>TRIB3|NM_021158|3'UTR
   1 GACCACCCTACTACACGCTCAGCTGCCAACAGTGGATTGAGTTTGGGGGTAGCTCCAAGCCTTCTCCTGCCTCTGAACTG
  81 AGCCAAACCTTCAGTGCCTTCCAGAAGGGAGAAAGGCAGAAGCCTGTGTGGAGTGTGCTGTGTACACATCTGCTTTGTTC
 161 CACACACATGCAGTTCCTGCTTGGGTGCTTATCAGGTGCCAAGCCCTGTTCTCGGTGCTGGGAGTACAGCAGTGAGCAAA
 241 GGAGACAATATTCCCTGCTCACAGAGATGACAAACTGGCATCCTTGAGCTGACAACACTTTTCCATGACCATAGGTCACT
 321 GTCTACACTGGGTACACTTTGTACCAGTGTCGGCCTCCACTGATGCTGGTGCTCAGGCACCTCTGTCCAAGGACAATCCC
 401 TTTCACAAACAAACCAGCTGCCTTTGTATCTTGTACCTTTTCAGAGAAAGGGAGGTATCCCTGTGCCAAAGGCTCCAGGC
 481 CTCTCCCCTGCAACTCAGGACCCAAGCCCAGCTCACTCTGGGAACTGTGTTCCCAGCATCTCTGTCCTCTTGATTAAGAG
 561 ATTCTCCTTCCAGGCCTAAGCCTGGGATTTGGGCCAGAGATAAGAATCCAAACTATGAGGCTAGTTCTTGTCTAACTCAA
 641 GACTGTTCTGGAATGAGGGTCCAGGCCTGTCAACCATGGGGCTTCTGACCTGAGCACCAAGGTTGAGGGACAGGATTAGG
 721 CAGGGTCTGTCCTGTGGCCACCTGGAAAGTCCCAGGTGGGACTCTTCTGGGGACACTTGGGGTCCACAATCCCAGGTCCA
 801 TACTCTAGGTTTTGGATACCATGAGTATGTATGTTTACCTGTGCCTAATAAAGGAGAATTATGAAATAAAAAAAAAAAAA
 881 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA

ID	Duplex structure	Position	Score	MFE
1	miRNA 3' auaACGUAGA------UAGGUUUGGAa 5' ||| ||| | |||||||| Target 5' tccTGCCTCTGAACTGAGCCAAACCTt 3'	65 - 91	156.00	-14.70
2	miRNA 3' auAACGUAGAU--AGGUUUGGAa 5' ||| : || |||||:||| Target 5' gtTTGGGGGTAGCTCCAAGCCTt 3'	41 - 63	141.00	-13.60
3	miRNA 3' auAACGUAGAUAGGUUUGGaa 5' || || | | |||||| Target 5' ccTTTCA-C-AAACAAACCag 3'	399 - 417	125.00	-5.60

Mutant ID	Mutant Position	Mutant Source
COSM316128	1	COSMIC
COSN31521652	42	COSMIC
COSN30489792	57	COSMIC
COSN30501150	60	COSMIC
COSN30463704	90	COSMIC
COSN30147612	103	COSMIC
COSN19566766	205	COSMIC
COSN29354843	232	COSMIC
COSN10015369	247	COSMIC
COSN31961813	351	COSMIC
COSN31543297	464	COSMIC
COSN31482446	482	COSMIC
COSN30176944	550	COSMIC
COSN30177003	565	COSMIC
COSN31483422	595	COSMIC

Mutant ID	Mutant Position	Mutant Source
rs771396793	8	dbSNP
rs776834364	12	dbSNP
rs759977026	16	dbSNP
rs759890273	17	dbSNP
rs765507830	18	dbSNP
rs1235908511	22	dbSNP
rs763062412	23	dbSNP
rs767371142	24	dbSNP
rs1357048045	26	dbSNP
rs1426151485	31	dbSNP
rs1477047761	33	dbSNP
rs780019539	38	dbSNP
rs1441997088	42	dbSNP
rs188020529	44	dbSNP
rs778272871	45	dbSNP
rs755972826	46	dbSNP
rs966171299	47	dbSNP
rs1466160557	49	dbSNP
rs766246372	53	dbSNP
rs900423317	61	dbSNP
rs556568862	62	dbSNP
rs1476305025	65	dbSNP
rs758744536	67	dbSNP
rs1321435934	75	dbSNP
rs6084315	90	dbSNP
rs977525080	91	dbSNP
rs996823999	95	dbSNP
rs1231058058	97	dbSNP
rs6051679	99	dbSNP
rs1028264674	102	dbSNP
rs952685720	110	dbSNP
rs1206557469	113	dbSNP
rs1442908833	127	dbSNP
rs780202035	130	dbSNP
rs936023029	132	dbSNP
rs1469360373	135	dbSNP
rs1182377595	136	dbSNP
rs1015638039	146	dbSNP
rs1467739910	161	dbSNP
rs192061190	172	dbSNP
rs1313039413	174	dbSNP
rs948610596	193	dbSNP
rs1045582422	194	dbSNP
rs535985314	195	dbSNP
rs939852649	196	dbSNP
rs928229395	204	dbSNP
rs1036774981	212	dbSNP
rs4352283	214	dbSNP
rs755089348	215	dbSNP
rs914930779	221	dbSNP
rs1418233844	229	dbSNP
rs1405530229	235	dbSNP
rs1410684385	249	dbSNP
rs1180350883	250	dbSNP
rs1290400509	253	dbSNP
rs1440223904	255	dbSNP
rs1343742711	257	dbSNP
rs1027911133	260	dbSNP
rs1211242068	262	dbSNP
rs868518762	264	dbSNP
rs889386390	272	dbSNP
rs6051682	284	dbSNP
rs1008198331	300	dbSNP
rs946328515	302	dbSNP
rs1345715311	316	dbSNP
rs1042540949	322	dbSNP
rs1202094739	324	dbSNP
rs923704772	329	dbSNP
rs944575156	336	dbSNP
rs142330335	339	dbSNP
rs1205467846	342	dbSNP
rs376258139	352	dbSNP
rs1370872943	353	dbSNP
rs544146672	360	dbSNP
rs527432999	361	dbSNP
rs558443192	366	dbSNP
rs748128309	369	dbSNP
rs769881992	370	dbSNP
rs1479239738	374	dbSNP
rs1368416943	379	dbSNP
rs578166429	399	dbSNP
rs1211334096	400	dbSNP
rs957405909	405	dbSNP
rs1198116969	429	dbSNP
rs1160213931	438	dbSNP
rs1420121739	443	dbSNP
rs1048942591	444	dbSNP
rs888449782	445	dbSNP
rs1394359868	453	dbSNP
rs777821030	459	dbSNP
rs1434337916	460	dbSNP
rs1016134661	464	dbSNP
rs915869369	466	dbSNP
rs1217762964	468	dbSNP
rs1264939892	468	dbSNP
rs1377697167	474	dbSNP
rs1347642767	476	dbSNP
rs11537607	477	dbSNP
rs567449867	492	dbSNP
rs563707076	500	dbSNP
rs770835467	509	dbSNP
rs183116089	522	dbSNP
rs928557639	523	dbSNP
rs1364311604	528	dbSNP
rs1299063378	529	dbSNP
rs1035199895	533	dbSNP
rs187050924	534	dbSNP
rs1400330445	535	dbSNP
rs939896193	548	dbSNP
rs959506757	550	dbSNP
rs991074650	561	dbSNP
rs879060394	562	dbSNP
rs192936575	571	dbSNP
rs1396235655	572	dbSNP
rs915464042	573	dbSNP
rs1036786322	583	dbSNP
rs1430745095	591	dbSNP
rs559537865	605	dbSNP
rs1363985576	614	dbSNP
rs968153899	615	dbSNP
rs773938324	617	dbSNP
rs1332846550	618	dbSNP
rs151258947	619	dbSNP
rs1251284119	620	dbSNP
rs1268306811	620	dbSNP
rs1341226383	621	dbSNP
rs551251219	622	dbSNP
rs1225284695	623	dbSNP
rs1320121606	636	dbSNP
rs889472198	640	dbSNP
rs944457107	641	dbSNP
rs2295491	646	dbSNP
rs1353871773	661	dbSNP
rs1310830070	664	dbSNP
rs530749662	668	dbSNP
rs1276477546	673	dbSNP
rs1489760173	680	dbSNP
rs931776239	682	dbSNP
rs1048973787	691	dbSNP
rs184131690	693	dbSNP
rs1459976806	706	dbSNP
rs1019650220	715	dbSNP
rs116353227	720	dbSNP
rs775085300	725	dbSNP
rs1415277968	726	dbSNP
rs3204117	728	dbSNP
rs1267461308	738	dbSNP
rs1037022015	740	dbSNP
rs1250370213	751	dbSNP
rs1194599708	757	dbSNP
rs1191688336	760	dbSNP
rs1459093607	761	dbSNP
rs3204118	765	dbSNP
rs1063081	768	dbSNP
rs546298462	774	dbSNP
rs1213205480	775	dbSNP
rs1332926750	777	dbSNP
rs566413053	778	dbSNP
rs1286211963	779	dbSNP
rs1246659493	782	dbSNP
rs1450601792	785	dbSNP
rs1170943514	786	dbSNP
rs1306122766	788	dbSNP
rs1035065807	801	dbSNP
rs189445101	804	dbSNP
rs765784366	807	dbSNP
rs1402449607	808	dbSNP
rs957455199	810	dbSNP
rs1012415292	818	dbSNP
rs1391781858	819	dbSNP
rs1294271241	822	dbSNP
rs1022592310	823	dbSNP
rs1393008047	824	dbSNP
rs766523952	828	dbSNP
rs1458679871	829	dbSNP
rs1023032803	832	dbSNP
rs978188414	834	dbSNP
rs1442072877	837	dbSNP
rs970492857	839	dbSNP
rs981463235	844	dbSNP
rs1435722126	852	dbSNP
rs149747048	853	dbSNP
rs961244072	859	dbSNP
rs1350321302	862	dbSNP
rs1259918689	867	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.