>SIX5|NM_175875|3'UTR
   1 CCCAGTGTGGCCCCGTGGCCTCTCCCGACATTGGTGCTGAAGACGCAGGGACAGGAATGGGAGGGGGGAGCCCCAGAAAT
  81 GCGGTTGCTGAAGACCCCAGTCACCACATCCTTCTGCCTGGGTGGCCTCTCCAAGCCCTGGTGGTGCTGGGGGTTGTATC
 161 CCCGGCCACCTCCTGTCCAGGTCTCCATCCCCCTTTGGATGGGAGGCCTCTCTGTTACAGCCCTCCCCATGCTGTGCCCT
 241 GCCATATACGTGGGGGACTCAGGGTCCTGACTCAGGGGCCCTGCCCCCTCCACTTGGTACTAGCTGTAAGCGGAACACCC
 321 TGCCCCAGGGCCGGACTTCCAGCCCCCAGAGCCCTCTCCCTGTCACTCCCTGAAACACTATTAATAGCTCTGCCGATAGC
 401 TGGTGTTGTCACAACTGCCTGGAATCCGAAGGTGGAGGACAGGCAGCCCCGCGCCCCTGAGACTGGAGACCCTCCCCAGT
 481 GTGGCATTTCCTGCCAGGGGCGGGGGGTGGGGCAGCTGTGGGGAGACGGGGGTCTTCCTTCACCAGCTCCCCTCGACTCA
 561 AGCCCTTGTCCTCATTATCCGGCCCAGACCAAAGATTCCCTCATCCCTGGGGGCAGCCCTGCCGCTGTGTCTCCTTTGTA
 641 TCCTAAATCTTTATTTTTCTAGGACATGTTATGCCTCCATTTTCAATTAAAATAAAGTTATCGGATTACACCACCAAAAA
 721 AAAAAAAAAAAAAAAAA

ID	Duplex structure	Position	Score	MFE
1	miRNA 3' aggaCUGGGGAUCUGGGUUGAc 5' |||:| :| ||::||| Target 5' ggggGACTCAGGGTCCTGACTc 3'	252 - 273	126.00	-15.50
2	miRNA 3' aggACUGGGGAUCUGGGUUGac 5' ||:||:|| |||:|| Target 5' ccgTGGCCTCT---CCCGACat 3'	13 - 31	124.00	-19.70
3	miRNA 3' agGACUGGGGAUCUGGGUUGAc 5' ||| |||| :|:|| :||| Target 5' ccCTG-CCCCAGGGCCGGACTt 3'	318 - 338	123.00	-24.50

Mutant ID	Mutant Position	Mutant Source
COSN30119032	26	COSMIC
COSN26994780	27	COSMIC
COSN30124668	49	COSMIC
COSN1216739	63	COSMIC
COSN30503343	78	COSMIC
COSN31547343	88	COSMIC
COSN26994775	117	COSMIC
COSN30525737	160	COSMIC
COSN30104079	218	COSMIC
COSN20079300	252	COSMIC
COSN20706405	270	COSMIC
COSN17465991	317	COSMIC
COSN31532127	334	COSMIC
COSN28682974	452	COSMIC
COSN31594174	501	COSMIC
COSN14666401	533	COSMIC
COSN31572778	580	COSMIC
COSN5438525	624	COSMIC

Mutant ID	Mutant Position	Mutant Source
rs748122958	3	dbSNP
rs1230948039	4	dbSNP
rs779940276	5	dbSNP
rs1413826890	6	dbSNP
rs772216581	7	dbSNP
rs1005950812	10	dbSNP
rs1381386631	13	dbSNP
rs373814605	14	dbSNP
rs918658376	15	dbSNP
rs1459499174	22	dbSNP
rs377764854	25	dbSNP
rs549470439	26	dbSNP
rs529275321	27	dbSNP
rs75443440	32	dbSNP
rs1019906076	35	dbSNP
rs547671488	37	dbSNP
rs779539387	39	dbSNP
rs7257701	44	dbSNP
rs7257515	45	dbSNP
rs386809783	46	dbSNP
rs199784167	47	dbSNP
rs759116973	49	dbSNP
rs1271862691	51	dbSNP
rs1482449555	52	dbSNP
rs1202525693	63	dbSNP
rs1011651283	64	dbSNP
rs1440639872	65	dbSNP
rs541507866	69	dbSNP
rs938008042	70	dbSNP
rs1306849119	73	dbSNP
rs891584801	81	dbSNP
rs191930690	82	dbSNP
rs1053263845	83	dbSNP
rs945556774	86	dbSNP
rs562416403	87	dbSNP
rs542711350	88	dbSNP
rs1404406763	93	dbSNP
rs914094981	94	dbSNP
rs1229334698	100	dbSNP
rs1297539005	102	dbSNP
rs1002691514	104	dbSNP
rs117997878	105	dbSNP
rs553395014	107	dbSNP
rs1357061451	112	dbSNP
rs1276319665	114	dbSNP
rs921023165	116	dbSNP
rs1208996875	118	dbSNP
rs111867295	131	dbSNP
rs948598307	139	dbSNP
rs962374755	141	dbSNP
rs916574317	153	dbSNP
rs1468510536	157	dbSNP
rs1447713347	160	dbSNP
rs544694134	161	dbSNP
rs1182845086	163	dbSNP
rs931303032	164	dbSNP
rs1246336409	167	dbSNP
rs1014096465	175	dbSNP
rs577947584	177	dbSNP
rs1449253049	183	dbSNP
rs1320433957	187	dbSNP
rs1055235053	193	dbSNP
rs1002188276	194	dbSNP
rs1299092608	196	dbSNP
rs1339498858	198	dbSNP
rs1218229521	205	dbSNP
rs972799203	207	dbSNP
rs965548013	210	dbSNP
rs558317052	212	dbSNP
rs538018125	214	dbSNP
rs569453470	215	dbSNP
rs1189650979	220	dbSNP
rs1292430467	225	dbSNP
rs954353486	226	dbSNP
rs1022292281	231	dbSNP
rs1386914419	232	dbSNP
rs1350278715	233	dbSNP
rs1459233673	236	dbSNP
rs577252141	239	dbSNP
rs934178908	244	dbSNP
rs779606423	249	dbSNP
rs555529276	250	dbSNP
rs955887775	252	dbSNP
rs1031434417	256	dbSNP
rs1287409376	259	dbSNP
rs1326829865	262	dbSNP
rs1210455970	276	dbSNP
rs535960214	278	dbSNP
rs1248657371	279	dbSNP
rs907045992	284	dbSNP
rs1022717583	285	dbSNP
rs1181746186	289	dbSNP
rs1410156922	300	dbSNP
rs60934577	306	dbSNP
rs1166626585	307	dbSNP
rs887739217	311	dbSNP
rs1049431660	312	dbSNP
rs1390711532	314	dbSNP
rs1404232761	319	dbSNP
rs1321094716	320	dbSNP
rs962346779	321	dbSNP
rs1405112384	330	dbSNP
rs60009313	331	dbSNP
rs527560484	332	dbSNP
rs1230045684	333	dbSNP
rs775851686	333	dbSNP
rs1266850291	336	dbSNP
rs1190723990	337	dbSNP
rs1488916326	341	dbSNP
rs769250354	342	dbSNP
rs1292044579	344	dbSNP
rs571484885	350	dbSNP
rs770083556	351	dbSNP
rs912643630	353	dbSNP
rs1248622298	357	dbSNP
rs985665247	359	dbSNP
rs1484230403	362	dbSNP
rs1024240877	364	dbSNP
rs1183064838	367	dbSNP
rs1368399531	369	dbSNP
rs1472055719	375	dbSNP
rs1165519953	380	dbSNP
rs558901544	382	dbSNP
rs1375713409	387	dbSNP
rs187437149	388	dbSNP
rs1269173126	390	dbSNP
rs958553952	391	dbSNP
rs1322114868	392	dbSNP
rs914859507	394	dbSNP
rs138057336	395	dbSNP
rs1445669080	399	dbSNP
rs1285917203	400	dbSNP
rs955752770	403	dbSNP
rs1360221216	406	dbSNP
rs1031256527	408	dbSNP
rs1227831822	410	dbSNP
rs1367725727	411	dbSNP
rs1272740969	412	dbSNP
rs1294885862	418	dbSNP
rs1196611476	419	dbSNP
rs981162538	421	dbSNP
rs1441067100	427	dbSNP
rs1432454784	428	dbSNP
rs1444692213	432	dbSNP
rs879240350	433	dbSNP
rs1387931958	437	dbSNP
rs1463147662	438	dbSNP
rs1168161114	440	dbSNP
rs1044081116	447	dbSNP
rs971152846	450	dbSNP
rs1022665173	451	dbSNP
rs182439328	452	dbSNP
rs1434464807	453	dbSNP
rs1295416540	454	dbSNP
rs1328286974	456	dbSNP
rs1228361181	459	dbSNP
rs542305939	463	dbSNP
rs887594543	481	dbSNP
rs529004512	495	dbSNP
rs900045929	497	dbSNP
rs1264285894	499	dbSNP
rs993797353	501	dbSNP
rs941075881	502	dbSNP
rs1028817522	508	dbSNP
rs1193416347	508	dbSNP
rs374223300	508	dbSNP
rs909641018	508	dbSNP
rs1376767358	513	dbSNP
rs1427354984	520	dbSNP
rs997756797	524	dbSNP
rs1178411219	527	dbSNP
rs982829360	530	dbSNP
rs929678323	532	dbSNP
rs901639771	533	dbSNP
rs1318482773	535	dbSNP
rs1249028253	539	dbSNP
rs1387174572	542	dbSNP
rs1211017511	543	dbSNP
rs1460356348	547	dbSNP
rs897163084	552	dbSNP
rs867983171	554	dbSNP
rs958523198	555	dbSNP
rs1234647945	559	dbSNP
rs1207343227	561	dbSNP
rs1263059142	562	dbSNP
rs1312195084	565	dbSNP
rs1037070262	570	dbSNP
rs746364119	574	dbSNP
rs1364099467	578	dbSNP
rs944016830	579	dbSNP
rs968506694	580	dbSNP
rs1429666595	581	dbSNP
rs529739397	589	dbSNP
rs1399832132	592	dbSNP
rs1009964583	595	dbSNP
rs1302121571	600	dbSNP
rs746350984	600	dbSNP
rs781776160	602	dbSNP
rs1293082772	606	dbSNP
rs1388672780	609	dbSNP
rs534912874	612	dbSNP
rs577584260	613	dbSNP
rs191289354	614	dbSNP
rs998433045	619	dbSNP
rs771328873	623	dbSNP
rs914702913	624	dbSNP
rs900098016	627	dbSNP
rs1264295594	634	dbSNP
rs1489653775	636	dbSNP
rs1224198206	642	dbSNP
rs1039814500	653	dbSNP
rs990420999	658	dbSNP
rs558136870	665	dbSNP
rs1179817349	666	dbSNP
rs1449055389	667	dbSNP
rs1419532343	672	dbSNP
rs1164009136	674	dbSNP
rs375018587	675	dbSNP
rs888171735	677	dbSNP
rs1190780353	678	dbSNP
rs1370250149	697	dbSNP
rs934872794	702	dbSNP
rs1046835709	703	dbSNP
rs924856486	709	dbSNP
rs929619880	711	dbSNP
rs1311254949	715	dbSNP
rs981110179	716	dbSNP
rs1247602670	717	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.

- mBio, 2013

UNLABELLED: The question of how HIV-1 interfaces with cellular microRNA (miRNA) biogenesis and effector mechanisms has been highly controversial. Here, we first used deep sequencing of small RNAs present in two different infected cell lines (TZM-bl and C8166) and two types of primary human cells (CD4(+) peripheral blood mononuclear cells [PBMCs] and macrophages) to unequivocally demonstrate that HIV-1 does not encode any viral miRNAs. Perhaps surprisingly, we also observed that infection of T cells by HIV-1 has only a modest effect on the expression of cellular miRNAs at early times after infection. Comprehensive analysis of miRNA binding to the HIV-1 genome using the photoactivatable ribonucleoside-induced cross-linking and immunoprecipitation (PAR-CLIP) technique revealed several binding sites for cellular miRNAs, a subset of which were shown to be capable of mediating miRNA-mediated repression of gene expression. However, the main finding from this analysis is that HIV-1 transcripts are largely refractory to miRNA binding, most probably due to extensive viral RNA secondary structure. Together, these data demonstrate that HIV-1 neither encodes viral miRNAs nor strongly influences cellular miRNA expression, at least early after infection, and imply that HIV-1 transcripts have evolved to avoid inhibition by preexisting cellular miRNAs by adopting extensive RNA secondary structures that occlude most potential miRNA binding sites. IMPORTANCE: MicroRNAs (miRNAs) are a ubiquitous class of small regulatory RNAs that serve as posttranscriptional regulators of gene expression. Previous work has suggested that HIV-1 might subvert the function of the cellular miRNA machinery by expressing viral miRNAs or by dramatically altering the level of cellular miRNA expression. Using very sensitive approaches, we now demonstrate that neither of these ideas is in fact correct. Moreover, HIV-1 transcripts appear to largely avoid regulation by cellular miRNAs by adopting an extensive RNA secondary structure that occludes the ability of cellular miRNAs to interact with viral mRNAs. Together, these data suggest that HIV-1, rather than seeking to control miRNA function in infected cells, has instead evolved a mechanism to become largely invisible to cellular miRNA effector mechanisms.