ID	Duplex structure	Position	Score	MFE
1	miRNA 3' ccGGGGUGG----GGUCAGAg 5' ||:|||: |||||:| Target 5' ctCCTCACTTTGGCCAGTTTg 3'	274 - 294	137.00	-15.80
2	miRNA 3' ccgGGGUGG---GGUCagag 5' |||||| |||| Target 5' acaCCCACCATGCCAGgggt 3'	58 - 77	98.00	-15.06
3	miRNA 3' ccgGGGUGGGGUCAGAg 5' :| :::||| ||| Target 5' caaTCGGTTCCA-TCTc 3'	80 - 95	94.00	-15.32

Mutant ID	Mutant Position	Mutant Source
COSN28851812	8	COSMIC
COSN25050402	9	COSMIC
COSN14328905	23	COSMIC
COSN30471326	27	COSMIC
COSN8518516	27	COSMIC
COSN31501911	28	COSMIC
COSN30471395	30	COSMIC
COSN28848191	43	COSMIC
COSN31487134	54	COSMIC
COSN30447993	66	COSMIC
COSN30090898	78	COSMIC
COSN31547076	95	COSMIC
COSN30506033	110	COSMIC
COSN28185036	117	COSMIC
COSN26440879	125	COSMIC
COSN21458430	138	COSMIC

Mutant ID	Mutant Position	Mutant Source
rs1432237394	4	dbSNP
rs1374155172	5	dbSNP
rs1424029885	5	dbSNP
rs772874297	9	dbSNP
rs747634210	10	dbSNP
rs530487645	17	dbSNP
rs981646065	19	dbSNP
rs1169830534	20	dbSNP
rs768643953	21	dbSNP
rs569332331	23	dbSNP
rs199821780	24	dbSNP
rs1184410264	26	dbSNP
rs1484672419	27	dbSNP
rs1315224176	28	dbSNP
rs1255297312	30	dbSNP
rs368201547	31	dbSNP
rs777983293	33	dbSNP
rs149098116	34	dbSNP
rs752882280	38	dbSNP
rs972965917	40	dbSNP
rs765403144	42	dbSNP
rs941531362	43	dbSNP
rs1412353085	49	dbSNP
rs538679997	51	dbSNP
rs1028101588	53	dbSNP
rs201726002	54	dbSNP
rs1383381363	61	dbSNP
rs1483363929	61	dbSNP
rs745822711	71	dbSNP
rs547668501	78	dbSNP
rs1429830393	82	dbSNP
rs1015375572	84	dbSNP
rs1432362223	85	dbSNP
rs985937227	95	dbSNP
rs750300562	96	dbSNP
rs890962345	105	dbSNP
rs1173488293	107	dbSNP
rs1049643170	110	dbSNP
rs34795284	113	dbSNP
rs954181105	114	dbSNP
rs1376408730	120	dbSNP
rs1364293876	122	dbSNP
rs36007795	125	dbSNP
rs922697343	126	dbSNP
rs934422832	127	dbSNP
rs565035183	129	dbSNP
rs976751081	134	dbSNP
rs185274718	135	dbSNP
rs1253838376	139	dbSNP
rs373408090	140	dbSNP
rs950156521	141	dbSNP
rs1020175926	154	dbSNP
rs1448192805	160	dbSNP
rs1010195711	164	dbSNP
rs1472510266	175	dbSNP
rs1462791645	179	dbSNP
rs991725254	180	dbSNP
rs781475326	184	dbSNP
rs1200797327	185	dbSNP
rs372926588	187	dbSNP
rs1457974776	192	dbSNP
rs1032874560	193	dbSNP
rs1001674111	200	dbSNP
rs1482826769	202	dbSNP
rs1432774284	208	dbSNP
rs1276599361	209	dbSNP
rs571270059	210	dbSNP
rs1218390875	214	dbSNP
rs546337870	222	dbSNP
rs1318289320	224	dbSNP
rs1229592662	229	dbSNP
rs962028513	230	dbSNP
rs1463198421	236	dbSNP
rs1045901717	238	dbSNP
rs1008955518	239	dbSNP
rs1013885764	242	dbSNP
rs1488443145	249	dbSNP
rs1384484041	252	dbSNP
rs896827770	263	dbSNP
rs1334461052	265	dbSNP
rs1037238796	266	dbSNP
rs1410688485	266	dbSNP
rs1400600897	267	dbSNP
rs1463037546	269	dbSNP
rs1324322356	286	dbSNP
rs73715869	294	dbSNP
rs910035657	307	dbSNP
rs1291560060	315	dbSNP
rs563754186	323	dbSNP
rs756729160	326	dbSNP
rs932828107	342	dbSNP
rs922679519	344	dbSNP
rs1287266056	346	dbSNP
rs1054118787	349	dbSNP
rs1430892117	357	dbSNP
rs1370517764	358	dbSNP
rs1229469634	363	dbSNP
rs1166741016	364	dbSNP
rs1446571153	371	dbSNP
rs1369237176	374	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.