ID	Duplex structure	Position	Score	MFE
1	miRNA 3' gcggcccgAGGGGCCCc 5' ||||:||| Target 5' ctagaacaTCCCTGGGc 3'	172 - 188	129.00	-14.40
2	miRNA 3' gcGGC-CCGAGGGGCCcc 5' ||| || |:|||| Target 5' cgCCGTGGGGCTCCGGag 3'	29 - 46	115.00	-25.70
3	miRNA 3' gcGGCCCGAGGGGCCCc 5' |:||| |:|||| | Target 5' gcCTGGGGTTCCCGAGg 3'	960 - 976	115.00	-25.90

Mutant ID	Mutant Position	Mutant Source
COSN30191026	4	COSMIC
COSN31493735	6	COSMIC
COSN31540972	6	COSMIC
COSN13546301	7	COSMIC
COSN30475936	17	COSMIC
COSN30104293	19	COSMIC
COSN30522118	20	COSMIC
COSN30100843	21	COSMIC
COSN30482587	28	COSMIC
COSN26991033	30	COSMIC
COSN31503622	33	COSMIC
COSN24297451	34	COSMIC
COSN31502564	37	COSMIC
COSN30193374	44	COSMIC
COSN16130872	45	COSMIC
COSN30150132	45	COSMIC
COSN13546303	59	COSMIC
COSN30502193	70	COSMIC
COSN30187324	73	COSMIC
COSN26635738	74	COSMIC
COSN30131488	80	COSMIC
COSN30495403	80	COSMIC
COSN31601381	95	COSMIC
COSN30161023	96	COSMIC
COSN26440585	162	COSMIC
COSN25575671	179	COSMIC
COSN4603780	307	COSMIC
COSN18777721	455	COSMIC
COSN25304224	498	COSMIC
COSN8470448	576	COSMIC
COSN26649852	687	COSMIC
COSN28808451	824	COSMIC
COSN19655896	851	COSMIC
COSN25554550	857	COSMIC
COSN8470449	871	COSMIC
COSN31487994	906	COSMIC
COSN16128175	1116	COSMIC
COSN16131707	1152	COSMIC
COSN31542479	1340	COSMIC
COSN31564540	1413	COSMIC
COSN31545846	1441	COSMIC
COSN26505494	1447	COSMIC
COSN16626360	1579	COSMIC
COSN31515421	1645	COSMIC
COSN16129668	1650	COSMIC
rs72673097	252	GWAS

Mutant ID	Mutant Position	Mutant Source
rs1256293636	3	dbSNP
rs755004036	4	dbSNP
rs1380633934	5	dbSNP
rs369551279	6	dbSNP
rs769423424	7	dbSNP
rs777303787	11	dbSNP
rs1237972970	12	dbSNP
rs748783332	13	dbSNP
rs775283573	14	dbSNP
rs373276106	15	dbSNP
rs1203940214	16	dbSNP
rs770382639	19	dbSNP
rs773894461	20	dbSNP
rs375151591	21	dbSNP
rs369952718	22	dbSNP
rs762085668	23	dbSNP
rs1467751161	25	dbSNP
rs765438541	25	dbSNP
rs373367448	30	dbSNP
rs377036580	31	dbSNP
rs751737122	33	dbSNP
rs754963221	34	dbSNP
rs973446485	40	dbSNP
rs368899845	43	dbSNP
rs929393703	44	dbSNP
rs752479708	46	dbSNP
rs1016479224	48	dbSNP
rs570547207	69	dbSNP
rs539468719	72	dbSNP
rs570743034	74	dbSNP
rs890961261	80	dbSNP
rs993667231	81	dbSNP
rs1210637730	82	dbSNP
rs772512205	84	dbSNP
rs1312177140	86	dbSNP
rs573467565	95	dbSNP
rs1335296174	96	dbSNP
rs749660576	98	dbSNP
rs899751880	117	dbSNP
rs536099288	118	dbSNP
rs954871692	125	dbSNP
rs1011636694	127	dbSNP
rs377470816	128	dbSNP
rs1021305345	131	dbSNP
rs773672788	139	dbSNP
rs757603415	140	dbSNP
rs1245977908	144	dbSNP
rs539467425	150	dbSNP
rs555727386	151	dbSNP
rs575781647	160	dbSNP
rs765005753	161	dbSNP
rs1256443433	162	dbSNP
rs544355533	163	dbSNP
rs1488842439	165	dbSNP
rs1286759350	166	dbSNP
rs564146178	167	dbSNP
rs1350630765	169	dbSNP
rs1266482496	170	dbSNP
rs991618545	175	dbSNP
rs1247104935	182	dbSNP
rs989487407	183	dbSNP
rs1023148068	184	dbSNP
rs913858411	188	dbSNP
rs1342553172	192	dbSNP
rs1315996282	211	dbSNP
rs1399827831	215	dbSNP
rs115324559	216	dbSNP
rs1164912012	219	dbSNP
rs974091953	228	dbSNP
rs919246218	231	dbSNP
rs950815987	233	dbSNP
rs1478613119	234	dbSNP
rs1239967247	242	dbSNP
rs1191496047	243	dbSNP
rs981971925	244	dbSNP
rs1249418061	248	dbSNP
rs1216093340	250	dbSNP
rs72673097	252	dbSNP
rs1182924276	253	dbSNP
rs371811751	256	dbSNP
rs1272649990	260	dbSNP
rs1383102237	262	dbSNP
rs1406910077	264	dbSNP
rs1165269674	266	dbSNP
rs1268577519	269	dbSNP
rs1344807978	270	dbSNP
rs911988594	271	dbSNP
rs560151700	276	dbSNP
rs943813889	277	dbSNP
rs1393582579	279	dbSNP
rs1039577702	285	dbSNP
rs1331480689	288	dbSNP
rs1055286072	290	dbSNP
rs1452478322	291	dbSNP
rs1166949604	297	dbSNP
rs921153062	302	dbSNP
rs55647429	303	dbSNP
rs941058331	317	dbSNP
rs150847540	322	dbSNP
rs1252844297	328	dbSNP
rs898110070	334	dbSNP
rs902848024	339	dbSNP
rs1229222107	340	dbSNP
rs562583701	341	dbSNP
rs1051941337	342	dbSNP
rs1056766164	343	dbSNP
rs895586096	347	dbSNP
rs1305388993	350	dbSNP
rs1315960926	352	dbSNP
rs369506012	353	dbSNP
rs114773270	354	dbSNP
rs1023119714	364	dbSNP
rs1352256477	367	dbSNP
rs1380540984	374	dbSNP
rs963903484	375	dbSNP
rs1414705472	387	dbSNP
rs995097672	388	dbSNP
rs1027017015	389	dbSNP
rs368342124	390	dbSNP
rs1010933949	391	dbSNP
rs1471220861	394	dbSNP
rs987473205	396	dbSNP
rs1182223779	397	dbSNP
rs6696481	401	dbSNP
rs539505691	406	dbSNP
rs139903281	409	dbSNP
rs566855750	413	dbSNP
rs535810053	417	dbSNP
rs1389416053	425	dbSNP
rs959475561	427	dbSNP
rs1334847442	430	dbSNP
rs990661793	442	dbSNP
rs1274529553	444	dbSNP
rs867714450	444	dbSNP
rs909664647	444	dbSNP
rs1310681702	445	dbSNP
rs868206752	447	dbSNP
rs376571493	449	dbSNP
rs1159832202	455	dbSNP
rs1449490195	458	dbSNP
rs575774447	459	dbSNP
rs538461167	471	dbSNP
rs558351526	489	dbSNP
rs1473135376	491	dbSNP
rs1259947873	493	dbSNP
rs921091187	501	dbSNP
rs750301676	520	dbSNP
rs756279907	521	dbSNP
rs1042942752	531	dbSNP
rs924523393	538	dbSNP
rs1283399650	543	dbSNP
rs1051972866	548	dbSNP
rs577824810	549	dbSNP
rs1008180077	556	dbSNP
rs1039183611	561	dbSNP
rs1340690769	563	dbSNP
rs1444064891	567	dbSNP
rs367863653	568	dbSNP
rs1056737655	579	dbSNP
rs1159005392	581	dbSNP
rs1406093385	585	dbSNP
rs780268019	586	dbSNP
rs1481964541	589	dbSNP
rs1163112648	593	dbSNP
rs1184123749	598	dbSNP
rs1475016251	607	dbSNP
rs754015175	609	dbSNP
rs1480263813	610	dbSNP
rs1044577370	616	dbSNP
rs1174358210	633	dbSNP
rs1427359827	636	dbSNP
rs1222174072	637	dbSNP
rs1336366121	641	dbSNP
rs1415485908	643	dbSNP
rs899323522	644	dbSNP
rs1353077744	650	dbSNP
rs995422537	655	dbSNP
rs1412033333	668	dbSNP
rs1026528622	677	dbSNP
rs1232112373	683	dbSNP
rs1350718047	688	dbSNP
rs755073476	690	dbSNP
rs1222596396	691	dbSNP
rs1318169310	692	dbSNP
rs1297206359	693	dbSNP
rs555395725	702	dbSNP
rs1003514222	706	dbSNP
rs190180934	707	dbSNP
rs748639663	708	dbSNP
rs1340026101	710	dbSNP
rs1460932811	715	dbSNP
rs1207014090	717	dbSNP
rs1373911207	718	dbSNP
rs959318449	721	dbSNP
rs1426558671	734	dbSNP
rs1418498407	736	dbSNP
rs1191499841	737	dbSNP
rs1252348915	738	dbSNP
rs1469788881	739	dbSNP
rs1250992405	740	dbSNP
rs974823813	744	dbSNP
rs1022837964	748	dbSNP
rs181616057	752	dbSNP
rs573572526	754	dbSNP
rs1306174417	767	dbSNP
rs747017196	770	dbSNP
rs968539485	772	dbSNP
rs979019140	773	dbSNP
rs1167450468	782	dbSNP
rs924521913	802	dbSNP
rs1235430791	821	dbSNP
rs1373844184	823	dbSNP
rs1301861648	825	dbSNP
rs934564551	826	dbSNP
rs1397261085	828	dbSNP
rs1300163680	838	dbSNP
rs1174039924	840	dbSNP
rs1388834214	840	dbSNP
rs1460675433	840	dbSNP
rs1192931591	845	dbSNP
rs1455378479	845	dbSNP
rs909729201	845	dbSNP
rs1432234372	846	dbSNP
rs1439816265	851	dbSNP
rs1252023288	858	dbSNP
rs962493628	861	dbSNP
rs1256163184	863	dbSNP
rs1130522	867	dbSNP
rs972457269	867	dbSNP
rs918299520	869	dbSNP
rs1234169272	870	dbSNP
rs1365350132	870	dbSNP
rs1336818223	871	dbSNP
rs1403895166	873	dbSNP
rs1313705349	874	dbSNP
rs1389675341	874	dbSNP
rs1436429730	874	dbSNP
rs933691590	874	dbSNP
rs1172989176	883	dbSNP
rs1373364410	883	dbSNP
rs1454269068	883	dbSNP
rs1365427413	887	dbSNP
rs1179053923	889	dbSNP
rs772742914	889	dbSNP
rs916911584	890	dbSNP
rs1486885342	894	dbSNP
rs201298308	894	dbSNP
rs1130523	895	dbSNP
rs879143289	895	dbSNP
rs879224963	895	dbSNP
rs912154098	895	dbSNP
rs145370622	896	dbSNP
rs1269134832	897	dbSNP
rs552049495	900	dbSNP
rs574957781	901	dbSNP
rs1294181157	903	dbSNP
rs1339963179	904	dbSNP
rs1039666862	905	dbSNP
rs1491332008	906	dbSNP
rs1230521070	907	dbSNP
rs756801665	907	dbSNP
rs1275011619	909	dbSNP
rs1358492931	910	dbSNP
rs946828468	921	dbSNP
rs1292251878	922	dbSNP
rs1042503740	924	dbSNP
rs1166402876	926	dbSNP
rs902595446	928	dbSNP
rs1256282727	932	dbSNP
rs1187296379	945	dbSNP
rs147659161	953	dbSNP
rs1452460366	956	dbSNP
rs1044118385	957	dbSNP
rs531475270	965	dbSNP
rs1235171432	971	dbSNP
rs1332969411	973	dbSNP
rs1035011584	974	dbSNP
rs1227969954	982	dbSNP
rs184834399	987	dbSNP
rs1048375566	989	dbSNP
rs1316193230	999	dbSNP
rs886637517	1008	dbSNP
rs570439684	1011	dbSNP
rs1384951802	1014	dbSNP
rs1416795452	1016	dbSNP
rs1168134296	1023	dbSNP
rs1475971446	1024	dbSNP
rs1019248904	1025	dbSNP
rs533296997	1026	dbSNP
rs1449426354	1034	dbSNP
rs1254104492	1037	dbSNP
rs996580855	1047	dbSNP
rs1022352595	1048	dbSNP
rs955106357	1060	dbSNP
rs1196580972	1064	dbSNP
rs1341676734	1066	dbSNP
rs986900163	1078	dbSNP
rs968549500	1088	dbSNP
rs978228889	1096	dbSNP
rs1371655689	1105	dbSNP
rs1305518758	1106	dbSNP
rs910901437	1107	dbSNP
rs942339134	1112	dbSNP
rs1329190750	1114	dbSNP
rs1411327865	1122	dbSNP
rs1319219646	1130	dbSNP
rs1166522124	1132	dbSNP
rs747462734	1132	dbSNP
rs540396539	1133	dbSNP
rs1031446213	1138	dbSNP
rs975026107	1139	dbSNP
rs915462374	1141	dbSNP
rs1182569447	1148	dbSNP
rs1437127404	1150	dbSNP
rs946903908	1156	dbSNP
rs1204246700	1158	dbSNP
rs1348322147	1164	dbSNP
rs1042578276	1165	dbSNP
rs1231969124	1168	dbSNP
rs1242312596	1169	dbSNP
rs1366764248	1174	dbSNP
rs1241264465	1179	dbSNP
rs955911907	1184	dbSNP
rs768586733	1206	dbSNP
rs1443657997	1213	dbSNP
rs1285797824	1214	dbSNP
rs902624796	1237	dbSNP
rs939405213	1242	dbSNP
rs1429556379	1243	dbSNP
rs1376418788	1247	dbSNP
rs537432031	1248	dbSNP
rs560451224	1251	dbSNP
rs1424997038	1252	dbSNP
rs1159228937	1254	dbSNP
rs775140763	1255	dbSNP
rs189730110	1257	dbSNP
rs1243041034	1269	dbSNP
rs566784404	1273	dbSNP
rs1422640136	1280	dbSNP
rs980195011	1281	dbSNP
rs1190042531	1287	dbSNP
rs535816870	1289	dbSNP
rs1284796799	1296	dbSNP
rs920329185	1302	dbSNP
rs549077723	1307	dbSNP
rs898415843	1309	dbSNP
rs993984319	1311	dbSNP
rs1415040960	1313	dbSNP
rs930376870	1317	dbSNP
rs1025418488	1319	dbSNP
rs1047499592	1326	dbSNP
rs1472887427	1329	dbSNP
rs955178920	1332	dbSNP
rs762617225	1334	dbSNP
rs944892808	1344	dbSNP
rs1473096018	1355	dbSNP
rs1405860425	1357	dbSNP
rs139767865	1358	dbSNP
rs986587237	1363	dbSNP
rs1320700084	1369	dbSNP
rs556138842	1370	dbSNP
rs900771133	1380	dbSNP
rs1394288697	1383	dbSNP
rs996161637	1386	dbSNP
rs1022703553	1388	dbSNP
rs903875751	1389	dbSNP
rs1266974682	1391	dbSNP
rs1238544108	1400	dbSNP
rs1291038850	1401	dbSNP
rs1227027159	1407	dbSNP
rs1000014440	1408	dbSNP
rs1378857763	1413	dbSNP
rs990214964	1413	dbSNP
rs1031079112	1414	dbSNP
rs1331544199	1420	dbSNP
rs538501568	1422	dbSNP
rs1461978532	1426	dbSNP
rs1229065870	1429	dbSNP
rs1163049890	1443	dbSNP
rs1423070787	1445	dbSNP
rs1262658604	1446	dbSNP
rs768132802	1447	dbSNP
rs773892267	1448	dbSNP
rs946936308	1455	dbSNP
rs558388767	1456	dbSNP
rs376077434	1458	dbSNP
rs1296785569	1459	dbSNP
rs571869696	1461	dbSNP
rs181200218	1462	dbSNP
rs1363660842	1468	dbSNP
rs1056558035	1472	dbSNP
rs1373250888	1476	dbSNP
rs553815311	1492	dbSNP
rs779452917	1498	dbSNP
rs1038314962	1499	dbSNP
rs1355266125	1520	dbSNP
rs573584395	1522	dbSNP
rs951786139	1526	dbSNP
rs1389548617	1527	dbSNP
rs983193555	1529	dbSNP
rs1455230320	1538	dbSNP
rs1250627130	1540	dbSNP
rs767502837	1541	dbSNP
rs1480759293	1551	dbSNP
rs994057787	1561	dbSNP
rs3189536	1565	dbSNP
rs1207134950	1581	dbSNP
rs1159256011	1590	dbSNP
rs1340478007	1595	dbSNP
rs542631623	1598	dbSNP
rs1235639855	1604	dbSNP
rs944829843	1607	dbSNP
rs145294623	1614	dbSNP
rs74511822	1616	dbSNP
rs1299287705	1619	dbSNP
rs922120744	1620	dbSNP
rs185205908	1625	dbSNP
rs1374406668	1630	dbSNP
rs1407804234	1632	dbSNP
rs1369689331	1633	dbSNP
rs1173976360	1639	dbSNP
rs932213811	1640	dbSNP
rs1375798842	1642	dbSNP
rs1304540801	1650	dbSNP
rs1419140651	1654	dbSNP
rs1252313381	1659	dbSNP
rs754039090	1661	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.

- Cell, 2013

The induction of pluripotency or trans-differentiation of one cell type to another can be accomplished with cell-lineage-specific transcription factors. Here, we report that repression of a single RNA binding polypyrimidine-tract-binding (PTB) protein, which occurs during normal brain development via the action of miR-124, is sufficient to induce trans-differentiation of fibroblasts into functional neurons. Besides its traditional role in regulated splicing, we show that PTB has a previously undocumented function in the regulation of microRNA functions, suppressing or enhancing microRNA targeting by competitive binding on target mRNA or altering local RNA secondary structure. A key event during neuronal induction is the relief of PTB-mediated blockage of microRNA action on multiple components of the REST complex, thereby derepressing a large array of neuronal genes, including miR-124 and multiple neuronal-specific transcription factors, in nonneuronal cells. This converts a negative feedback loop to a positive one to elicit cellular reprogramming to the neuronal lineage.

- 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.

- Genome research, 2016

DNA damage activates TP53-regulated surveillance mechanisms that are crucial in suppressing tumorigenesis. TP53 orchestrates these responses directly by transcriptionally modulating genes, including microRNAs (miRNAs), and by regulating miRNA biogenesis through interacting with the DROSHA complex. However, whether the association between miRNAs and AGO2 is regulated following DNA damage is not yet known. Here, we show that, following DNA damage, TP53 interacts with AGO2 to induce or reduce AGO2's association of a subset of miRNAs, including multiple let-7 family members. Furthermore, we show that specific mutations in TP53 decrease rather than increase the association of let-7 family miRNAs, reducing their activity without preventing TP53 from interacting with AGO2. This is consistent with the oncogenic properties of these mutants. Using AGO2 RIP-seq and PAR-CLIP-seq, we show that the DNA damage-induced increase in binding of let-7 family members to the RISC complex is functional. We unambiguously determine the global miRNA-mRNA interaction networks involved in the DNA damage response, validating them through the identification of miRNA-target chimeras formed by endogenous ligation reactions. We find that the target complementary region of the let-7 seed tends to have highly fixed positions and more variable ones. Additionally, we observe that miRNAs, whose cellular abundance or differential association with AGO2 is regulated by TP53, are involved in an intricate network of regulatory feedback and feedforward circuits. TP53-mediated regulation of AGO2-miRNA interaction represents a new mechanism of miRNA regulation in carcinogenesis.