ID	Duplex structure	Position	Score	MFE
1	miRNA 3' gaGGUAAAAGGUGGUCUCGACGu 5' :| | ||| || ||||||| Target 5' ccTCCTCCTCCTCC-GAGCTGCt 3'	236 - 257	156.00	-23.50
2	miRNA 3' gaggUAAAAGGUGGUCUCGACGu 5' | ||| |::||||||: Target 5' ttgaACTTT---CTGGAGCTGTt 3'	713 - 732	136.00	-13.10
3	miRNA 3' gaGGUAAAAGGUGGUCUCGACGu 5' ||||| | |: | |||||: Target 5' caCCATTGT-AATAAAAGCTGTt 3'	786 - 807	116.00	-11.90

Mutant ID	Mutant Position	Mutant Source
COSN22177850	8	COSMIC
COSN30137786	14	COSMIC
COSN19671987	19	COSMIC
COSN30495100	20	COSMIC
COSN26964998	24	COSMIC
COSN28223872	27	COSMIC
COSN26964999	34	COSMIC
COSN4894029	70	COSMIC
COSN14273436	76	COSMIC
COSN30105208	90	COSMIC
COSN30528465	140	COSMIC
COSN30539361	141	COSMIC
COSN30106886	142	COSMIC
COSN31485296	143	COSMIC
COSN30167895	157	COSMIC
COSN1345688	236	COSMIC
COSN7969213	243	COSMIC
COSN1345689	382	COSMIC
COSN30175920	390	COSMIC
COSN6358760	480	COSMIC
COSN31536468	503	COSMIC
COSN21502176	545	COSMIC
COSN30542659	599	COSMIC
COSN7969214	611	COSMIC
COSN31542695	686	COSMIC
COSN28665473	760	COSMIC

Mutant ID	Mutant Position	Mutant Source
rs756444090	7	dbSNP
rs144608640	14	dbSNP
rs376102692	15	dbSNP
rs778301772	16	dbSNP
rs771970905	17	dbSNP
rs377688816	19	dbSNP
rs752545388	20	dbSNP
rs1249449510	23	dbSNP
rs1480197469	24	dbSNP
rs1236536011	25	dbSNP
rs770872299	30	dbSNP
rs1408732778	31	dbSNP
rs1244895928	34	dbSNP
rs371526661	35	dbSNP
rs373617906	36	dbSNP
rs1377408077	41	dbSNP
rs1393563770	42	dbSNP
rs768908419	43	dbSNP
rs774359081	46	dbSNP
rs367789719	47	dbSNP
rs1041387292	48	dbSNP
rs377449083	50	dbSNP
rs558325298	51	dbSNP
rs774724016	52	dbSNP
rs1273793034	61	dbSNP
rs914548418	65	dbSNP
rs946138676	72	dbSNP
rs999794991	73	dbSNP
rs758128650	75	dbSNP
rs1233146595	77	dbSNP
rs1373541902	89	dbSNP
rs758948012	92	dbSNP
rs764154405	93	dbSNP
rs902041574	95	dbSNP
rs1314008743	99	dbSNP
rs1437060925	107	dbSNP
rs573400192	114	dbSNP
rs779492260	115	dbSNP
rs1173360718	120	dbSNP
rs1192535564	123	dbSNP
rs1050704249	127	dbSNP
rs540833114	128	dbSNP
rs117268662	129	dbSNP
rs1175599470	133	dbSNP
rs1469690183	135	dbSNP
rs529567291	139	dbSNP
rs1427726127	140	dbSNP
rs1023710986	141	dbSNP
rs1017024794	142	dbSNP
rs1459805604	143	dbSNP
rs541390295	145	dbSNP
rs1317182628	146	dbSNP
rs756803293	147	dbSNP
rs1221633573	148	dbSNP
rs11103	151	dbSNP
rs918598814	157	dbSNP
rs530501255	161	dbSNP
rs1354061051	165	dbSNP
rs1025337299	167	dbSNP
rs1431898195	168	dbSNP
rs1347244572	172	dbSNP
rs1157183622	173	dbSNP
rs1400286651	174	dbSNP
rs1361474545	175	dbSNP
rs755806147	176	dbSNP
rs1255277374	179	dbSNP
rs981239466	180	dbSNP
rs182137136	181	dbSNP
rs942581642	182	dbSNP
rs780449321	183	dbSNP
rs1213218669	185	dbSNP
rs1464130050	186	dbSNP
rs187242851	189	dbSNP
rs1451704908	198	dbSNP
rs1223062696	199	dbSNP
rs1312633450	200	dbSNP
rs1215586091	202	dbSNP
rs1240015808	203	dbSNP
rs1430300850	207	dbSNP
rs779506539	207	dbSNP
rs990057961	208	dbSNP
rs914578551	212	dbSNP
rs1194203382	214	dbSNP
rs1459934159	222	dbSNP
rs1041459312	224	dbSNP
rs191862750	228	dbSNP
rs148492658	229	dbSNP
rs1184509561	231	dbSNP
rs1215097177	233	dbSNP
rs368701446	233	dbSNP
rs374373895	233	dbSNP
rs567703179	233	dbSNP
rs967390997	234	dbSNP
rs749728009	235	dbSNP
rs568327048	243	dbSNP
rs369090329	250	dbSNP
rs868337676	251	dbSNP
rs1372084355	254	dbSNP
rs1407179847	259	dbSNP
rs923347106	263	dbSNP
rs1156943848	264	dbSNP
rs1438904305	265	dbSNP
rs933352343	267	dbSNP
rs1390113995	269	dbSNP
rs1050592446	271	dbSNP
rs1344839460	292	dbSNP
rs1462453735	310	dbSNP
rs62494975	320	dbSNP
rs1023743843	324	dbSNP
rs1353916546	332	dbSNP
rs116421517	334	dbSNP
rs1003598716	335	dbSNP
rs1452117366	342	dbSNP
rs569319164	343	dbSNP
rs1481928003	353	dbSNP
rs951420520	353	dbSNP
rs1037939770	356	dbSNP
rs184834948	359	dbSNP
rs188548495	360	dbSNP
rs1352604441	363	dbSNP
rs1330695086	367	dbSNP
rs1046838126	369	dbSNP
rs193153093	370	dbSNP
rs1002547309	371	dbSNP
rs1162346486	374	dbSNP
rs1484586889	377	dbSNP
rs202175559	383	dbSNP
rs1186522591	394	dbSNP
rs1034163723	395	dbSNP
rs958546276	409	dbSNP
rs1011935985	427	dbSNP
rs534104954	433	dbSNP
rs977172249	449	dbSNP
rs1175610792	464	dbSNP
rs924325288	479	dbSNP
rs1159279160	481	dbSNP
rs1420335860	497	dbSNP
rs781481989	498	dbSNP
rs967821716	500	dbSNP
rs555943741	502	dbSNP
rs1209149893	504	dbSNP
rs1054527980	506	dbSNP
rs977451582	507	dbSNP
rs1160708631	511	dbSNP
rs185576736	516	dbSNP
rs560058957	523	dbSNP
rs986192271	524	dbSNP
rs1409172509	525	dbSNP
rs906710180	533	dbSNP
rs1003629796	536	dbSNP
rs1394061197	542	dbSNP
rs1401124181	545	dbSNP
rs1158797444	552	dbSNP
rs910748803	554	dbSNP
rs1409167080	559	dbSNP
rs1157709775	562	dbSNP
rs189172069	569	dbSNP
rs769614331	572	dbSNP
rs777600178	577	dbSNP
rs1277306011	580	dbSNP
rs1262799743	583	dbSNP
rs1005573699	585	dbSNP
rs1038395727	587	dbSNP
rs1484995210	593	dbSNP
rs1375490291	602	dbSNP
rs536990548	604	dbSNP
rs964050988	605	dbSNP
rs975346353	607	dbSNP
rs1318679268	608	dbSNP
rs1383583179	622	dbSNP
rs1029546861	625	dbSNP
rs955202355	631	dbSNP
rs1461504772	639	dbSNP
rs574936364	641	dbSNP
rs371669922	661	dbSNP
rs545785644	663	dbSNP
rs1472719963	664	dbSNP
rs957331810	665	dbSNP
rs1202333659	666	dbSNP
rs1046726643	684	dbSNP
rs1427016408	686	dbSNP
rs180910954	688	dbSNP
rs1214456965	691	dbSNP
rs1440434815	692	dbSNP
rs906852666	694	dbSNP
rs1002599889	702	dbSNP
rs915579547	703	dbSNP
rs989884907	703	dbSNP
rs1355491004	705	dbSNP
rs375893071	736	dbSNP
rs1270599410	742	dbSNP
rs1229298064	748	dbSNP
rs1362671097	753	dbSNP
rs1393519181	754	dbSNP
rs948372072	758	dbSNP
rs1045295423	759	dbSNP
rs1173597260	763	dbSNP
rs928211920	765	dbSNP
rs1405318465	766	dbSNP
rs146009072	776	dbSNP
rs1170069914	781	dbSNP
rs939561275	800	dbSNP
rs1047198977	814	dbSNP
rs1194506119	815	dbSNP
rs887227694	825	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.