' tggGAGGCCAAGGCAGGCAGAt 3'	12 - 33	119.00	-17.16
2	miRNA 3' cggUUCCCUUACCGUCCCUUUa 5' :||| : ||:||| :|| Target 5' cggGAGGCTGAGGTAGGAGAAt 3'	147 - 168	111.00	-15.50
3	miRNA 3' cgGUUCCCUUACCGUCCCUUUa 5' | :|| || | || ||:| Target 5' gcCTGGGCAACAG-AGCGAGAc 3'	226 - 246	103.00	-9.30

Mutant ID	Mutant Position	Mutant Source
COSN20067606	28	COSMIC
COSN30168725	41	COSMIC
COSN14312544	82	COSMIC
COSN30184441	107	COSMIC
COSN31540438	111	COSMIC
COSN30103387	121	COSMIC
COSN15103100	226	COSMIC

Mutant ID	Mutant Position	Mutant Source
rs1176434642	3	dbSNP
rs1479925312	5	dbSNP
rs1375524437	9	dbSNP
rs1336346778	12	dbSNP
rs775212234	13	dbSNP
rs1460807965	15	dbSNP
rs765819482	17	dbSNP
rs1419446010	20	dbSNP
rs1249802686	22	dbSNP
rs1196687613	23	dbSNP
rs1181290937	25	dbSNP
rs11559273	26	dbSNP
rs1462542777	29	dbSNP
rs375965460	30	dbSNP
rs946345348	31	dbSNP
rs746297912	32	dbSNP
rs1343195018	35	dbSNP
rs779412504	42	dbSNP
rs1240296959	45	dbSNP
rs757876962	46	dbSNP
rs749788141	47	dbSNP
rs1192052799	58	dbSNP
rs192140804	60	dbSNP
rs1460823136	63	dbSNP
rs1173240087	64	dbSNP
rs1401731949	71	dbSNP
rs11559272	76	dbSNP
rs548681261	82	dbSNP
rs1335230345	84	dbSNP
rs1054761574	88	dbSNP
rs187263300	89	dbSNP
rs1357453937	91	dbSNP
rs1306257138	96	dbSNP
rs1295179364	100	dbSNP
rs1324890794	100	dbSNP
rs565848000	103	dbSNP
rs769764970	109	dbSNP
rs1397457381	110	dbSNP
rs1322484283	111	dbSNP
rs112828549	112	dbSNP
rs1456733660	116	dbSNP
rs1349601728	118	dbSNP
rs1264872767	120	dbSNP
rs532257031	122	dbSNP
rs1476469323	123	dbSNP
rs1409200049	127	dbSNP
rs1204002579	128	dbSNP
rs191527346	136	dbSNP
rs1429910306	138	dbSNP
rs760419567	144	dbSNP
rs1424788563	146	dbSNP
rs982003597	147	dbSNP
rs540060067	148	dbSNP
rs971611641	161	dbSNP
rs1174949498	162	dbSNP
rs918812224	163	dbSNP
rs369707322	186	dbSNP
rs543390757	187	dbSNP
rs1016951128	191	dbSNP
rs531319374	209	dbSNP
rs1215557073	210	dbSNP
rs1326979128	211	dbSNP
rs560576856	220	dbSNP
rs1279012353	232	dbSNP
rs1238460589	234	dbSNP
rs772907032	241	dbSNP
rs375957912	244	dbSNP
rs771547591	246	dbSNP
rs1303371242	247	dbSNP
rs1312678484	249	dbSNP
rs1309438255	250	dbSNP
rs1003102112	252	dbSNP
rs1258423956	253	dbSNP
rs1029777814	264	dbSNP
rs1044410807	265	dbSNP
rs1216898064	265	dbSNP
rs1326975976	269	dbSNP
rs1490300921	269	dbSNP
rs1197690761	278	dbSNP
rs1427940723	280	dbSNP
rs998401508	283	dbSNP
rs529503677	284	dbSNP
rs571817379	285	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, 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.