>COL4A1|NM_001845|3'UTR
   1 TGAAGCCTGACTCAGCTAATGTCACAACATGGTGCTACTTCTTCTTCTTTTTGTTAACAGCAACGAACCCTAGAAATATA
  81 TCCTGTGTACCTCACTGTCCAATATGAAAACCGTAAAGTGCCTTATAGGAATTTGCGTAACTAACACACCCTGCTTCATT
 161 GACCTCTACTTGCTGAAGGAGAAAAAGACAGCGATAAGCTTTCAATAGTGGCATACCAAATGGCACTTTTGATGAAATAA
 241 AATATCAATATTTTCTGCAATCCAATGCACTGATGTGTGAAGTGAGAACTCCATCAGAAAACCAAAGGGTGCTAGGAGGT
 321 GTGGGTGCCTTCCATACTGTTTGCCCATTTTCATTCTTGTATTATAATTAATTTTCTACCCCCAGAGATAAATGTTTGTT
 401 TATATCACTGTCTAGCTGTTTCAAAATTTAGGTCCCTTGGTCTGTACAAATAATAGCAATGTAAAAATGGTTTTTTGAAC
 481 CTCCAAATGGAATTACAGACTCAGTAGCCATATCTTCCAACCCCCCAGTATAAATTTCTGTCTTTCTGCTATGTGTGGTA
 561 CTTTGCAGCTGCTTTTGCAGAAATCACAATTTTCCTGTGGAATAAAGATGGTCCAAAAATAGTCAAAAATTAAATATATA
 641 TATATATTAGTAATTTATATAGATGTCAGCAATTAGGCAGATCAAGGTTTAGTTTAACTTCCACTGTTAAAATAAAGCTT
 721 ACATAGTTTTCTTCCTTTGAAAGACTGTGCTGTCCTTTAACATAGGTTTTTAAAGACTAGGATATTGAATGTGAAACATC
 801 CGTTTTCATTGTTCACTTCTAAACCAAAAATTATGTGTTGCCAAAACCAAACCCAGGTTCATGAATATGGTGTCTATTAT
 881 AGTGAAACATGTACTTTGAGCTTATTGTTTTTATTCTGTATTAAATATTTTCAGGGTTTTAAACACTAATCACAAACTGA
 961 ATGACTTGACTTCAAAAGCAACAACCTTAAAGGCCGTCATTTCATTAGTATTCCTCATTCTGCATCCTGGCTTGAAAAAC
1041 AGCTCTGTTGAATCACAGTATCAGTATTTTCACACGTAAGCACATTCGGGCCATTTCCGTGGTTTCTCATGAGCTGTGTT
1121 CACAGACCTCAGCAGGGCATCGCATGGACCGCAGGAGGGCAGATTCGGACCACTAGGCCTGAAATGACATTTCACTAAAA
1201 GTCTCCAAAACATTTCTAAGACTACTAAGGCCTTTTATGTAATTTCTTTAAATGTGTATTTCTTAAGAATTCAAATTTGT
1281 AATAAAACTATTTGTATAAAAATTAAGCTTTTATTAATTTGTTGCTAGTATTGCCACAGACGCATTAAAAGAAACTTACT
1361 GCACAAGCTGCTAATAAATTTGTAAGCTTTGCATACCTTAGATTA

ID	Duplex structure	Position	Score	MFE
1	miRNA 3' gacacccUCGGUGUCCCACGAc 5' | ||| |||||||| Target 5' atcagaaAACCAAAGGGTGCTa 3'	293 - 314	159.00	-17.60
2	miRNA 3' gacACCCUCGGUGUCCCACGAc 5' || | | ||| |||||| Target 5' taaTGTCA-CAACATGGTGCTa 3'	17 - 37	126.00	-13.40
3	miRNA 3' gacacccUCGGUGUCCCACGAc 5' | :: |||||| :| Target 5' attaaatATTTTCAGGGTTTTa 3'	920 - 941	103.00	-7.80

Mutant ID	Mutant Position	Mutant Source
311018	6	ClinVar
689433	31	ClinVar
689434	32	ClinVar
689435	32	ClinVar
689432	35	ClinVar
311017	137	ClinVar
311016	176	ClinVar
311015	265	ClinVar
883801	433	ClinVar
311014	477	ClinVar
311013	510	ClinVar
883019	530	ClinVar
311012	531	ClinVar
311011	587	ClinVar
311010	609	ClinVar
311009	648	ClinVar
311008	766	ClinVar
881850	838	ClinVar
311007	888	ClinVar
881849	952	ClinVar
311006	975	ClinVar
881414	995	ClinVar
311005	1014	ClinVar
311004	1039	ClinVar
311003	1099	ClinVar
COSN30478202	7	COSMIC
COSN32059364	13	COSMIC
COSN31597111	37	COSMIC
COSN9742694	37	COSMIC
COSN30447441	41	COSMIC
COSN1155497	68	COSMIC
COSN26647153	68	COSMIC
COSN30124039	78	COSMIC
COSN30558311	83	COSMIC
COSN30610201	85	COSMIC
COSN30138138	91	COSMIC
COSN30140885	112	COSMIC
COSN20054554	113	COSMIC
COSN26369913	136	COSMIC
COSN26466224	192	COSMIC
COSN26637704	224	COSMIC
COSN31565945	428	COSMIC
COSN31544157	453	COSMIC
COSN25070980	470	COSMIC
COSN7393099	532	COSMIC
COSN31489769	631	COSMIC
COSN31489762	633	COSMIC
COSN19298923	652	COSMIC
COSN31487444	680	COSMIC
COSN8774475	724	COSMIC
COSN31608766	874	COSMIC
COSN9742693	893	COSMIC
COSN7393098	895	COSMIC
COSN20062356	993	COSMIC
COSN31566401	997	COSMIC
COSN8126113	1075	COSMIC
COSN31556116	1077	COSMIC
COSN31552169	1087	COSMIC
COSN19709830	1142	COSMIC
COSN30687588	1150	COSMIC
COSN30541781	1166	COSMIC
COSN17182092	1185	COSMIC
COSN26574938	1196	COSMIC
COSN7393097	1232	COSMIC
COSN31515233	1246	COSMIC
COSN31526850	1333	COSMIC
COSN30161829	1341	COSMIC
COSN31524385	1342	COSMIC
COSN31544877	1395	COSMIC
rs13260	587	GWAS
rs143486029	838	GWAS

Mutant ID	Mutant Position	Mutant Source
rs1439503961	1	dbSNP
rs762512053	6	dbSNP
rs987088251	9	dbSNP
rs749916077	16	dbSNP
rs764627917	19	dbSNP
rs1393714011	20	dbSNP
rs761118951	22	dbSNP
rs776017720	27	dbSNP
rs772336809	40	dbSNP
rs1161710304	41	dbSNP
rs1175572126	42	dbSNP
rs551436530	50	dbSNP
rs759877577	50	dbSNP
rs1420474423	52	dbSNP
rs1298583418	58	dbSNP
rs1346814230	60	dbSNP
rs562272486	64	dbSNP
rs1342177406	65	dbSNP
rs1379763146	66	dbSNP
rs899975533	79	dbSNP
rs1039775459	87	dbSNP
rs548862332	91	dbSNP
rs1247573605	96	dbSNP
rs1278550283	101	dbSNP
rs921448063	103	dbSNP
rs184801410	112	dbSNP
rs1285899844	121	dbSNP
rs1445690133	127	dbSNP
rs888509133	130	dbSNP
rs886049956	137	dbSNP
rs1304507686	139	dbSNP
rs1484499025	141	dbSNP
rs1467697666	143	dbSNP
rs1181837222	147	dbSNP
rs1384610791	148	dbSNP
rs767579092	150	dbSNP
rs1440389099	154	dbSNP
rs1160736554	157	dbSNP
rs929966407	170	dbSNP
rs1033126202	173	dbSNP
rs560166628	175	dbSNP
rs11545877	176	dbSNP
rs1476938845	177	dbSNP
rs992043935	180	dbSNP
rs1334605453	181	dbSNP
rs1024604449	189	dbSNP
rs577604834	192	dbSNP
rs939182559	193	dbSNP
rs1348055506	203	dbSNP
rs926420988	207	dbSNP
rs980583307	210	dbSNP
rs1014181226	213	dbSNP
rs1326282347	217	dbSNP
rs967852447	223	dbSNP
rs1194759335	224	dbSNP
rs752062690	231	dbSNP
rs140945148	236	dbSNP
rs1180553929	245	dbSNP
rs544296306	246	dbSNP
rs575054149	248	dbSNP
rs1254763029	252	dbSNP
rs55935428	255	dbSNP
rs555157539	265	dbSNP
rs1346208318	279	dbSNP
rs1483315122	282	dbSNP
rs1250227626	286	dbSNP
rs1196393751	293	dbSNP
rs1157788289	301	dbSNP
rs1319487664	303	dbSNP
rs1470826122	312	dbSNP
rs1174249948	318	dbSNP
rs1258469792	319	dbSNP
rs1446931062	323	dbSNP
rs1029876658	327	dbSNP
rs998364027	332	dbSNP
rs964196873	343	dbSNP
rs898904947	345	dbSNP
rs1275068665	348	dbSNP
rs1347841469	370	dbSNP
rs1018419945	371	dbSNP
rs1036082893	377	dbSNP
rs1263104272	382	dbSNP
rs1006118676	397	dbSNP
rs1338469205	402	dbSNP
rs888570995	409	dbSNP
rs1437311634	411	dbSNP
rs192991532	432	dbSNP
rs1051748243	433	dbSNP
rs1271293444	445	dbSNP
rs1380017346	453	dbSNP
rs1481318932	461	dbSNP
rs886049955	477	dbSNP
rs921552159	480	dbSNP
rs1466028166	483	dbSNP
rs572779381	486	dbSNP
rs116538870	491	dbSNP
rs1450512110	492	dbSNP
rs1461296622	499	dbSNP
rs1056414883	504	dbSNP
rs886049954	510	dbSNP
rs1403522078	511	dbSNP
rs112581425	513	dbSNP
rs926004804	514	dbSNP
rs977537146	521	dbSNP
rs1367057466	524	dbSNP
rs1190261827	525	dbSNP
rs939274227	526	dbSNP
rs34197107	527	dbSNP
rs926515437	529	dbSNP
rs967749737	530	dbSNP
rs886049953	531	dbSNP
rs1294265561	532	dbSNP
rs1044939792	533	dbSNP
rs1219998415	535	dbSNP
rs946540076	573	dbSNP
rs914999289	584	dbSNP
rs13260	587	dbSNP
rs1176162077	588	dbSNP
rs879229722	590	dbSNP
rs12876590	593	dbSNP
rs1474816703	599	dbSNP
rs11545876	604	dbSNP
rs189966143	609	dbSNP
rs1367073564	610	dbSNP
rs548562512	622	dbSNP
rs1422300773	637	dbSNP
rs1302928640	640	dbSNP
rs958630346	646	dbSNP
rs1034258617	648	dbSNP
rs886049952	648	dbSNP
rs550752680	649	dbSNP
rs1245645341	662	dbSNP
rs1212654272	665	dbSNP
rs922247243	668	dbSNP
rs1357566444	671	dbSNP
rs185390916	680	dbSNP
rs1014587332	701	dbSNP
rs568638168	702	dbSNP
rs1286989162	704	dbSNP
rs1004641903	705	dbSNP
rs1206639310	708	dbSNP
rs1266943152	717	dbSNP
rs1245453025	723	dbSNP
rs530176460	732	dbSNP
rs1183682707	747	dbSNP
rs548825515	754	dbSNP
rs1442227199	755	dbSNP
rs1306990842	756	dbSNP
rs755352953	759	dbSNP
rs747373232	764	dbSNP
rs371130027	766	dbSNP
rs780463565	772	dbSNP
rs1051433399	776	dbSNP
rs758930260	779	dbSNP
rs1018470725	782	dbSNP
rs1339269000	784	dbSNP
rs1380745409	792	dbSNP
rs1451973622	797	dbSNP
rs146744560	802	dbSNP
rs996276836	808	dbSNP
rs1240943034	812	dbSNP
rs1258675491	829	dbSNP
rs952960450	834	dbSNP
rs1388461450	835	dbSNP
rs143486029	838	dbSNP
rs1244871113	843	dbSNP
rs1459621000	852	dbSNP
rs1182403216	864	dbSNP
rs1458870429	867	dbSNP
rs552877576	869	dbSNP
rs1250826679	876	dbSNP
rs994637483	886	dbSNP
rs886049951	888	dbSNP
rs1157381691	889	dbSNP
rs1380294255	897	dbSNP
rs1363655335	901	dbSNP
rs537564307	906	dbSNP
rs1470497579	907	dbSNP
rs1157368793	917	dbSNP
rs1039998862	931	dbSNP
rs895886534	945	dbSNP
rs1404497962	948	dbSNP
rs936116388	955	dbSNP
rs750546844	965	dbSNP
rs1375813412	967	dbSNP
rs28362515	975	dbSNP
rs1192647457	985	dbSNP
rs1335000496	989	dbSNP
rs769502575	995	dbSNP
rs1264965111	996	dbSNP
rs1045346667	1003	dbSNP
rs1202502720	1004	dbSNP
rs1251318462	1007	dbSNP
rs564150639	1010	dbSNP
rs139916479	1014	dbSNP
rs146497932	1017	dbSNP
rs1485416009	1024	dbSNP
rs1249350814	1031	dbSNP
rs759122507	1034	dbSNP
rs776016334	1039	dbSNP
rs1242192012	1050	dbSNP
rs1469685166	1052	dbSNP
rs1355988040	1054	dbSNP
rs1356419873	1058	dbSNP
rs1460517500	1069	dbSNP
rs11545879	1071	dbSNP
rs1297860053	1072	dbSNP
rs1366385263	1073	dbSNP
rs561468041	1075	dbSNP
rs927189766	1076	dbSNP
rs1232826581	1084	dbSNP
rs1343572837	1087	dbSNP
rs973295428	1088	dbSNP
rs1296196088	1093	dbSNP
rs976419885	1098	dbSNP
rs193065628	1099	dbSNP
rs1325768090	1102	dbSNP
rs142553288	1106	dbSNP
rs963146049	1108	dbSNP
rs552943976	1112	dbSNP
rs1014701451	1118	dbSNP
rs1187675833	1127	dbSNP
rs1480311427	1127	dbSNP
rs1422013396	1129	dbSNP
rs757412494	1131	dbSNP
rs7273	1132	dbSNP
rs1422233104	1138	dbSNP
rs1005161543	1141	dbSNP
rs952929520	1142	dbSNP
rs1171420971	1145	dbSNP
rs1169767699	1148	dbSNP
rs1476755766	1150	dbSNP
rs1026258027	1151	dbSNP
rs972913085	1154	dbSNP
rs1435473435	1164	dbSNP
rs1446256618	1166	dbSNP
rs1260717852	1167	dbSNP
rs372541562	1171	dbSNP
rs1035774859	1174	dbSNP
rs546124548	1187	dbSNP
rs1001538860	1198	dbSNP
rs905829018	1206	dbSNP
rs1296150360	1230	dbSNP
rs571719457	1234	dbSNP
rs746472246	1239	dbSNP
rs995835658	1242	dbSNP
rs1023566122	1244	dbSNP
rs577157939	1254	dbSNP
rs1289121581	1263	dbSNP
rs777816814	1267	dbSNP
rs1490302702	1292	dbSNP
rs1011215110	1338	dbSNP
rs900173832	1341	dbSNP
rs557357803	1342	dbSNP
rs1485146648	1348	dbSNP
rs1039946132	1349	dbSNP
rs1386014704	1360	dbSNP
rs772122903	1362	dbSNP
rs935156170	1369	dbSNP
rs1276880202	1372	dbSNP
rs1384814625	1377	dbSNP
rs537517944	1382	dbSNP
rs551689044	1387	dbSNP
rs568536001	1392	dbSNP
rs946235168	1393	dbSNP
rs942385853	1397	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.