ID	Duplex structure	Position	Score	MFE
1	miRNA 3' gcucacacucuagUGUGGAGGg 5' :||||||| Target 5' cctcacctctccgGCACCTCCt 3'	700 - 721	141.00	-13.20
2	miRNA 3' gcUCAC---ACU-CUAGUGUGGAGGg 5' |||| | | || : |||||:| Target 5' tcAGTGCCTTCATGAATTCACCTTCc 3'	773 - 798	136.00	-15.00
3	miRNA 3' gcUCAC--ACU----CU-AGUGUGGAGGg 5' |||| ||| || |:::|:|||| Target 5' tcAGTGGCTGACACGGACTTGTATCTCCt 3'	571 - 599	128.00	-13.90

Mutant ID	Mutant Position	Mutant Source
COSN31588548	3	COSMIC
COSN30515397	10	COSMIC
COSN30489174	12	COSMIC
COSN31576967	14	COSMIC
COSN28189276	17	COSMIC
COSN30157074	28	COSMIC
COSN14005227	38	COSMIC
COSN30462493	42	COSMIC
COSN30499808	43	COSMIC
COSN31505451	44	COSMIC
COSN30120692	54	COSMIC
COSN31522104	62	COSMIC
COSN30489213	70	COSMIC
COSN15906567	71	COSMIC
COSN30517808	73	COSMIC
COSN31581393	86	COSMIC
COSN29429545	89	COSMIC
COSN31572399	95	COSMIC
COSN31526630	144	COSMIC
COSN27176412	162	COSMIC
COSN31571522	193	COSMIC
COSN29509260	737	COSMIC

Mutant ID	Mutant Position	Mutant Source
rs370635955	6	dbSNP
rs533708008	15	dbSNP
rs1438593027	21	dbSNP
rs781875236	22	dbSNP
rs782700461	26	dbSNP
rs782643159	27	dbSNP
rs17006424	30	dbSNP
rs1056911887	31	dbSNP
rs782445651	35	dbSNP
rs1218222195	36	dbSNP
rs144452787	37	dbSNP
rs140660157	38	dbSNP
rs782162189	39	dbSNP
rs376522449	49	dbSNP
rs1452682893	53	dbSNP
rs946907468	54	dbSNP
rs1239833085	59	dbSNP
rs1474825109	60	dbSNP
rs1193788794	61	dbSNP
rs1425239471	68	dbSNP
rs568266745	71	dbSNP
rs1474026923	72	dbSNP
rs1163924799	74	dbSNP
rs1414343184	76	dbSNP
rs1406986155	85	dbSNP
rs1316191633	87	dbSNP
rs1344557367	88	dbSNP
rs1399436935	92	dbSNP
rs116070623	95	dbSNP
rs76441599	96	dbSNP
rs934327828	109	dbSNP
rs1283972226	128	dbSNP
rs1357548125	139	dbSNP
rs1230507910	142	dbSNP
rs562823755	143	dbSNP
rs190774979	145	dbSNP
rs371710720	148	dbSNP
rs1264771531	151	dbSNP
rs1484480925	170	dbSNP
rs74392937	171	dbSNP
rs545749043	172	dbSNP
rs1473627381	173	dbSNP
rs1156624912	180	dbSNP
rs1407077670	192	dbSNP
rs921074641	198	dbSNP
rs1420246271	205	dbSNP
rs1159316521	207	dbSNP
rs540751386	208	dbSNP
rs1413136498	215	dbSNP
rs186059238	218	dbSNP
rs962569793	223	dbSNP
rs1341324351	225	dbSNP
rs1016858599	227	dbSNP
rs183556916	232	dbSNP
rs951325569	235	dbSNP
rs1241584290	253	dbSNP
rs1287499418	254	dbSNP
rs1035039508	255	dbSNP
rs1345179880	261	dbSNP
rs1004011327	264	dbSNP
rs1199408366	267	dbSNP
rs1256372733	270	dbSNP
rs782715836	277	dbSNP
rs769058777	278	dbSNP
rs1179329023	279	dbSNP
rs544529240	283	dbSNP
rs1440234295	284	dbSNP
rs142322494	285	dbSNP
rs148723258	287	dbSNP
rs2110980	289	dbSNP
rs386647176	290	dbSNP
rs144214899	298	dbSNP
rs1416435211	299	dbSNP
rs782779696	301	dbSNP
rs1376674859	311	dbSNP
rs1448141948	316	dbSNP
rs924244198	323	dbSNP
rs1369467014	338	dbSNP
rs1231801267	344	dbSNP
rs1050801757	346	dbSNP
rs782132003	350	dbSNP
rs3732245	352	dbSNP
rs1346669852	359	dbSNP
rs921009755	380	dbSNP
rs975198834	386	dbSNP
rs533902922	388	dbSNP
rs1257161554	390	dbSNP
rs568121999	399	dbSNP
rs782023297	400	dbSNP
rs909723379	401	dbSNP
rs982666690	406	dbSNP
rs1378342968	418	dbSNP
rs548367482	422	dbSNP
rs782818242	423	dbSNP
rs1168862040	451	dbSNP
rs1035371554	453	dbSNP
rs1333794908	460	dbSNP
rs982119542	472	dbSNP
rs1386764979	483	dbSNP
rs1301359150	496	dbSNP
rs140562210	512	dbSNP
rs1224768193	516	dbSNP
rs1277129839	517	dbSNP
rs1318196089	535	dbSNP
rs1200227884	544	dbSNP
rs1488111993	550	dbSNP
rs17656758	552	dbSNP
rs1268115339	553	dbSNP
rs1010950752	561	dbSNP
rs893943355	564	dbSNP
rs1453350528	567	dbSNP
rs1031144305	569	dbSNP
rs1423099987	577	dbSNP
rs1478278468	584	dbSNP
rs1173256391	585	dbSNP
rs191974180	595	dbSNP
rs1457816988	604	dbSNP
rs1294684361	606	dbSNP
rs772022119	608	dbSNP
rs552535044	609	dbSNP
rs1297050393	610	dbSNP
rs1052475188	613	dbSNP
rs1220156010	615	dbSNP
rs1291175460	617	dbSNP
rs532530758	619	dbSNP
rs1320942069	622	dbSNP
rs1245272445	638	dbSNP
rs1267099161	644	dbSNP
rs1348460653	648	dbSNP
rs1214470007	655	dbSNP
rs1262642723	661	dbSNP
rs560496919	662	dbSNP
rs1196172837	665	dbSNP
rs933668801	667	dbSNP
rs1254485391	682	dbSNP
rs1423553617	683	dbSNP
rs1165968685	686	dbSNP
rs1370641813	693	dbSNP
rs1418427663	697	dbSNP
rs546746764	704	dbSNP
rs530224381	711	dbSNP
rs782339783	712	dbSNP
rs1039437149	717	dbSNP
rs187218297	720	dbSNP
rs1396325046	724	dbSNP
rs1314629282	725	dbSNP
rs1315042764	728	dbSNP
rs745911300	731	dbSNP
rs1285360883	732	dbSNP
rs1354567102	742	dbSNP
rs544779826	749	dbSNP
rs1254445891	759	dbSNP
rs531041582	763	dbSNP
rs1182750358	777	dbSNP
rs982593007	781	dbSNP
rs1438345671	783	dbSNP
rs1178617149	786	dbSNP
rs1381495650	792	dbSNP
rs1420940860	807	dbSNP
rs1173348099	818	dbSNP
rs1358156788	827	dbSNP
rs1466283199	834	dbSNP
rs929825454	838	dbSNP
rs1304364440	839	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.