ID	Duplex structure	Position	Score	MFE
1	miRNA 3' ucuguguaaACC---UC---UCCCUUGg 5' ||| || ||||||| Target 5' tttagaaggTGGAAAAGCCAAGGGAACg 3'	330 - 357	141.00	-11.80
2	miRNA 3' ucuguguaaaCCUC--UCCCUUGg 5' |||| ||| ||| Target 5' ----------GGAGACAGGAAACt 3'	1 - 14	118.00	-8.50
3	miRNA 3' ucugugUAAACCUCUCCCUUGg 5' :| | :|| ||||| Target 5' tctagaGTCTCCGGAAGGAACa 3'	366 - 387	116.00	-7.50

Mutant ID	Mutant Position	Mutant Source
COSN30476289	3	COSMIC
COSN30476242	5	COSMIC
COSN30454168	10	COSMIC
COSN30751073	17	COSMIC
COSN19730937	18	COSMIC
COSN30153984	29	COSMIC
COSN30709053	71	COSMIC

Mutant ID	Mutant Position	Mutant Source
rs1204136392	2	dbSNP
rs745485687	7	dbSNP
rs1267368823	9	dbSNP
rs375634508	10	dbSNP
rs1178832946	13	dbSNP
rs754697184	14	dbSNP
rs777879022	15	dbSNP
rs527283732	17	dbSNP
rs768342890	18	dbSNP
rs1224523824	29	dbSNP
rs548109033	30	dbSNP
rs761701313	32	dbSNP
rs765324777	34	dbSNP
rs1357726837	35	dbSNP
rs763146014	36	dbSNP
rs766529555	38	dbSNP
rs13005572	41	dbSNP
rs1408143788	45	dbSNP
rs974866482	48	dbSNP
rs536520937	53	dbSNP
rs1029159248	54	dbSNP
rs1164422575	64	dbSNP
rs952261615	72	dbSNP
rs1427301735	78	dbSNP
rs1390049969	85	dbSNP
rs142892925	87	dbSNP
rs28928300	88	dbSNP
rs939692867	89	dbSNP
rs192730679	94	dbSNP
rs1269733795	101	dbSNP
rs1463386423	104	dbSNP
rs911081592	109	dbSNP
rs972453268	114	dbSNP
rs558782359	115	dbSNP
rs1482797821	119	dbSNP
rs752483382	121	dbSNP
rs944108569	121	dbSNP
rs759330602	122	dbSNP
rs1341191137	123	dbSNP
rs1473484616	130	dbSNP
rs949820700	134	dbSNP
rs891789502	136	dbSNP
rs1044242877	137	dbSNP
rs1304610434	154	dbSNP
rs374511346	160	dbSNP
rs1369444076	166	dbSNP
rs1420157403	167	dbSNP
rs184514993	174	dbSNP
rs1162024188	176	dbSNP
rs28928301	182	dbSNP
rs1412188458	184	dbSNP
rs1043298252	189	dbSNP
rs904791584	191	dbSNP
rs1457109365	192	dbSNP
rs1379565936	194	dbSNP
rs1180341296	201	dbSNP
rs1472300613	207	dbSNP
rs1252699646	208	dbSNP
rs758033369	219	dbSNP
rs1001677746	222	dbSNP
rs749440714	225	dbSNP
rs1337623201	239	dbSNP
rs1439418904	247	dbSNP
rs1199618949	248	dbSNP
rs147412734	249	dbSNP
rs1034910814	252	dbSNP
rs1445875211	257	dbSNP
rs187644874	259	dbSNP
rs960262416	262	dbSNP
rs891767352	268	dbSNP
rs1010641974	271	dbSNP
rs1357882201	273	dbSNP
rs1018972761	277	dbSNP
rs901935115	285	dbSNP
rs1408844522	294	dbSNP
rs1157196675	296	dbSNP
rs1472352063	299	dbSNP
rs28929168	300	dbSNP
rs1290140898	304	dbSNP
rs1471865788	305	dbSNP
rs1235647198	322	dbSNP
rs1326805445	323	dbSNP
rs28928302	327	dbSNP
rs952613613	333	dbSNP
rs1206609455	335	dbSNP
rs952230600	340	dbSNP
rs1268392415	352	dbSNP
rs775112257	358	dbSNP
rs1376387320	361	dbSNP
rs1284116899	365	dbSNP
rs192462873	366	dbSNP
rs1449478200	370	dbSNP
rs911039383	377	dbSNP
rs139645400	378	dbSNP
rs28928303	379	dbSNP
rs1457071893	387	dbSNP
rs1389594546	395	dbSNP
rs1161619300	397	dbSNP
rs28928304	402	dbSNP
rs1413250196	404	dbSNP
rs913329105	405	dbSNP
rs28928305	407	dbSNP
rs1244902191	413	dbSNP
rs1043095321	434	dbSNP
rs1470204986	447	dbSNP
rs1464310771	457	dbSNP
rs916953087	462	dbSNP
rs1248222677	465	dbSNP
rs1217580216	469	dbSNP
rs1319386072	471	dbSNP
rs1288455677	475	dbSNP
rs530361237	480	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.