>GLO1|NM_006708|3'UTR
   1 TGCTGTGAGAATTCTCCTTTGAGATTTCAGAAGAAAGGAAACAATGTGATTCAAGATATTTACATACCAGAAGCATCTAG
  81 GACTGATGGATCACTGTCCCGATTCAAATTATTCTTCAGTCCATTTCCCCTTCCTATTTCAGCTGTTCCTTTTCACCTAA
 161 CTGTTCAGTCATTCTGGTTTTCAAGCAGTGCTTTATCTCATGTCCTTGAATATAGTTGTGTAACTTTATTTTTTAGGTAA
 241 TAATTAGAACAGTTCCCTTCAGAGGCTGCATTTGCCTTCTTCTGCCACCTAAATATTACTTCCCTTCAAATCTGCCTTTG
 321 AATCATCATTTTTAAAAAAAAATTAACATGTTTTTGTTGTAGTTATCTTCTGGGGTTTCAATTCCTCAGAAACAACTTTT
 401 TTCACAACGGAAAGGAAAGAACACTAGTGTTCTTTCAGTAAAGTACAAAGTGTTTATTTTACAAAAGAGTAGGTACTCTT
 481 GAGAGCAATTCAAATCATGCTGACAAGGATACTGATAGAAAAAGTGATTTCTTCTTATTATAAAGTACATTTAAAGTTCA
 561 AGGACTAACCTTATTTATTTGGGAAAGGGGAGGAGGAAGGAAATGATATGGTACCCAGACACTGGGCTAGGCTGCAACTT
 641 TATCTCATTTAATACTCCCAGCTGTCATGTGAGAAAGAAAGCAGGCTAGGCATGTGAAATCACTTTCATGGATTATTAAT
 721 GGATTTAAGAGGGCATCAATCAGCTCAACTCAAGATTTCATAATCATTTTTAGTATTTAGATTGTGCCTCAAAGTTGTAG
 801 TACCTCACAATACCTCCACTGGTTTCCTGTTGTAAAAACCTTCAGTGAGTTTGACCATTGTGCTCTTGGCTCTTGGGCTG
 881 GAGTACCGTGGTGAGGGAGTAAACACTAGAAGTCTTTAGTACAAAACTGCTCTAGGGACACCTGGTGATTCCTACACAAG
 961 TGATGTTTATATTTCTCATAAAGAGTCTTCCCTATCCCAAGGTCTTCATGATGCCAGTAGCCATATATGATAAATTATGT
1041 TCAGTGATAACTTAGTTATCAGAAATCAGCTCAGTGGTCTTCCCCGCCATGATTCACATTTGATGAGTTTTTAAAAATCA
1121 AAGTGATTTTGAAAATCTCTAATGGCTCAGAAAATAAAAACATCCAGTTTGTGGATGACTATATTTAGATTTCTCTAGAC
1201 TCTAGTGGAAGACCTTTGGAAAGGCCATGCCAACCGTGCTTGTACTGCTAGAAGCACTTTATGTTTCCTTTTTGGGTGAA
1281 ATGGATTTATGTGAGTGCTTTAAACAAATAGCAATACTTATAGACTGAAATAAAATGAAACTTCAAATAAGACTATGTTT
1361 AATTTGTAAAAAAAAAAAAAAAAAAAAAAAAAAA

ID	Duplex structure	Position	Score	MFE
1	miRNA 3' caGUGGUAGAAGGGAAGa 5' :|::| ||||||||| Target 5' aaTATTA-CTTCCCTTCa 3'	292 - 308	155.00	-15.20
2	miRNA 3' cagUGGUAGAAGGGAAGa 5' | || |||||||| Target 5' tagAACA-GTTCCCTTCa 3'	245 - 261	146.00	-11.30
3	miRNA 3' caguGGUAGAAGGGAAGa 5' ||||:| |||||| Target 5' cagtCCATTTCCCCTTCc 3'	117 - 134	134.00	-15.90

Mutant ID	Mutant Position	Mutant Source
COSN30109469	37	COSMIC
COSN31523520	66	COSMIC
COSN30124737	86	COSMIC
COSN30705930	115	COSMIC
COSN7790188	334	COSMIC
COSN7872184	343	COSMIC
COSN21440530	741	COSMIC
COSN14876005	842	COSMIC
COSN17198017	1155	COSMIC

Mutant ID	Mutant Position	Mutant Source
rs1238721754	5	dbSNP
rs372960211	9	dbSNP
rs748249302	16	dbSNP
rs1398872032	17	dbSNP
rs779122254	21	dbSNP
rs1446222418	29	dbSNP
rs755608541	31	dbSNP
rs754339809	38	dbSNP
rs1355045513	42	dbSNP
rs761808625	49	dbSNP
rs1053170132	52	dbSNP
rs908001034	53	dbSNP
rs41273110	62	dbSNP
rs930421249	64	dbSNP
rs916330118	65	dbSNP
rs1363736179	67	dbSNP
rs1454890826	73	dbSNP
rs1313950780	76	dbSNP
rs923734769	77	dbSNP
rs772914774	88	dbSNP
rs1339464007	96	dbSNP
rs1367432363	98	dbSNP
rs982352377	99	dbSNP
rs949271637	100	dbSNP
rs2293868	101	dbSNP
rs550808645	110	dbSNP
rs1266131562	111	dbSNP
rs1462633702	114	dbSNP
rs1182181685	122	dbSNP
rs577076975	123	dbSNP
rs1423393909	124	dbSNP
rs556946001	152	dbSNP
rs554635238	159	dbSNP
rs1034918236	162	dbSNP
rs990765097	163	dbSNP
rs16890915	164	dbSNP
rs11544287	168	dbSNP
rs369417583	176	dbSNP
rs1387066266	193	dbSNP
rs1471256409	200	dbSNP
rs1026612975	205	dbSNP
rs1215646472	214	dbSNP
rs761324247	217	dbSNP
rs11544285	223	dbSNP
rs201683245	229	dbSNP
rs1393875083	232	dbSNP
rs961105841	237	dbSNP
rs775925376	238	dbSNP
rs1019397103	239	dbSNP
rs1227218068	242	dbSNP
rs1008792357	245	dbSNP
rs1285936700	266	dbSNP
rs1325538740	272	dbSNP
rs954264426	276	dbSNP
rs1255134269	277	dbSNP
rs1482144010	278	dbSNP
rs893236728	281	dbSNP
rs1028962477	283	dbSNP
rs1254213433	286	dbSNP
rs745836149	290	dbSNP
rs1029068039	294	dbSNP
rs1011853100	302	dbSNP
rs1409890127	304	dbSNP
rs770231594	312	dbSNP
rs1292792744	314	dbSNP
rs1177445234	315	dbSNP
rs746424331	321	dbSNP
rs1464829877	322	dbSNP
rs776834649	329	dbSNP
rs567882403	333	dbSNP
rs75200860	334	dbSNP
rs1430496857	341	dbSNP
rs1005102574	343	dbSNP
rs1305565245	343	dbSNP
rs115662320	346	dbSNP
rs1049733592	350	dbSNP
rs930809111	358	dbSNP
rs916329139	372	dbSNP
rs566571027	388	dbSNP
rs1412460547	397	dbSNP
rs949213833	405	dbSNP
rs747233390	408	dbSNP
rs778149215	409	dbSNP
rs546578131	410	dbSNP
rs533317351	411	dbSNP
rs752561926	413	dbSNP
rs1489499454	418	dbSNP
rs1425053137	419	dbSNP
rs939024319	419	dbSNP
rs919879751	420	dbSNP
rs142823052	423	dbSNP
rs977722194	424	dbSNP
rs1391169369	428	dbSNP
rs1185534119	437	dbSNP
rs1166314998	438	dbSNP
rs1351323393	439	dbSNP
rs961051327	446	dbSNP
rs966639544	447	dbSNP
rs1292489583	460	dbSNP
rs1365351259	488	dbSNP
rs1383888845	494	dbSNP
rs915145911	494	dbSNP
rs544860359	498	dbSNP
rs986577740	502	dbSNP
rs954328781	507	dbSNP
rs953872981	508	dbSNP
rs1451037144	509	dbSNP
rs1323781219	527	dbSNP
rs1028493772	531	dbSNP
rs758496839	556	dbSNP
rs377664484	564	dbSNP
rs772595921	583	dbSNP
rs1214398782	587	dbSNP
rs1246231852	602	dbSNP
rs1487752678	606	dbSNP
rs1029508075	609	dbSNP
rs9470916	610	dbSNP
rs562246078	611	dbSNP
rs1018989300	615	dbSNP
rs541994930	634	dbSNP
rs1405621601	664	dbSNP
rs1163418405	678	dbSNP
rs1004883304	679	dbSNP
rs886714543	681	dbSNP
rs1321127189	684	dbSNP
rs1364455997	689	dbSNP
rs1432607370	690	dbSNP
rs1031953518	703	dbSNP
rs995432628	705	dbSNP
rs1229105448	710	dbSNP
rs547833846	712	dbSNP
rs778954901	715	dbSNP
rs895277587	716	dbSNP
rs762891015	720	dbSNP
rs1210739816	733	dbSNP
rs1269282260	742	dbSNP
rs1370926400	743	dbSNP
rs998844178	757	dbSNP
rs572966196	760	dbSNP
rs927717777	770	dbSNP
rs1042061793	791	dbSNP
rs553064775	798	dbSNP
rs1472886061	799	dbSNP
rs945033667	802	dbSNP
rs915159066	804	dbSNP
rs371858314	810	dbSNP
rs1397441657	813	dbSNP
rs1169110038	821	dbSNP
rs568110423	822	dbSNP
rs1455603348	832	dbSNP
rs1421204816	833	dbSNP
rs1046208485	843	dbSNP
rs1359538870	844	dbSNP
rs921070294	849	dbSNP
rs11544277	856	dbSNP
rs1353842503	857	dbSNP
rs1453514678	863	dbSNP
rs966155729	865	dbSNP
rs1019022119	872	dbSNP
rs894941334	883	dbSNP
rs1329038617	885	dbSNP
rs188973590	887	dbSNP
rs950723608	888	dbSNP
rs1209941478	891	dbSNP
rs1028324406	896	dbSNP
rs1421470049	905	dbSNP
rs753862662	906	dbSNP
rs919822842	918	dbSNP
rs1456366409	922	dbSNP
rs995066743	932	dbSNP
rs1471535179	938	dbSNP
rs1236475806	942	dbSNP
rs1036936508	949	dbSNP
rs11544286	950	dbSNP
rs1203906028	953	dbSNP
rs939651136	956	dbSNP
rs912245903	964	dbSNP
rs1425864485	975	dbSNP
rs1308361336	978	dbSNP
rs895380307	980	dbSNP
rs986916463	997	dbSNP
rs1332000251	998	dbSNP
rs1373819117	1001	dbSNP
rs1411937385	1015	dbSNP
rs1033849876	1016	dbSNP
rs1349968637	1021	dbSNP
rs1237047742	1025	dbSNP
rs537338882	1028	dbSNP
rs1346376711	1032	dbSNP
rs1218986450	1033	dbSNP
rs772019736	1038	dbSNP
rs1483792933	1039	dbSNP
rs111411963	1063	dbSNP
rs185037650	1067	dbSNP
rs921046715	1072	dbSNP
rs750688747	1075	dbSNP
rs1028924838	1081	dbSNP
rs1042094735	1082	dbSNP
rs1200418162	1082	dbSNP
rs755941564	1084	dbSNP
rs765409451	1085	dbSNP
rs1477668215	1086	dbSNP
rs957555128	1086	dbSNP
rs1031899765	1097	dbSNP
rs1431803044	1116	dbSNP
rs554337343	1123	dbSNP
rs932618050	1144	dbSNP
rs921176220	1154	dbSNP
rs548690487	1164	dbSNP
rs1325669969	1168	dbSNP
rs977688758	1183	dbSNP
rs762046072	1184	dbSNP
rs1436394346	1189	dbSNP
rs1297172040	1198	dbSNP
rs1442290005	1202	dbSNP
rs943839883	1215	dbSNP
rs143734257	1235	dbSNP
rs192487325	1236	dbSNP
rs1024319406	1245	dbSNP
rs1290011061	1263	dbSNP
rs1433887702	1270	dbSNP
rs547025736	1273	dbSNP
rs7604	1275	dbSNP
rs1191687502	1295	dbSNP
rs894559467	1300	dbSNP
rs1249889345	1311	dbSNP
rs149374228	1318	dbSNP
rs551020297	1321	dbSNP
rs1389760219	1323	dbSNP
rs1437821799	1327	dbSNP
rs1165006656	1334	dbSNP
rs1391559486	1337	dbSNP
rs1404896656	1343	dbSNP
rs1324466156	1347	dbSNP
rs1368017854	1350	dbSNP
rs1436244904	1351	dbSNP
rs1297348701	1354	dbSNP
rs1407143606	1355	dbSNP
rs149705108	1357	dbSNP
rs1480962104	1370	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.