ID	Duplex structure	Position	Score	MFE
1	miRNA 3' ggggggaggggCCCUGGg 5' |||||| Target 5' gcttgcttgaaGGGACCc 3'	625 - 642	120.00	-19.00
2	miRNA 3' ggggggaggggCCCUGGg 5' |||||| Target 5' ataaacccaggGGGACCa 3'	951 - 968	120.00	-17.00
3	miRNA 3' gggggGAGG--GGCCCUGGg 5' |||| | |||||: Target 5' ggcggCTCCAGCAGGGACTa 3'	923 - 942	107.00	-16.60

Mutant ID	Mutant Position	Mutant Source
COSN24297432	32	COSMIC
COSN28866274	91	COSMIC
COSN30538432	94	COSMIC
COSN31544104	130	COSMIC
COSN30173523	174	COSMIC
COSN20237851	185	COSMIC
COSN21994754	545	COSMIC
COSN19322641	968	COSMIC
COSN31571814	1048	COSMIC
COSN31541954	1049	COSMIC
COSN1103527	1071	COSMIC

Mutant ID	Mutant Position	Mutant Source
rs753668634	2	dbSNP
rs1167165755	4	dbSNP
rs887228686	5	dbSNP
rs1378852436	11	dbSNP
rs1396850927	13	dbSNP
rs75817414	14	dbSNP
rs1305882763	15	dbSNP
rs751812100	16	dbSNP
rs754956677	19	dbSNP
rs781317782	25	dbSNP
rs752785686	31	dbSNP
rs1255221308	32	dbSNP
rs768539494	41	dbSNP
rs1183283894	42	dbSNP
rs1259190412	43	dbSNP
rs1341651963	47	dbSNP
rs1477246536	49	dbSNP
rs756581218	56	dbSNP
rs529573626	59	dbSNP
rs1276708323	67	dbSNP
rs1467673244	72	dbSNP
rs1174516485	78	dbSNP
rs58718331	79	dbSNP
rs1009488987	83	dbSNP
rs776248027	83	dbSNP
rs757649362	85	dbSNP
rs1304883965	86	dbSNP
rs778468809	87	dbSNP
rs745545529	88	dbSNP
rs1399575355	89	dbSNP
rs904195693	89	dbSNP
rs541917030	90	dbSNP
rs747996133	90	dbSNP
rs769563259	91	dbSNP
rs867441673	91	dbSNP
rs563328250	92	dbSNP
rs1342402151	97	dbSNP
rs1254225258	101	dbSNP
rs1346994049	102	dbSNP
rs1031297174	103	dbSNP
rs1258232185	105	dbSNP
rs1486784067	108	dbSNP
rs1464598872	110	dbSNP
rs1277798671	111	dbSNP
rs1312596978	114	dbSNP
rs1403452832	115	dbSNP
rs766019488	116	dbSNP
rs1258649806	118	dbSNP
rs1487765325	119	dbSNP
rs1296688571	120	dbSNP
rs1008590796	135	dbSNP
rs1219673368	139	dbSNP
rs530779480	154	dbSNP
rs72659625	157	dbSNP
rs972159618	159	dbSNP
rs964139284	180	dbSNP
rs976076172	181	dbSNP
rs952043046	185	dbSNP
rs920222502	186	dbSNP
rs759244376	187	dbSNP
rs1194192429	188	dbSNP
rs982826928	189	dbSNP
rs1266871002	204	dbSNP
rs1162957805	206	dbSNP
rs908530973	212	dbSNP
rs552165192	215	dbSNP
rs368706575	216	dbSNP
rs1021511697	221	dbSNP
rs1157346429	222	dbSNP
rs570447840	225	dbSNP
rs538307425	230	dbSNP
rs547360504	231	dbSNP
rs1302933608	237	dbSNP
rs1366383854	239	dbSNP
rs1427567583	242	dbSNP
rs915750403	243	dbSNP
rs948548401	250	dbSNP
rs565739553	251	dbSNP
rs1355786460	257	dbSNP
rs575147294	261	dbSNP
rs1216986424	267	dbSNP
rs904259701	268	dbSNP
rs1487602605	270	dbSNP
rs1193115886	275	dbSNP
rs1384949494	283	dbSNP
rs904480015	284	dbSNP
rs999162226	286	dbSNP
rs889401856	288	dbSNP
rs1164467664	289	dbSNP
rs1052750297	299	dbSNP
rs1459812577	301	dbSNP
rs536310795	303	dbSNP
rs898005114	304	dbSNP
rs1008602197	306	dbSNP
rs1017272606	307	dbSNP
rs1445328752	317	dbSNP
rs964807265	339	dbSNP
rs1306460927	340	dbSNP
rs1378973916	343	dbSNP
rs997062489	345	dbSNP
rs1311986252	359	dbSNP
rs555088804	367	dbSNP
rs1027547992	369	dbSNP
rs994049047	371	dbSNP
rs953019633	373	dbSNP
rs1027741647	375	dbSNP
rs952072483	379	dbSNP
rs1028089629	382	dbSNP
rs1196748774	382	dbSNP
rs558923918	387	dbSNP
rs1278859253	392	dbSNP
rs528036413	396	dbSNP
rs537681976	397	dbSNP
rs1225422442	407	dbSNP
rs1425911947	409	dbSNP
rs1033675348	414	dbSNP
rs1464808992	429	dbSNP
rs1328631548	431	dbSNP
rs752565362	434	dbSNP
rs908562204	435	dbSNP
rs1270682159	443	dbSNP
rs1490939542	444	dbSNP
rs756063234	456	dbSNP
rs559208662	458	dbSNP
rs1317474135	465	dbSNP
rs1217056345	468	dbSNP
rs1260288454	473	dbSNP
rs1200663303	477	dbSNP
rs1458245263	478	dbSNP
rs992747401	481	dbSNP
rs959989881	484	dbSNP
rs992920862	489	dbSNP
rs916033180	496	dbSNP
rs577581923	499	dbSNP
rs1182766013	500	dbSNP
rs1469021373	516	dbSNP
rs1477076279	518	dbSNP
rs917127759	527	dbSNP
rs948814294	529	dbSNP
rs945921453	534	dbSNP
rs978643382	544	dbSNP
rs1332941773	560	dbSNP
rs1408741753	568	dbSNP
rs1357289239	570	dbSNP
rs925713103	572	dbSNP
rs535338767	573	dbSNP
rs1339570257	575	dbSNP
rs935745940	587	dbSNP
rs754334677	596	dbSNP
rs12046738	597	dbSNP
rs944342116	598	dbSNP
rs1367739414	599	dbSNP
rs1211416764	611	dbSNP
rs1040647552	624	dbSNP
rs1487512389	628	dbSNP
rs898032303	629	dbSNP
rs993671399	631	dbSNP
rs1475537608	635	dbSNP
rs1171438551	644	dbSNP
rs1405294005	647	dbSNP
rs1415729329	647	dbSNP
rs1174150096	649	dbSNP
rs934611258	653	dbSNP
rs750495760	655	dbSNP
rs1052925660	660	dbSNP
rs1327892246	668	dbSNP
rs1049248268	671	dbSNP
rs1299812259	671	dbSNP
rs890125737	674	dbSNP
rs79080032	679	dbSNP
rs1038671861	680	dbSNP
rs1235205700	691	dbSNP
rs900272399	697	dbSNP
rs550951605	698	dbSNP
rs1219160482	703	dbSNP
rs1287225269	704	dbSNP
rs149256824	707	dbSNP
rs201597802	707	dbSNP
rs1293464982	710	dbSNP
rs1193781770	713	dbSNP
rs200433534	714	dbSNP
rs1359765909	732	dbSNP
rs780306954	737	dbSNP
rs11545627	738	dbSNP
rs1160186737	748	dbSNP
rs1385375243	753	dbSNP
rs867620004	754	dbSNP
rs1321827050	755	dbSNP
rs1024230909	770	dbSNP
rs1441658431	789	dbSNP
rs1308627949	797	dbSNP
rs1375271219	798	dbSNP
rs967666430	806	dbSNP
rs1280692109	811	dbSNP
rs1356050901	818	dbSNP
rs541556602	830	dbSNP
rs1239376883	831	dbSNP
rs1452987375	832	dbSNP
rs1444060675	856	dbSNP
rs1161792212	857	dbSNP
rs1437334301	865	dbSNP
rs747142608	866	dbSNP
rs1364382519	867	dbSNP
rs563424892	871	dbSNP
rs1161261794	872	dbSNP
rs1416150175	875	dbSNP
rs1462189693	884	dbSNP
rs1330701650	886	dbSNP
rs1425481974	894	dbSNP
rs957142791	912	dbSNP
rs1167569197	916	dbSNP
rs985855669	917	dbSNP
rs768926702	919	dbSNP
rs1242995040	920	dbSNP
rs992869885	927	dbSNP
rs1329442368	930	dbSNP
rs1023371141	936	dbSNP
rs910268547	939	dbSNP
rs1197099481	942	dbSNP
rs1251086078	947	dbSNP
rs970199041	957	dbSNP
rs1449796898	966	dbSNP
rs1192742069	967	dbSNP
rs1198636498	967	dbSNP
rs1228892659	967	dbSNP
rs1251421146	967	dbSNP
rs1259577224	967	dbSNP
rs1261227558	967	dbSNP
rs1314830122	967	dbSNP
rs1344150995	967	dbSNP
rs1369997656	967	dbSNP
rs1430525677	967	dbSNP
rs1485872965	967	dbSNP
rs1491298970	967	dbSNP
rs371112044	967	dbSNP
rs56974171	967	dbSNP
rs570824683	967	dbSNP
rs71831349	967	dbSNP
rs759215590	967	dbSNP
rs1491127280	968	dbSNP
rs764651842	969	dbSNP
rs1464645113	970	dbSNP
rs1040409428	971	dbSNP
rs1226171373	974	dbSNP
rs1249271383	975	dbSNP
rs1419424010	986	dbSNP
rs1337835645	990	dbSNP
rs1197973885	993	dbSNP
rs919549936	1003	dbSNP
rs1461227320	1009	dbSNP
rs1182312015	1011	dbSNP
rs1244981245	1012	dbSNP
rs1364121455	1013	dbSNP
rs1424477915	1014	dbSNP
rs1329967665	1016	dbSNP
rs1215539500	1017	dbSNP
rs1230518912	1017	dbSNP
rs188515142	1017	dbSNP
rs1283661084	1018	dbSNP
rs934452970	1019	dbSNP
rs575330822	1026	dbSNP
rs988594704	1030	dbSNP
rs1267023645	1032	dbSNP
rs1431501005	1037	dbSNP
rs1195596034	1040	dbSNP
rs201506039	1041	dbSNP
rs944606748	1046	dbSNP
rs1439658745	1047	dbSNP
rs1002345511	1049	dbSNP
rs143571041	1059	dbSNP
rs900137264	1060	dbSNP
rs930428161	1068	dbSNP
rs1049249014	1100	dbSNP
rs1382806205	1104	dbSNP
rs1381214091	1105	dbSNP
rs781363836	1112	dbSNP
rs768666059	1113	dbSNP

- 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.

- Genes & development, 2013

When adapting to environmental stress, cells attenuate and reprogram their translational output. In part, these altered translation profiles are established through changes in the interactions between RNA-binding proteins and mRNAs. The Argonaute 2 (Ago2)/microRNA (miRNA) machinery has been shown to participate in stress-induced translational up-regulation of a particular mRNA, CAT-1; however, a detailed, transcriptome-wide understanding of the involvement of Ago2 in the process has been lacking. Here, we profiled the overall changes in Ago2-mRNA interactions upon arsenite stress by cross-linking immunoprecipitation (CLIP) followed by high-throughput sequencing (CLIP-seq). Ago2 displayed a significant remodeling of its transcript occupancy, with the majority of 3' untranslated region (UTR) and coding sequence (CDS) sites exhibiting stronger interaction. Interestingly, target sites that were destined for release from Ago2 upon stress were depleted in miRNA complementarity signatures, suggesting an alternative mode of interaction. To compare the changes in Ago2-binding patterns across transcripts with changes in their translational states, we measured mRNA profiles on ribosome/polysome gradients by RNA sequencing (RNA-seq). Increased Ago2 occupancy correlated with stronger repression of translation for those mRNAs, as evidenced by a shift toward lighter gradient fractions upon stress, while release of Ago2 was associated with the limited number of transcripts that remained translated. Taken together, these data point to a role for Ago2 and the mammalian miRNAs in mediating the translational component of the stress response.

- Breast cancer research and treatment, 2014

miRNAs regulate the expression of genes in both normal physiology and disease. While miRNAs have been demonstrated to play a pivotal role in aspects of cancer biology, these reports have generally focused on the regulation of single genes. Such single-gene approaches have significant limitations, relying on miRNA expression levels and heuristic predictions of mRNA-binding sites. This results in only circumstantial evidence of miRNA-target interaction and typically leads to large numbers of false positive predictions. Here, we used a genome-wide approach (high-throughput sequencing of RNA isolated by crosslinking immunoprecipitation, HITS-CLIP) to define direct miRNA-mRNA interactions in three breast cancer subtypes (estrogen receptor positive, Her2 amplified, and triple negative). Focusing on steroid receptor signaling, we identified two novel regulators of the ER pathway (miR-9-5p and miR-193a/b-3p), which together target multiple genes involved in ER signaling. Moreover, this approach enabled the definition of miR-9-5p as a global regulator of steroid receptor signaling in breast cancer. We show that miRNA targets and networks defined by HITS-CLIP under physiologic conditions are predictive of patient outcomes and provide global insight into miRNA regulation in breast cancer.

- Nucleic acids research, 2016

MicroRNAs (miRs) have emerged as key biological effectors in human health and disease. These small noncoding RNAs are incorporated into Argonaute (Ago) proteins, where they direct post-transcriptional gene silencing via base-pairing with target transcripts. Although miRs have become intriguing biological entities and attractive therapeutic targets, the translational impacts of miR research remain limited by a paucity of empirical miR targeting data, particularly in human primary tissues. Here, to improve our understanding of the diverse roles miRs play in cardiovascular function and disease, we applied high-throughput methods to globally profile miR:target interactions in human heart tissues. We deciphered Ago2:RNA interactions using crosslinking immunoprecipitation coupled with high-throughput sequencing (HITS-CLIP) to generate the first transcriptome-wide map of miR targeting events in human myocardium, detecting 4000 cardiac Ago2 binding sites across >2200 target transcripts. Our initial exploration of this interactome revealed an abundance of miR target sites in gene coding regions, including several sites pointing to new miR-29 functions in regulating cardiomyocyte calcium, growth and metabolism. Also, we uncovered several clinically-relevant interactions involving common genetic variants that alter miR targeting events in cardiomyopathy-associated genes. Overall, these data provide a critical resource for bolstering translational miR research in heart, and likely beyond.