>LYPLA2|NM_007260|3'UTR
   1 CTAGTCGCTGGCCCCAGTGCAGTACCCCAGCTCATGGGGGACTCAGCAAGCAAGCGTGGCACCATCTTGGATCTGAGCCG
  81 GTCGAGCCCCTGTCCCCACCCTTCCTGACCTGTCCTTTTCCCACAGGCCTCTGGGGGCAGGTGGCAAGGCCTGGCCGGGC
 161 CTTCCTTCCTGGCCTTAGCCACCTGGCTCTGTCTGCAGCAGGGGCAGGCTGCTTTCTTATCCATTTCCCTGGAGGCGGGC
 241 CCCCCTGGCAGCAGTATTGGAGGGGCTACAGGCAGCTGGAGAAAGGGGCCCAGCCGCTGACCCACTCACTCAGGACCTCA
 321 CTCACTAGCCCCGCTTTGGGCCCCCTCCTGTGACCTCAGGGTTTGGCCCATGGGGCCCCCCCAGGCCCCTGCCCCAACTG
 401 ATTCTGCCCAGATAATCGTGTCTCCTGCCTCCACTCAGCTGCTTCTCAGTCATGAATGTGGCCATGGCCCCGGGGTCCCC
 481 TTGCTGCTGTGGGCTCCCTGTCCCTGGGCAGGAGTGCTGGTGAGGAGGTGGAGCCTTTTGAGGGGGGCCTTCCCTCAGCT
 561 GTTTCCCCACACTGGGGGGCTGGGCCCTGCCTCCCCGTTACCCTCCTTCCCTGCAGGCCTGGAGCCTGTAGGGCTGGACT
 641 GAGGTTCAGGTCTCCCCCCAGCTGTCTCACCCCCACTTTGTCCCCACTCTAGAGCAGGGAGGCAGTGGGGGAGGAGTTGT
 721 GTCTCGTCTTCTGTCTCCATGTGGTTTTTGGGTGTTTTTCTTGTTGTGTCCTGGATTCCGATAAAATTAAAGAAATTGCT
 801 TCCTCAAAAAAAAAAAAAAAAAAAAAAAAAA

ID	Duplex structure	Position	Score	MFE
1	miRNA 3' uuGGUGGUCGGGUGAGg 5' ||:|:: ||||||| Target 5' agCCGCTGACCCACTCa 3'	292 - 308	155.00	-22.30
2	miRNA 3' uuGGUG-GUC--GGGUGAGg 5' |||| : | ||||||| Target 5' ccCCACTTTGTCCCCACTCt 3'	671 - 690	145.00	-17.50
3	miRNA 3' uuGGUGGUCGGGUGAGg 5' |::|| :|||||| Target 5' tcCTGCC--TCCACTCa 3'	423 - 437	131.00	-14.80

Mutant ID	Mutant Position	Mutant Source
COSN30115561	17	COSMIC
COSN23014280	59	COSMIC
COSN30157439	64	COSMIC
COSN30520006	67	COSMIC
COSN30131338	84	COSMIC
COSN26506772	380	COSMIC
COSN28756488	458	COSMIC
COSN28756477	472	COSMIC
COSN31528427	472	COSMIC
COSN15606474	597	COSMIC
COSN30108171	694	COSMIC

Mutant ID	Mutant Position	Mutant Source
rs974026835	6	dbSNP
rs769903641	7	dbSNP
rs773284290	8	dbSNP
rs1415570208	9	dbSNP
rs1270807759	12	dbSNP
rs767150495	12	dbSNP
rs752549143	13	dbSNP
rs760603558	15	dbSNP
rs764121267	17	dbSNP
rs1342834824	21	dbSNP
rs201420801	22	dbSNP
rs753863755	23	dbSNP
rs865808026	25	dbSNP
rs1429784004	29	dbSNP
rs1170659969	35	dbSNP
rs1277865117	36	dbSNP
rs200324733	37	dbSNP
rs747193347	41	dbSNP
rs1238912271	42	dbSNP
rs768743441	45	dbSNP
rs1459658827	51	dbSNP
rs1050385989	52	dbSNP
rs1327718579	55	dbSNP
rs753115075	56	dbSNP
rs767438572	57	dbSNP
rs1283454662	58	dbSNP
rs1038249482	63	dbSNP
rs1040145158	64	dbSNP
rs1216424720	66	dbSNP
rs902918749	73	dbSNP
rs1216338341	80	dbSNP
rs998552907	81	dbSNP
rs1054116657	84	dbSNP
rs1469201801	85	dbSNP
rs765063417	90	dbSNP
rs1240898000	92	dbSNP
rs549846053	95	dbSNP
rs2232984	98	dbSNP
rs2232985	102	dbSNP
rs1042028816	112	dbSNP
rs902308453	115	dbSNP
rs971269386	129	dbSNP
rs1000550545	134	dbSNP
rs1456532256	136	dbSNP
rs1316069497	150	dbSNP
rs1346943405	152	dbSNP
rs1378695665	156	dbSNP
rs2232986	157	dbSNP
rs1015701736	158	dbSNP
rs961427403	166	dbSNP
rs974077850	183	dbSNP
rs1333432112	188	dbSNP
rs565797797	190	dbSNP
rs539132646	191	dbSNP
rs1355042840	196	dbSNP
rs1413102774	203	dbSNP
rs1295354508	204	dbSNP
rs1026939216	206	dbSNP
rs1443723710	207	dbSNP
rs879091021	209	dbSNP
rs559109969	223	dbSNP
rs957505295	225	dbSNP
rs954005770	227	dbSNP
rs1215881500	230	dbSNP
rs1375654910	234	dbSNP
rs985735913	237	dbSNP
rs912775583	238	dbSNP
rs981886022	240	dbSNP
rs1469417332	242	dbSNP
rs570917319	245	dbSNP
rs944245338	252	dbSNP
rs1199187053	255	dbSNP
rs1278524249	257	dbSNP
rs978654608	258	dbSNP
rs1175290952	260	dbSNP
rs1374859004	261	dbSNP
rs924391993	263	dbSNP
rs1314945704	265	dbSNP
rs1356397479	265	dbSNP
rs1441898786	266	dbSNP
rs961477708	270	dbSNP
rs376717618	274	dbSNP
rs538425401	287	dbSNP
rs934397022	295	dbSNP
rs1054168782	296	dbSNP
rs974143016	297	dbSNP
rs556466651	302	dbSNP
rs574774946	317	dbSNP
rs1280273126	318	dbSNP
rs919772562	320	dbSNP
rs1212455852	325	dbSNP
rs1439261154	326	dbSNP
rs1194536221	331	dbSNP
rs892815975	333	dbSNP
rs1480794521	334	dbSNP
rs754866944	341	dbSNP
rs1470393968	342	dbSNP
rs1192888348	345	dbSNP
rs1476924442	349	dbSNP
rs948360929	368	dbSNP
rs1393218804	376	dbSNP
rs932436169	376	dbSNP
rs1063433	380	dbSNP
rs1403179197	381	dbSNP
rs1409669690	382	dbSNP
rs907095496	386	dbSNP
rs1356598868	388	dbSNP
rs1397120113	391	dbSNP
rs553722404	392	dbSNP
rs1303279491	394	dbSNP
rs1369481386	399	dbSNP
rs1235844080	405	dbSNP
rs1328659219	406	dbSNP
rs1398961858	412	dbSNP
rs572503667	417	dbSNP
rs545933557	418	dbSNP
rs1329054435	419	dbSNP
rs1212890894	420	dbSNP
rs1251031459	421	dbSNP
rs760682242	425	dbSNP
rs1231528447	430	dbSNP
rs1274676725	439	dbSNP
rs1340653890	440	dbSNP
rs1221025062	441	dbSNP
rs1378219076	444	dbSNP
rs995550870	448	dbSNP
rs564593318	453	dbSNP
rs1166317661	468	dbSNP
rs1421973072	468	dbSNP
rs1256190913	472	dbSNP
rs531450404	473	dbSNP
rs1392900979	476	dbSNP
rs902172382	480	dbSNP
rs1000581853	498	dbSNP
rs543583696	499	dbSNP
rs1214485056	505	dbSNP
rs1053444392	510	dbSNP
rs1325314133	515	dbSNP
rs535542189	517	dbSNP
rs1224641279	522	dbSNP
rs1269719202	524	dbSNP
rs954081903	525	dbSNP
rs1271550502	533	dbSNP
rs1339712163	542	dbSNP
rs1450156727	543	dbSNP
rs561998925	548	dbSNP
rs1271103654	552	dbSNP
rs1019896771	554	dbSNP
rs757674539	558	dbSNP
rs555024569	560	dbSNP
rs529170295	565	dbSNP
rs1446474361	566	dbSNP
rs924109430	567	dbSNP
rs1244054385	569	dbSNP
rs1478304660	574	dbSNP
rs1164495575	575	dbSNP
rs1461497336	576	dbSNP
rs1416057499	577	dbSNP
rs936789718	580	dbSNP
rs145040732	585	dbSNP
rs1385923629	587	dbSNP
rs1015633703	588	dbSNP
rs961341044	597	dbSNP
rs534365460	598	dbSNP
rs1319801043	604	dbSNP
rs376109675	608	dbSNP
rs879594790	628	dbSNP
rs1340734326	629	dbSNP
rs879606870	635	dbSNP
rs1413728117	637	dbSNP
rs948436633	642	dbSNP
rs1044440722	645	dbSNP
rs367816671	647	dbSNP
rs1260037760	651	dbSNP
rs1348532368	653	dbSNP
rs1203452499	657	dbSNP
rs912379603	659	dbSNP
rs1187441737	660	dbSNP
rs943981221	661	dbSNP
rs907151213	671	dbSNP
rs1160816397	675	dbSNP
rs938594186	675	dbSNP
rs1042256764	676	dbSNP
rs1233974061	685	dbSNP
rs1267345357	690	dbSNP
rs1310673925	691	dbSNP
rs1357012937	696	dbSNP
rs1354479296	699	dbSNP
rs16831105	705	dbSNP
rs1036868191	708	dbSNP
rs558060122	710	dbSNP
rs1262085567	713	dbSNP
rs1053476181	714	dbSNP
rs896999339	716	dbSNP
rs1262382631	717	dbSNP
rs1210323771	720	dbSNP
rs370323512	724	dbSNP
rs2745	726	dbSNP
rs533057160	727	dbSNP
rs1201379659	729	dbSNP
rs1417712777	731	dbSNP
rs74062786	732	dbSNP
rs1027043837	738	dbSNP
rs889857350	743	dbSNP
rs1453231874	745	dbSNP
rs1044984416	746	dbSNP
rs907357598	751	dbSNP
rs1466179338	752	dbSNP
rs1006928970	762	dbSNP
rs2744	764	dbSNP
rs1003142382	773	dbSNP
rs1394014673	779	dbSNP
rs1015831784	780	dbSNP
rs1457058721	781	dbSNP
rs1309863729	789	dbSNP
rs577566076	789	dbSNP
rs1233653632	800	dbSNP
rs1301414351	801	dbSNP
rs1314040173	803	dbSNP
rs181470499	804	dbSNP
rs965370085	806	dbSNP
rs999788615	808	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.