ID	Duplex structure	Position	Score	MFE
1	miRNA 3' cgcUCUCAC---GCCCGGGGUCCUc 5' |||||| :||||||| ||: Target 5' ttcAGAGTGGGCTGGGCCCCTGGGc 3'	396 - 420	131.00	-28.90
2	miRNA 3' cgcucucacgcccggGGUCCUc 5' |||||| Target 5' ggcatctttttaataCCAGGAa 3'	441 - 462	120.00	-9.52
3	miRNA 3' cgcucucacgccCGGGGUCcuc 5' ||||||| Target 5' tgtaaaggaacaGCCCCAGtgc 3'	119 - 140	110.00	-13.70

Mutant ID	Mutant Position	Mutant Source
COSN31510581	57	COSMIC
COSN30146431	82	COSMIC
COSN30146512	86	COSMIC
COSN5186746	87	COSMIC
COSN30460002	96	COSMIC
COSN5264377	99	COSMIC
COSN30543141	106	COSMIC
COSN30466023	107	COSMIC
COSN30107216	147	COSMIC
COSN30138190	163	COSMIC
COSN31526256	249	COSMIC
COSN26552882	254	COSMIC
COSN20092481	265	COSMIC
COSN20159021	300	COSMIC
COSN31514180	329	COSMIC
COSN31565941	374	COSMIC
COSN26563523	420	COSMIC
COSN31546047	421	COSMIC
COSN20109111	505	COSMIC
COSN20109112	506	COSMIC
COSN24304322	506	COSMIC
COSN31481080	583	COSMIC

Mutant ID	Mutant Position	Mutant Source
rs779691620	1	dbSNP
rs867781306	8	dbSNP
rs750214515	11	dbSNP
rs112636750	16	dbSNP
rs1273637417	16	dbSNP
rs761705137	23	dbSNP
rs1157649676	24	dbSNP
rs753811207	27	dbSNP
rs1204902675	29	dbSNP
rs375386448	30	dbSNP
rs760852905	39	dbSNP
rs371501457	43	dbSNP
rs772457322	46	dbSNP
rs878925203	47	dbSNP
rs767355615	49	dbSNP
rs1317314787	51	dbSNP
rs1026021792	54	dbSNP
rs368227033	56	dbSNP
rs898161450	57	dbSNP
rs906891732	64	dbSNP
rs1425134528	69	dbSNP
rs1045444455	72	dbSNP
rs1409991756	74	dbSNP
rs1023353657	79	dbSNP
rs1174865663	86	dbSNP
rs570774016	88	dbSNP
rs949588155	94	dbSNP
rs2267968	99	dbSNP
rs533871420	102	dbSNP
rs1470481248	104	dbSNP
rs1336439164	106	dbSNP
rs1419734968	117	dbSNP
rs1343592635	129	dbSNP
rs577551370	144	dbSNP
rs1430126065	145	dbSNP
rs896262857	151	dbSNP
rs1057310026	157	dbSNP
rs938868035	169	dbSNP
rs1460714638	175	dbSNP
rs1243473404	177	dbSNP
rs1052995369	183	dbSNP
rs903432569	190	dbSNP
rs936895933	191	dbSNP
rs773139218	201	dbSNP
rs1446125427	205	dbSNP
rs1216061990	206	dbSNP
rs1264754189	208	dbSNP
rs1479158467	213	dbSNP
rs1259755508	222	dbSNP
rs975545195	229	dbSNP
rs964113156	231	dbSNP
rs912531996	232	dbSNP
rs975462047	238	dbSNP
rs750504212	243	dbSNP
rs1400381177	248	dbSNP
rs1299003110	250	dbSNP
rs951259791	254	dbSNP
rs1244360282	257	dbSNP
rs1403136217	259	dbSNP
rs1382544674	260	dbSNP
rs1025551283	261	dbSNP
rs543601543	265	dbSNP
rs962597553	270	dbSNP
rs1025524050	271	dbSNP
rs537546275	279	dbSNP
rs1288508376	280	dbSNP
rs1224042570	281	dbSNP
rs568613560	287	dbSNP
rs1454380601	291	dbSNP
rs1365548815	295	dbSNP
rs1001262309	306	dbSNP
rs1162623037	308	dbSNP
rs1443886449	313	dbSNP
rs1385748246	322	dbSNP
rs1185243377	323	dbSNP
rs1201600356	324	dbSNP
rs906968692	327	dbSNP
rs1362467724	331	dbSNP
rs1045384516	340	dbSNP
rs753633533	350	dbSNP
rs1009913036	351	dbSNP
rs1422834837	354	dbSNP
rs549124129	372	dbSNP
rs15150	374	dbSNP
rs1391539970	378	dbSNP
rs1260683825	381	dbSNP
rs1334974455	381	dbSNP
rs73045994	382	dbSNP
rs1311010071	383	dbSNP
rs1356755849	389	dbSNP
rs1244778659	390	dbSNP
rs1011949659	392	dbSNP
rs1357820993	413	dbSNP
rs1212172072	415	dbSNP
rs896231811	421	dbSNP
rs1034809657	422	dbSNP
rs1240400230	437	dbSNP
rs1443081176	438	dbSNP
rs1244565740	442	dbSNP
rs1369176629	446	dbSNP
rs1003003276	449	dbSNP
rs192895387	456	dbSNP
rs1316335574	461	dbSNP
rs903359032	465	dbSNP
rs547247769	468	dbSNP
rs1451520213	477	dbSNP
rs533487633	479	dbSNP
rs1312923662	484	dbSNP
rs1012261922	485	dbSNP
rs1324984555	486	dbSNP
rs1295142846	494	dbSNP
rs1382941424	495	dbSNP
rs1002749830	498	dbSNP
rs1339371591	498	dbSNP
rs893416063	499	dbSNP
rs779392929	502	dbSNP
rs1301417409	503	dbSNP
rs77870850	504	dbSNP
rs1297228802	505	dbSNP
rs1039670385	506	dbSNP
rs754174255	506	dbSNP
rs758479656	506	dbSNP
rs564494202	513	dbSNP
rs1478147644	517	dbSNP
rs1165387894	518	dbSNP
rs1159682210	519	dbSNP
rs1403657308	519	dbSNP
rs201057993	519	dbSNP
rs762151199	519	dbSNP
rs780818304	519	dbSNP
rs1294315230	520	dbSNP
rs1340563175	520	dbSNP
rs912607102	525	dbSNP
rs1321895564	527	dbSNP
rs928601410	527	dbSNP
rs1209776028	529	dbSNP
rs1447437393	533	dbSNP
rs892712894	533	dbSNP
rs1372242027	543	dbSNP
rs1203614271	546	dbSNP
rs1193495550	553	dbSNP
rs1488627935	574	dbSNP
rs1195793174	575	dbSNP
rs1427031448	575	dbSNP
rs918433356	579	dbSNP
rs929782468	579	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.

- Nature, 2013

Circular RNAs (circRNAs) in animals are an enigmatic class of RNA with unknown function. To explore circRNAs systematically, we sequenced and computationally analysed human, mouse and nematode RNA. We detected thousands of well-expressed, stable circRNAs, often showing tissue/developmental-stage-specific expression. Sequence analysis indicated important regulatory functions for circRNAs. We found that a human circRNA, antisense to the cerebellar degeneration-related protein 1 transcript (CDR1as), is densely bound by microRNA (miRNA) effector complexes and harbours 63 conserved binding sites for the ancient miRNA miR-7. Further analyses indicated that CDR1as functions to bind miR-7 in neuronal tissues. Human CDR1as expression in zebrafish impaired midbrain development, similar to knocking down miR-7, suggesting that CDR1as is a miRNA antagonist with a miRNA-binding capacity ten times higher than any other known transcript. Together, our data provide evidence that circRNAs form a large class of post-transcriptional regulators. Numerous circRNAs form by head-to-tail splicing of exons, suggesting previously unrecognized regulatory potential of coding sequences.

- 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.