ID	Duplex structure	Position	Score	MFE
1	miRNA 3' uuugagcgaCUCGGGGu 5' ||||||| Target 5' tggcaccagGAGCCCCt 3'	11 - 27	140.00	-13.70
2	miRNA 3' uuUGAGCG-ACUCGGGGu 5' | | || ||||||: Target 5' ggAGTAGCAGGAGCCCTt 3'	368 - 385	127.00	-12.40
3	miRNA 3' uuugagcgaCUCGGGGu 5' ||||||: Target 5' atgagacggGAGCCCTt 3'	409 - 425	124.00	-14.20

Mutant ID	Mutant Position	Mutant Source
COSN30447286	4	COSMIC
COSN26967660	32	COSMIC
COSN31604253	38	COSMIC
COSN19768776	44	COSMIC
COSN30586409	58	COSMIC
COSN30175928	115	COSMIC
COSN23015005	156	COSMIC
COSN31523748	169	COSMIC
COSN31555978	218	COSMIC
COSN28685527	243	COSMIC
COSN20078579	289	COSMIC
COSN31523752	329	COSMIC
COSN32063723	396	COSMIC
COSN19114940	456	COSMIC
COSN20855472	551	COSMIC

Mutant ID	Mutant Position	Mutant Source
rs1384208204	2	dbSNP
rs148267118	3	dbSNP
rs541865959	4	dbSNP
rs201534157	7	dbSNP
rs778143240	8	dbSNP
rs370081613	9	dbSNP
rs1355203078	10	dbSNP
rs781142694	12	dbSNP
rs745833144	15	dbSNP
rs769554669	16	dbSNP
rs373118920	17	dbSNP
rs748935001	20	dbSNP
rs910064044	23	dbSNP
rs768232860	25	dbSNP
rs940161337	26	dbSNP
rs773889321	27	dbSNP
rs761340949	29	dbSNP
rs771515196	30	dbSNP
rs760172496	31	dbSNP
rs1335387351	32	dbSNP
rs73235273	33	dbSNP
rs760538647	36	dbSNP
rs763420504	36	dbSNP
rs764326012	37	dbSNP
rs1399780839	38	dbSNP
rs1451710371	39	dbSNP
rs1331573569	40	dbSNP
rs1399268321	41	dbSNP
rs1346099890	43	dbSNP
rs1378683349	44	dbSNP
rs751759297	45	dbSNP
rs1008666966	49	dbSNP
rs757327377	50	dbSNP
rs781177624	52	dbSNP
rs750345947	53	dbSNP
rs889413976	54	dbSNP
rs1010834320	55	dbSNP
rs1022601421	56	dbSNP
rs1322055743	57	dbSNP
rs1222608147	58	dbSNP
rs1260296457	61	dbSNP
rs1241400208	67	dbSNP
rs995830140	68	dbSNP
rs1188422109	71	dbSNP
rs879104682	71	dbSNP
rs1033378182	73	dbSNP
rs1248702967	74	dbSNP
rs546120104	78	dbSNP
rs1358898751	79	dbSNP
rs902361174	79	dbSNP
rs117893382	80	dbSNP
rs1270083608	81	dbSNP
rs1182246135	84	dbSNP
rs1429082748	86	dbSNP
rs1351973612	89	dbSNP
rs1303457172	91	dbSNP
rs1034854750	94	dbSNP
rs531910558	95	dbSNP
rs1363224147	97	dbSNP
rs960155805	99	dbSNP
rs866805341	102	dbSNP
rs1020124161	106	dbSNP
rs1184647411	108	dbSNP
rs1478918758	110	dbSNP
rs1247061911	111	dbSNP
rs1223553189	112	dbSNP
rs550082439	116	dbSNP
rs111789216	117	dbSNP
rs970003465	119	dbSNP
rs1157917271	124	dbSNP
rs1272997748	125	dbSNP
rs927361892	127	dbSNP
rs181731147	128	dbSNP
rs1404668655	129	dbSNP
rs910150074	130	dbSNP
rs1343289279	132	dbSNP
rs1309398767	134	dbSNP
rs974099533	135	dbSNP
rs1320701601	136	dbSNP
rs940271188	137	dbSNP
rs529274864	139	dbSNP
rs1168318430	140	dbSNP
rs919882771	141	dbSNP
rs1429797320	145	dbSNP
rs1198442364	147	dbSNP
rs1479308281	148	dbSNP
rs922763242	151	dbSNP
rs1379628856	154	dbSNP
rs7499959	156	dbSNP
rs1304581866	158	dbSNP
rs1049469275	160	dbSNP
rs912750811	161	dbSNP
rs910902676	164	dbSNP
rs946350281	166	dbSNP
rs944170973	168	dbSNP
rs1040177931	169	dbSNP
rs748443231	169	dbSNP
rs749072947	169	dbSNP
rs566083498	171	dbSNP
rs1460891194	173	dbSNP
rs995880538	175	dbSNP
rs1202340057	176	dbSNP
rs1245433819	178	dbSNP
rs1449517537	179	dbSNP
rs1175532549	188	dbSNP
rs1483860428	189	dbSNP
rs1413901995	194	dbSNP
rs1054128498	196	dbSNP
rs1419874974	199	dbSNP
rs1250029761	201	dbSNP
rs1406211569	201	dbSNP
rs902464535	205	dbSNP
rs533976080	208	dbSNP
rs552432138	210	dbSNP
rs1270377355	213	dbSNP
rs1020596724	215	dbSNP
rs1315989845	219	dbSNP
rs186837941	222	dbSNP
rs538100519	224	dbSNP
rs1002648672	225	dbSNP
rs1382808791	226	dbSNP
rs1336064856	231	dbSNP
rs1441368811	232	dbSNP
rs1296282300	234	dbSNP
rs1375208094	239	dbSNP
rs1230490599	242	dbSNP
rs1452734419	243	dbSNP
rs1056705990	244	dbSNP
rs896290063	248	dbSNP
rs1322918760	249	dbSNP
rs958785724	254	dbSNP
rs770421375	255	dbSNP
rs1221829475	256	dbSNP
rs1280806694	259	dbSNP
rs974531094	263	dbSNP
rs1183556627	265	dbSNP
rs1022982771	266	dbSNP
rs970098853	267	dbSNP
rs144377121	268	dbSNP
rs951435403	269	dbSNP
rs1258593417	273	dbSNP
rs1223292582	274	dbSNP
rs1016926701	279	dbSNP
rs1247179188	282	dbSNP
rs1231558173	283	dbSNP
rs1296125040	285	dbSNP
rs961970073	300	dbSNP
rs1287408536	307	dbSNP
rs972970213	307	dbSNP
rs1366324827	314	dbSNP
rs369288051	320	dbSNP
rs372643761	323	dbSNP
rs1267820633	325	dbSNP
rs1442814982	335	dbSNP
rs1194442947	336	dbSNP
rs985223529	340	dbSNP
rs912807178	349	dbSNP
rs1490418951	351	dbSNP
rs199514280	351	dbSNP
rs975578279	351	dbSNP
rs910996094	361	dbSNP
rs1226603852	364	dbSNP
rs946480579	368	dbSNP
rs1405278282	369	dbSNP
rs764630349	370	dbSNP
rs1425225077	374	dbSNP
rs535150161	375	dbSNP
rs1315168583	376	dbSNP
rs1302707399	378	dbSNP
rs553821168	382	dbSNP
rs1422833460	383	dbSNP
rs1398705789	384	dbSNP
rs935255048	390	dbSNP
rs191518470	393	dbSNP
rs1054582490	394	dbSNP
rs896342253	409	dbSNP
rs1012059577	411	dbSNP
rs1197343692	412	dbSNP
rs1265440976	413	dbSNP
rs1410130312	416	dbSNP
rs1480929927	417	dbSNP
rs1044864843	419	dbSNP
rs892822002	422	dbSNP
rs1196825568	426	dbSNP
rs1250581414	427	dbSNP
rs905989554	431	dbSNP
rs1005630922	438	dbSNP
rs1041664041	439	dbSNP
rs1302298312	449	dbSNP
rs1017351530	456	dbSNP
rs1356507323	456	dbSNP
rs1282947202	457	dbSNP
rs1434573179	458	dbSNP
rs1337650703	468	dbSNP
rs1345174369	469	dbSNP
rs546356872	476	dbSNP
rs961367285	486	dbSNP
rs1002707703	489	dbSNP
rs1179144250	494	dbSNP
rs994838764	496	dbSNP
rs894284364	497	dbSNP
rs1173865992	501	dbSNP
rs995623276	510	dbSNP
rs1363966196	511	dbSNP
rs1180502692	512	dbSNP
rs557902541	513	dbSNP
rs1276727812	514	dbSNP
rs1027469301	523	dbSNP
rs1345758554	526	dbSNP
rs1204205741	527	dbSNP
rs1460757367	530	dbSNP
rs1214522194	534	dbSNP
rs1029894768	535	dbSNP
rs955588055	537	dbSNP
rs1260987815	538	dbSNP
rs1206393140	539	dbSNP
rs1225212473	539	dbSNP
rs1291474425	540	dbSNP
rs1353149862	541	dbSNP
rs1489743787	541	dbSNP
rs1407412215	543	dbSNP
rs367837141	554	dbSNP
rs1018453014	559	dbSNP
rs968207781	560	dbSNP
rs1339354272	561	dbSNP
rs1474763619	563	dbSNP
rs749968317	565	dbSNP
rs1019919177	566	dbSNP
rs576239677	567	dbSNP
rs1405875075	568	dbSNP
rs965620719	572	dbSNP
rs1430312799	575	dbSNP
rs979173308	577	dbSNP
rs1162745298	581	dbSNP
rs1363449472	584	dbSNP
rs1385224250	585	dbSNP
rs1423008752	586	dbSNP
rs1325720064	591	dbSNP
rs975627244	592	dbSNP
rs921443405	594	dbSNP
rs923615720	596	dbSNP
rs1430188934	611	dbSNP
rs183383846	612	dbSNP
rs1368034033	613	dbSNP
rs370324575	616	dbSNP
rs1229751623	617	dbSNP
rs1314835577	621	dbSNP
rs991768941	622	dbSNP
rs989938917	623	dbSNP
rs1211281883	625	dbSNP
rs562092346	630	dbSNP
rs1290068507	631	dbSNP
rs1317228044	632	dbSNP
rs1246738706	634	dbSNP
rs1382734101	639	dbSNP
rs914292713	644	dbSNP
rs779884254	649	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.

- 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.