ID	Duplex structure	Position	Score	MFE
1	miRNA 3' gugcagucacUGACGCGGGGGa 5' ||| ||||||| Target 5' gggacacaaaACTCCGCCCCCa 3'	564 - 585	152.00	-17.90
2	miRNA 3' gugcaGUCACUGACGCGGGGGa 5' || || :| :|||||| Target 5' gagccCA-TG-TTCTGCCCCCa 3'	62 - 81	131.00	-17.00
3	miRNA 3' guGCAGUCACU-GACGCGGGGGa 5' | || ||| | |||||:| Target 5' agCATC-CTGAGCCCCGCCCTCt 3'	593 - 614	131.00	-14.50

Mutant ID	Mutant Position	Mutant Source
560773	16	ClinVar
305312	89	ClinVar
305311	104	ClinVar
880309	126	ClinVar
580649	133	ClinVar
305310	185	ClinVar
879089	245	ClinVar
305309	272	ClinVar
305308	302	ClinVar
305307	307	ClinVar
305306	309	ClinVar
878508	341	ClinVar
305305	373	ClinVar
305304	392	ClinVar
878507	400	ClinVar
446503	412	ClinVar
305303	438	ClinVar
305302	470	ClinVar
305301	527	ClinVar
305300	529	ClinVar
305299	533	ClinVar
305298	557	ClinVar
305297	560	ClinVar
305296	570	ClinVar
877477	693	ClinVar
305295	794	ClinVar
572762	821	ClinVar
COSN32057079	20	COSMIC
COSN26984199	28	COSMIC
COSN13339832	42	COSMIC
COSN30458209	45	COSMIC
COSN30159763	73	COSMIC
COSN26602536	83	COSMIC
COSN31492395	85	COSMIC
COSN30473338	90	COSMIC
COSN31506324	126	COSMIC
COSN21014258	225	COSMIC
COSN24157640	241	COSMIC
COSN22079254	550	COSMIC
COSN31516045	770	COSMIC
COSN31520248	805	COSMIC

Mutant ID	Mutant Position	Mutant Source
rs955479842	1	dbSNP
rs1258520848	2	dbSNP
rs769076890	3	dbSNP
rs749702261	9	dbSNP
rs1266059159	14	dbSNP
rs1276106671	15	dbSNP
rs140924477	16	dbSNP
rs756547560	17	dbSNP
rs71581749	18	dbSNP
rs746452984	20	dbSNP
rs781117541	25	dbSNP
rs768424332	35	dbSNP
rs1312973646	37	dbSNP
rs749255998	38	dbSNP
rs757368629	41	dbSNP
rs994749940	42	dbSNP
rs751711071	48	dbSNP
rs764327356	50	dbSNP
rs758136062	51	dbSNP
rs962969824	55	dbSNP
rs866086933	58	dbSNP
rs1012529849	61	dbSNP
rs1057067406	62	dbSNP
rs934731720	69	dbSNP
rs894138469	70	dbSNP
rs1274602417	80	dbSNP
rs1352103616	81	dbSNP
rs886048478	89	dbSNP
rs1002540892	96	dbSNP
rs1266352169	102	dbSNP
rs886048477	104	dbSNP
rs1214571397	105	dbSNP
rs1269817005	110	dbSNP
rs1256611314	113	dbSNP
rs1196539126	121	dbSNP
rs138595686	126	dbSNP
rs1161196544	131	dbSNP
rs1385818012	135	dbSNP
rs945887648	137	dbSNP
rs910398618	145	dbSNP
rs914432880	146	dbSNP
rs933233074	156	dbSNP
rs1054765306	157	dbSNP
rs922925005	167	dbSNP
rs971796209	172	dbSNP
rs1286939851	173	dbSNP
rs942624965	174	dbSNP
rs1314877234	175	dbSNP
rs1245663728	183	dbSNP
rs1329070414	183	dbSNP
rs111895237	185	dbSNP
rs986801624	189	dbSNP
rs1382219825	190	dbSNP
rs1209421368	192	dbSNP
rs1310257524	200	dbSNP
rs769487374	200	dbSNP
rs1449350739	205	dbSNP
rs1374357126	209	dbSNP
rs1184060315	210	dbSNP
rs1409756384	215	dbSNP
rs1164926878	218	dbSNP
rs1472208065	218	dbSNP
rs1369646443	224	dbSNP
rs1297435677	231	dbSNP
rs955407339	235	dbSNP
rs1456094484	253	dbSNP
rs1016047144	259	dbSNP
rs1458312160	260	dbSNP
rs1351572569	261	dbSNP
rs918686885	267	dbSNP
rs972866675	269	dbSNP
rs577302942	270	dbSNP
rs563783609	272	dbSNP
rs868213743	274	dbSNP
rs1423462563	275	dbSNP
rs1017137197	277	dbSNP
rs371871320	284	dbSNP
rs1013086815	286	dbSNP
rs1244346373	287	dbSNP
rs959620501	294	dbSNP
rs1275688507	295	dbSNP
rs1804849	302	dbSNP
rs1804848	307	dbSNP
rs143341556	309	dbSNP
rs906939612	311	dbSNP
rs555709836	324	dbSNP
rs1043117142	326	dbSNP
rs184826203	333	dbSNP
rs888918274	335	dbSNP
rs1163446665	336	dbSNP
rs892949876	341	dbSNP
rs747634476	342	dbSNP
rs573165205	343	dbSNP
rs1050285525	344	dbSNP
rs1370297215	361	dbSNP
rs1242543802	362	dbSNP
rs1305046348	365	dbSNP
rs942554403	370	dbSNP
rs886048476	373	dbSNP
rs553038299	382	dbSNP
rs886048475	392	dbSNP
rs933222929	393	dbSNP
rs1351825181	400	dbSNP
rs911148642	407	dbSNP
rs1051063442	409	dbSNP
rs972128957	412	dbSNP
rs933961932	416	dbSNP
rs1306638101	418	dbSNP
rs918625400	420	dbSNP
rs973221244	436	dbSNP
rs908891279	437	dbSNP
rs886048474	438	dbSNP
rs869238838	441	dbSNP
rs1182498496	442	dbSNP
rs1217417677	444	dbSNP
rs1450978350	447	dbSNP
rs1291715712	449	dbSNP
rs1186207592	455	dbSNP
rs1389958587	456	dbSNP
rs1404323797	457	dbSNP
rs969115913	461	dbSNP
rs1178679937	462	dbSNP
rs778272737	470	dbSNP
rs1159960277	472	dbSNP
rs1465963052	479	dbSNP
rs991654558	492	dbSNP
rs1390879815	495	dbSNP
rs991013729	498	dbSNP
rs555937274	503	dbSNP
rs1362874005	508	dbSNP
rs1035973744	513	dbSNP
rs1035254901	516	dbSNP
rs545890111	526	dbSNP
rs886048473	527	dbSNP
rs886048472	529	dbSNP
rs967379721	530	dbSNP
rs879327862	533	dbSNP
rs1268214233	538	dbSNP
rs971023190	542	dbSNP
rs1465814134	543	dbSNP
rs147116273	550	dbSNP
rs1206267959	551	dbSNP
rs1011661416	552	dbSNP
rs886048471	557	dbSNP
rs1193337869	558	dbSNP
rs886048470	560	dbSNP
rs1269989512	567	dbSNP
rs886048469	570	dbSNP
rs768323266	575	dbSNP
rs1480415097	576	dbSNP
rs368065487	580	dbSNP
rs1414302099	585	dbSNP
rs556981901	590	dbSNP
rs537254362	592	dbSNP
rs1350728945	595	dbSNP
rs1263949976	601	dbSNP
rs1438813212	602	dbSNP
rs1218919014	606	dbSNP
rs1050234163	621	dbSNP
rs1365137075	629	dbSNP
rs1222834423	630	dbSNP
rs372763032	631	dbSNP
rs901689181	633	dbSNP
rs1234332034	634	dbSNP
rs1313731853	637	dbSNP
rs1252758728	639	dbSNP
rs1451846610	642	dbSNP
rs1223262259	643	dbSNP
rs548368376	643	dbSNP
rs1033225242	644	dbSNP
rs1006740105	645	dbSNP
rs528803192	646	dbSNP
rs1036261231	647	dbSNP
rs71581759	652	dbSNP
rs1804850	653	dbSNP
rs1471880385	655	dbSNP
rs1158089809	657	dbSNP
rs1049236547	658	dbSNP
rs552183901	660	dbSNP
rs916352656	662	dbSNP
rs1303053053	663	dbSNP
rs1349503161	664	dbSNP
rs1467302868	665	dbSNP
rs991602212	672	dbSNP
rs1352309871	677	dbSNP
rs996117310	677	dbSNP
rs1407869147	679	dbSNP
rs933930799	680	dbSNP
rs928814450	681	dbSNP
rs1356356073	682	dbSNP
rs1229690026	693	dbSNP
rs1287373530	700	dbSNP
rs71581758	704	dbSNP
rs1358284019	708	dbSNP
rs977661445	709	dbSNP
rs897145871	711	dbSNP
rs1254391907	714	dbSNP
rs770837677	718	dbSNP
rs1379702993	719	dbSNP
rs1037038302	722	dbSNP
rs34171410	724	dbSNP
rs1480369461	725	dbSNP
rs375525393	736	dbSNP
rs941410112	741	dbSNP
rs1473848200	743	dbSNP
rs1180187004	751	dbSNP
rs909983687	759	dbSNP
rs1384890200	779	dbSNP
rs990926419	782	dbSNP
rs1430618196	793	dbSNP
rs117705251	794	dbSNP
rs1408145935	797	dbSNP
rs748927986	816	dbSNP
rs928163083	817	dbSNP
rs1021625358	819	dbSNP
rs982319626	821	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.