ID	Duplex structure	Position	Score	MFE
1	miRNA 3' auGUA--GGUUUUCUAGUGUAAc 5' ||| |: : | ||||||| Target 5' ttCATTCCTTGCTGCTCACATTc 3'	845 - 867	145.00	-8.30
2	miRNA 3' auGUAGGUUUUCUAGUGUAAc 5' ||||| | ||::||| Target 5' ccCATCC----GTTCGTATTt 3'	584 - 600	121.00	-9.90
3	miRNA 3' augUAGGUUU-UCUAGUGUAac 5' ||::|:: :| |||| Target 5' gtgATTTAGGTTTGTAACATcc 3'	763 - 784	94.00	-6.50

Mutant ID	Mutant Position	Mutant Source
COSN26641407	20	COSMIC
COSN26979188	21	COSMIC
COSN31512486	22	COSMIC
COSN30447311	26	COSMIC
COSN26979187	34	COSMIC
COSN30189576	36	COSMIC
COSN17132602	44	COSMIC
COSN23016971	47	COSMIC
COSN8516345	53	COSMIC
COSN19699473	104	COSMIC
COSN30481464	105	COSMIC
COSN30450661	125	COSMIC
COSN7976334	131	COSMIC
COSN30110692	137	COSMIC
COSN31483393	158	COSMIC
COSN8516344	176	COSMIC
COSN30139131	184	COSMIC
COSN30139114	185	COSMIC
COSN20076179	233	COSMIC
COSN26570685	249	COSMIC
COSN31545477	277	COSMIC
COSN26566789	314	COSMIC
COSN18723409	395	COSMIC
COSN20103984	398	COSMIC
COSN32063234	401	COSMIC
COSN20857089	636	COSMIC
COSN31594658	794	COSMIC
COSN30206725	816	COSMIC
COSN31562052	842	COSMIC
COSN31516212	881	COSMIC

Mutant ID	Mutant Position	Mutant Source
rs1383682218	8	dbSNP
rs778557985	9	dbSNP
rs1210222291	11	dbSNP
rs1459928148	17	dbSNP
rs377427078	18	dbSNP
rs753788812	19	dbSNP
rs779731853	20	dbSNP
rs193202877	21	dbSNP
rs750612423	23	dbSNP
rs1428117220	26	dbSNP
rs767668046	27	dbSNP
rs757456899	28	dbSNP
rs374216046	29	dbSNP
rs764128970	31	dbSNP
rs763419268	33	dbSNP
rs71554076	34	dbSNP
rs1168371262	35	dbSNP
rs1369218757	37	dbSNP
rs1412266012	38	dbSNP
rs776018013	39	dbSNP
rs765553961	40	dbSNP
rs776644792	40	dbSNP
rs199885709	44	dbSNP
rs1315033027	47	dbSNP
rs772754901	50	dbSNP
rs879129544	53	dbSNP
rs1245185344	56	dbSNP
rs1321081789	57	dbSNP
rs1404238988	58	dbSNP
rs1412672107	61	dbSNP
rs1161256517	62	dbSNP
rs373103767	63	dbSNP
rs369993289	64	dbSNP
rs1471500619	68	dbSNP
rs1410900248	81	dbSNP
rs1207292707	82	dbSNP
rs1388775151	83	dbSNP
rs1491090074	83	dbSNP
rs59078276	83	dbSNP
rs748193368	83	dbSNP
rs770426477	83	dbSNP
rs772195135	83	dbSNP
rs796959362	83	dbSNP
rs879148850	83	dbSNP
rs879160023	83	dbSNP
rs1176840408	84	dbSNP
rs1359103325	84	dbSNP
rs1491498968	84	dbSNP
rs1488895704	85	dbSNP
rs924627235	88	dbSNP
rs1380134199	95	dbSNP
rs73071548	104	dbSNP
rs1296593013	105	dbSNP
rs1362691389	112	dbSNP
rs1230341877	114	dbSNP
rs369064106	115	dbSNP
rs534471475	118	dbSNP
rs1207382074	124	dbSNP
rs1257282750	125	dbSNP
rs867271066	127	dbSNP
rs997525298	129	dbSNP
rs1052770356	130	dbSNP
rs1230738358	132	dbSNP
rs1189651223	133	dbSNP
rs201851892	145	dbSNP
rs1425027914	147	dbSNP
rs1431997321	150	dbSNP
rs934943116	151	dbSNP
rs904741230	152	dbSNP
rs572221578	155	dbSNP
rs1318706801	157	dbSNP
rs1391146507	163	dbSNP
rs1220166255	166	dbSNP
rs1270600442	168	dbSNP
rs948891829	172	dbSNP
rs1217468589	173	dbSNP
rs1302745845	175	dbSNP
rs1015461492	180	dbSNP
rs1238965757	182	dbSNP
rs186936655	188	dbSNP
rs992902096	189	dbSNP
rs887972629	193	dbSNP
rs538913360	195	dbSNP
rs1455511596	197	dbSNP
rs1472281855	199	dbSNP
rs1157062445	200	dbSNP
rs570012832	210	dbSNP
rs1176593586	222	dbSNP
rs377638703	224	dbSNP
rs1318717339	233	dbSNP
rs1349142963	237	dbSNP
rs1434042410	243	dbSNP
rs1295150492	249	dbSNP
rs1346108572	253	dbSNP
rs1027532948	255	dbSNP
rs1285973411	257	dbSNP
rs1045251003	258	dbSNP
rs1427570798	259	dbSNP
rs766238805	260	dbSNP
rs896745916	262	dbSNP
rs1289600272	269	dbSNP
rs1056609748	277	dbSNP
rs1248655429	278	dbSNP
rs1270166968	292	dbSNP
rs182660365	292	dbSNP
rs923607933	297	dbSNP
rs1463983265	302	dbSNP
rs867913576	308	dbSNP
rs979617050	309	dbSNP
rs550191787	310	dbSNP
rs946498460	318	dbSNP
rs757710426	325	dbSNP
rs1411901325	327	dbSNP
rs1268048341	328	dbSNP
rs910936888	337	dbSNP
rs1366092333	348	dbSNP
rs1043285785	354	dbSNP
rs78128603	355	dbSNP
rs1276093745	360	dbSNP
rs1442319214	367	dbSNP
rs894671965	375	dbSNP
rs1057225470	386	dbSNP
rs1203707233	390	dbSNP
rs1293003116	390	dbSNP
rs1342068348	390	dbSNP
rs938801173	390	dbSNP
rs536661534	395	dbSNP
rs567608456	396	dbSNP
rs1029618716	398	dbSNP
rs397774469	399	dbSNP
rs1473926167	400	dbSNP
rs972642229	408	dbSNP
rs1385709645	409	dbSNP
rs1429015651	409	dbSNP
rs5883060	409	dbSNP
rs1303324915	411	dbSNP
rs1409990050	411	dbSNP
rs1467433110	423	dbSNP
rs1338301506	427	dbSNP
rs1449857815	429	dbSNP
rs1357160133	434	dbSNP
rs1364846147	442	dbSNP
rs567990174	442	dbSNP
rs1434283193	447	dbSNP
rs1226652432	450	dbSNP
rs1300391954	460	dbSNP
rs1391007579	462	dbSNP
rs140825617	464	dbSNP
rs3173606	469	dbSNP
rs1199919766	472	dbSNP
rs1447702541	475	dbSNP
rs973371332	479	dbSNP
rs1014912959	481	dbSNP
rs1204617461	482	dbSNP
rs769575199	484	dbSNP
rs1448581920	485	dbSNP
rs1182902967	492	dbSNP
rs1006607490	493	dbSNP
rs1186480330	494	dbSNP
rs747461779	496	dbSNP
rs887887294	498	dbSNP
rs1024100635	501	dbSNP
rs1254563250	509	dbSNP
rs987270578	512	dbSNP
rs1012380051	523	dbSNP
rs527845187	524	dbSNP
rs896652983	526	dbSNP
rs761556113	527	dbSNP
rs1399508181	529	dbSNP
rs1415694475	537	dbSNP
rs1336904258	538	dbSNP
rs1387491413	538	dbSNP
rs998941104	539	dbSNP
rs1300327749	545	dbSNP
rs373398214	545	dbSNP
rs968442991	545	dbSNP
rs776295764	551	dbSNP
rs902742812	562	dbSNP
rs1273143440	563	dbSNP
rs1276325673	565	dbSNP
rs1347148967	565	dbSNP
rs571220331	570	dbSNP
rs1267701551	580	dbSNP
rs1463749998	582	dbSNP
rs1013208410	586	dbSNP
rs1358998268	597	dbSNP
rs1263663743	603	dbSNP
rs1447496140	606	dbSNP
rs1340811801	609	dbSNP
rs1198010148	619	dbSNP
rs946333879	624	dbSNP
rs910979983	625	dbSNP
rs768222041	627	dbSNP
rs13437725	632	dbSNP
rs551584553	636	dbSNP
rs147756101	640	dbSNP
rs1410745004	655	dbSNP
rs1455355117	668	dbSNP
rs1290996142	673	dbSNP
rs1397646769	674	dbSNP
rs922410264	677	dbSNP
rs531878676	682	dbSNP
rs1322078866	688	dbSNP
rs1333367301	688	dbSNP
rs1405582372	689	dbSNP
rs1002956911	691	dbSNP
rs1327330634	694	dbSNP
rs35319600	699	dbSNP
rs1376723810	702	dbSNP
rs1230524557	710	dbSNP
rs879190320	715	dbSNP
rs1261543079	720	dbSNP
rs548139740	724	dbSNP
rs972673216	726	dbSNP
rs1978133	727	dbSNP
rs909767732	728	dbSNP
rs1490834702	736	dbSNP
rs1199471981	743	dbSNP
rs984811560	771	dbSNP
rs1250515063	772	dbSNP
rs1047111138	775	dbSNP
rs931373309	776	dbSNP
rs1371447871	778	dbSNP
rs189593465	784	dbSNP
rs1427930918	785	dbSNP
rs1023757568	786	dbSNP
rs1166114764	792	dbSNP
rs1426014053	793	dbSNP
rs1254666984	794	dbSNP
rs1187760433	796	dbSNP
rs1012286766	802	dbSNP
rs1040106533	805	dbSNP
rs1354013530	805	dbSNP
rs574377091	813	dbSNP
rs186657751	815	dbSNP
rs1243765302	825	dbSNP
rs146417277	835	dbSNP
rs1361499463	837	dbSNP
rs910434689	838	dbSNP
rs1035139769	845	dbSNP
rs1481750875	851	dbSNP
rs1202521375	867	dbSNP
rs999623127	868	dbSNP
rs1480041747	872	dbSNP
rs541106928	878	dbSNP
rs13437722	881	dbSNP
rs1246340423	886	dbSNP
rs1319926888	889	dbSNP
rs1422932627	889	dbSNP
rs1292565899	906	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.

- 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.