ID	Duplex structure	Position	Score	MFE
1	miRNA 3' cgGGUCUGGUCUCG-----ACCGAAGu 5' || |:| :|:|| ||||||| Target 5' tcCCTGGCAGGGGCCCTCGTGGCTTCt 3'	534 - 560	156.00	-23.70
2	miRNA 3' cgGGUCUGGUCUCGACCGAAGu 5' |::||||| | ||||| || Target 5' aaCTGGACCA-A-CTGGCCTCt 3'	211 - 230	134.00	-18.50
3	miRNA 3' cgGGUCUGGUCUCGACCGAAGu 5' |::|||: |: || ||||| Target 5' tgCTGGACT-GGCCTTGCTTCt 3'	392 - 412	131.00	-16.40

Mutant ID	Mutant Position	Mutant Source
COSN26997828	13	COSMIC
COSN30485277	29	COSMIC
COSN28874178	32	COSMIC
COSN30504899	33	COSMIC
COSN26997825	55	COSMIC
COSN30144364	57	COSMIC
COSN19468763	63	COSMIC
COSN31532205	92	COSMIC
COSN7180421	93	COSMIC
COSN31488945	98	COSMIC
COSN30187376	102	COSMIC
COSN30476353	102	COSMIC
COSN31593894	117	COSMIC
COSN28759140	145	COSMIC
COSN30465674	169	COSMIC
COSN30481606	183	COSMIC
COSN21669104	263	COSMIC
COSN31540483	268	COSMIC
COSN31561917	268	COSMIC
COSN28397925	297	COSMIC
COSN31484487	299	COSMIC

Mutant ID	Mutant Position	Mutant Source
rs1277269551	2	dbSNP
rs1440208969	3	dbSNP
rs577289067	4	dbSNP
rs1374463045	7	dbSNP
rs1360080306	11	dbSNP
rs11556956	13	dbSNP
rs769569595	17	dbSNP
rs1437337060	20	dbSNP
rs1393830646	21	dbSNP
rs1324480453	23	dbSNP
rs1467593140	25	dbSNP
rs970685163	27	dbSNP
rs1424817296	30	dbSNP
rs747951609	32	dbSNP
rs1427078383	34	dbSNP
rs780897933	44	dbSNP
rs755260441	46	dbSNP
rs1291324805	74	dbSNP
rs36076633	80	dbSNP
rs1329365111	96	dbSNP
rs113008022	106	dbSNP
rs1392483953	109	dbSNP
rs139865543	119	dbSNP
rs1181500572	120	dbSNP
rs1242357582	125	dbSNP
rs1445162763	130	dbSNP
rs1165397920	140	dbSNP
rs530323201	146	dbSNP
rs1408310219	150	dbSNP
rs1169880789	153	dbSNP
rs1355315070	162	dbSNP
rs1449355688	169	dbSNP
rs1335138735	170	dbSNP
rs1428823016	173	dbSNP
rs1453938813	183	dbSNP
rs1388097172	185	dbSNP
rs562868802	187	dbSNP
rs1170350470	193	dbSNP
rs960273987	205	dbSNP
rs11556953	221	dbSNP
rs1273154202	225	dbSNP
rs1319540106	226	dbSNP
rs181751868	229	dbSNP
rs1201457841	232	dbSNP
rs879131629	236	dbSNP
rs1015624267	237	dbSNP
rs1461613401	240	dbSNP
rs11556950	251	dbSNP
rs1004218482	264	dbSNP
rs952800390	271	dbSNP
rs1196903363	273	dbSNP
rs1453525518	274	dbSNP
rs1026919840	275	dbSNP
rs1420404224	278	dbSNP
rs1269805252	280	dbSNP
rs1174567447	283	dbSNP
rs1204739138	290	dbSNP
rs1405744171	297	dbSNP
rs1340392052	301	dbSNP
rs1277225282	302	dbSNP
rs531171681	303	dbSNP
rs1430715112	304	dbSNP
rs899734635	305	dbSNP
rs774365514	309	dbSNP
rs1221243323	311	dbSNP
rs1273698101	314	dbSNP
rs1008478129	316	dbSNP
rs1201942590	323	dbSNP
rs892341152	324	dbSNP
rs115070391	337	dbSNP
rs1216421048	341	dbSNP
rs759589237	345	dbSNP
rs1303311513	346	dbSNP
rs1197483487	350	dbSNP
rs1408854485	355	dbSNP
rs1480912732	371	dbSNP
rs1368458644	381	dbSNP
rs1174660977	387	dbSNP
rs1052277935	390	dbSNP
rs1400566098	395	dbSNP
rs1170331553	402	dbSNP
rs1319571170	410	dbSNP
rs146132606	412	dbSNP
rs1402519585	413	dbSNP
rs1302041859	417	dbSNP
rs1424439077	418	dbSNP
rs763342436	425	dbSNP
rs553650730	426	dbSNP
rs1277492371	427	dbSNP
rs1349711225	432	dbSNP
rs1224227916	442	dbSNP
rs553922888	468	dbSNP
rs1489849830	487	dbSNP
rs916144154	488	dbSNP
rs1430072935	493	dbSNP
rs1452398958	495	dbSNP
rs1181654327	502	dbSNP
rs1362363724	512	dbSNP
rs1049905	522	dbSNP
rs1482228778	533	dbSNP
rs1254411503	537	dbSNP
rs1350386568	537	dbSNP
rs1423363137	538	dbSNP
rs35792571	538	dbSNP
rs993128238	541	dbSNP
rs938944357	551	dbSNP
rs1442327270	552	dbSNP
rs753847255	560	dbSNP
rs1277074209	569	dbSNP
rs541705576	577	dbSNP
rs574762239	578	dbSNP
rs766422525	593	dbSNP
rs1311241677	594	dbSNP
rs1221440334	595	dbSNP
rs1357169020	598	dbSNP
rs1245235990	608	dbSNP
rs1291044770	612	dbSNP
rs1211809182	614	dbSNP
rs1324998878	623	dbSNP
rs982930510	625	dbSNP
rs1179639349	627	dbSNP
rs1049974	633	dbSNP
rs952770842	636	dbSNP
rs556532800	639	dbSNP
rs1027057089	645	dbSNP
rs1348288957	650	dbSNP
rs760675434	665	dbSNP
rs370592800	677	dbSNP
rs1442607920	678	dbSNP
rs538155785	682	dbSNP
rs772236706	686	dbSNP
rs954536818	687	dbSNP

- 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.