ID	Duplex structure	Position	Score	MFE
1	miRNA 3' ggguggucgacgaggGACCGggu 5' ||||| Target 5' ----------cacaaCTGGCaga 3'	1 - 13	100.00	-7.62
2	miRNA 3' ggguggUCGACGAGG-GACCGGGu 5' :| ||||:: ||| :|: Target 5' acaaaaGGGTGCTTTGCTGTTCTt 3'	446 - 469	93.00	-13.10
3	miRNA 3' ggguggUCGACGAGGGACCGGgu 5' | || : :||||: Target 5' aaaaaaAACTTTGAATTGGCTat 3'	252 - 274	89.00	-7.30

Mutant ID	Mutant Position	Mutant Source
COSN5068179	2	COSMIC
COSN30483451	21	COSMIC
COSN6510237	41	COSMIC
COSN20050036	66	COSMIC
COSN20050034	67	COSMIC
COSN30470072	80	COSMIC
COSN1306243	91	COSMIC
COSN24787946	108	COSMIC
COSN15665927	109	COSMIC
COSN30162499	119	COSMIC
COSN22088707	155	COSMIC
COSN26574747	156	COSMIC
COSN31548185	265	COSMIC
COSN31563790	273	COSMIC
COSN28767871	380	COSMIC
COSN16730628	428	COSMIC
COSN14791497	567	COSMIC
COSN29323315	603	COSMIC

Mutant ID	Mutant Position	Mutant Source
rs1407480023	6	dbSNP
rs1446109445	7	dbSNP
rs367741833	13	dbSNP
rs754818746	19	dbSNP
rs370559562	21	dbSNP
rs766018743	22	dbSNP
rs760961856	24	dbSNP
rs966611319	32	dbSNP
rs1022532778	34	dbSNP
rs750629331	36	dbSNP
rs146229593	37	dbSNP
rs776662400	37	dbSNP
rs397999141	38	dbSNP
rs889673529	38	dbSNP
rs534440216	39	dbSNP
rs750956100	39	dbSNP
rs1276792180	41	dbSNP
rs1402259967	44	dbSNP
rs566741336	44	dbSNP
rs757629304	44	dbSNP
rs1341630855	46	dbSNP
rs1476610386	46	dbSNP
rs371305785	48	dbSNP
rs1389183109	64	dbSNP
rs546924735	64	dbSNP
rs10552214	67	dbSNP
rs1165001978	68	dbSNP
rs1366095543	68	dbSNP
rs1404740701	68	dbSNP
rs1427190555	68	dbSNP
rs1431234627	68	dbSNP
rs1491249003	68	dbSNP
rs70988555	68	dbSNP
rs776432929	68	dbSNP
rs879117036	68	dbSNP
rs759094553	69	dbSNP
rs1328194378	71	dbSNP
rs1401011719	72	dbSNP
rs374923857	73	dbSNP
rs1388165287	78	dbSNP
rs1433233167	86	dbSNP
rs1217395423	103	dbSNP
rs528773387	103	dbSNP
rs879309374	103	dbSNP
rs1293309453	104	dbSNP
rs1052129559	108	dbSNP
rs375067091	112	dbSNP
rs1375782890	113	dbSNP
rs1313748779	127	dbSNP
rs984369909	133	dbSNP
rs1436758212	134	dbSNP
rs1184789583	135	dbSNP
rs952975270	143	dbSNP
rs1373856169	146	dbSNP
rs1472911038	148	dbSNP
rs370088217	155	dbSNP
rs41471149	156	dbSNP
rs1470852697	157	dbSNP
rs1338876227	158	dbSNP
rs1462534862	160	dbSNP
rs994767969	162	dbSNP
rs960255813	170	dbSNP
rs940769022	181	dbSNP
rs144971686	188	dbSNP
rs1049679405	194	dbSNP
rs751815540	201	dbSNP
rs567307852	202	dbSNP
rs764327393	207	dbSNP
rs1327466828	215	dbSNP
rs1225754707	220	dbSNP
rs45605533	221	dbSNP
rs1010767619	232	dbSNP
rs893751784	239	dbSNP
rs568220009	240	dbSNP
rs990495191	246	dbSNP
rs1252110486	250	dbSNP
rs939035257	255	dbSNP
rs935135822	259	dbSNP
rs1176608534	260	dbSNP
rs1189639407	260	dbSNP
rs1481256607	260	dbSNP
rs1378411095	261	dbSNP
rs927614009	273	dbSNP
rs1465770575	274	dbSNP
rs901018027	280	dbSNP
rs1277469134	281	dbSNP
rs977862191	283	dbSNP
rs966848797	287	dbSNP
rs1340832647	290	dbSNP
rs1307902023	296	dbSNP
rs1041158533	298	dbSNP
rs1349184091	298	dbSNP
rs942504488	298	dbSNP
rs910883156	307	dbSNP
rs569167704	309	dbSNP
rs745623572	310	dbSNP
rs1230658907	317	dbSNP
rs983818433	320	dbSNP
rs1342193106	322	dbSNP
rs45560934	327	dbSNP
rs989695576	333	dbSNP
rs918821021	336	dbSNP
rs953991548	353	dbSNP
rs1191533297	357	dbSNP
rs1355858600	358	dbSNP
rs1266453724	362	dbSNP
rs1431258020	369	dbSNP
rs1294965268	372	dbSNP
rs15577	380	dbSNP
rs1338966840	384	dbSNP
rs1333729034	390	dbSNP
rs1369235826	395	dbSNP
rs565854333	396	dbSNP
rs998049379	410	dbSNP
rs901890796	412	dbSNP
rs1035868498	415	dbSNP
rs1398682685	419	dbSNP
rs1297191658	426	dbSNP
rs1166670643	428	dbSNP
rs980589450	436	dbSNP
rs1294830317	442	dbSNP
rs1018883508	443	dbSNP
rs1465513194	447	dbSNP
rs1004994190	464	dbSNP
rs1419191378	464	dbSNP
rs1167632264	467	dbSNP
rs374302222	467	dbSNP
rs868222264	472	dbSNP
rs1206681800	478	dbSNP
rs45561935	485	dbSNP
rs1236582437	497	dbSNP
rs1450391259	499	dbSNP
rs1011555424	502	dbSNP
rs1425668673	506	dbSNP
rs891814866	512	dbSNP
rs1349825650	518	dbSNP
rs1049245498	522	dbSNP
rs1456708811	525	dbSNP
rs532211426	534	dbSNP
rs1247720959	537	dbSNP
rs999457043	539	dbSNP
rs1318161782	549	dbSNP
rs900963151	553	dbSNP
rs1311840638	556	dbSNP
rs1319928240	557	dbSNP
rs776092278	559	dbSNP
rs76739889	560	dbSNP
rs528160347	562	dbSNP
rs35413555	567	dbSNP
rs1055425984	568	dbSNP
rs1208302915	573	dbSNP
rs1246448830	581	dbSNP
rs770898737	582	dbSNP
rs1355322876	587	dbSNP
rs746832553	595	dbSNP
rs1283860194	600	dbSNP
rs927645304	603	dbSNP
rs1042046703	604	dbSNP
rs1443122648	617	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.