ID	Duplex structure	Position	Score	MFE
1	miRNA 3' uguUUCAAGACAUC--ACGUGACu 5' ||| ||| || ||||| | Target 5' tacAAGGGCTGGAGTCTGCACGGg 3'	582 - 605	129.00	-14.30
2	miRNA 3' ugUUUCAAGAC--AUCACGUGACu 5' ||| ||| || ||| ||| Target 5' gaAAA---CTGGCTACTGCTCTGt 3'	428 - 448	123.00	-8.70
3	miRNA 3' ugUUUCAAGACAU----CACGUGACu 5' ::|| || | | |||::||| Target 5' ggGGAGCTCAGGAAGGGGTGTGCTGa 3'	751 - 776	122.00	-10.50

Mutant ID	Mutant Position	Mutant Source
338185	56	ClinVar
338186	71	ClinVar
898982	76	ClinVar
338187	91	ClinVar
898983	102	ClinVar
898984	113	ClinVar
338188	114	ClinVar
338189	184	ClinVar
338190	240	ClinVar
338191	289	ClinVar
894849	313	ClinVar
338192	444	ClinVar
338193	561	ClinVar
338194	578	ClinVar
894850	603	ClinVar
894851	655	ClinVar
338195	748	ClinVar
338196	755	ClinVar
896292	764	ClinVar
896293	766	ClinVar
338197	828	ClinVar
896294	833	ClinVar
896295	896	ClinVar
897912	931	ClinVar
338198	943	ClinVar
338199	1062	ClinVar
338200	1077	ClinVar
897913	1133	ClinVar
338201	1311	ClinVar
338202	1333	ClinVar
338203	1337	ClinVar
338204	1351	ClinVar
338205	1406	ClinVar
COSN30487825	20	COSMIC
COSN1869824	30	COSMIC
COSN26576975	71	COSMIC
COSN30191553	81	COSMIC
COSN31500901	83	COSMIC
COSN30502323	105	COSMIC
COSN30461780	137	COSMIC
COSN21718997	237	COSMIC
COSN28880924	299	COSMIC
COSN27396199	300	COSMIC
COSN9125903	407	COSMIC
COSN1869825	600	COSMIC
COSN15034566	655	COSMIC
COSN31584979	706	COSMIC
COSN31529173	824	COSMIC
COSN20784013	966	COSMIC
COSN31486563	1096	COSMIC
COSN20691743	1100	COSMIC
COSN25616654	1118	COSMIC
COSN25665289	1119	COSMIC
COSN31513864	1224	COSMIC
COSN31515331	1232	COSMIC
COSN31568665	1310	COSMIC
COSN20116394	1319	COSMIC
COSN24489005	1337	COSMIC
COSN31606679	1406	COSMIC

Mutant ID	Mutant Position	Mutant Source
rs375334650	3	dbSNP
rs1288426724	7	dbSNP
rs1359872576	23	dbSNP
rs369433698	24	dbSNP
rs771148897	25	dbSNP
rs373165422	26	dbSNP
rs1347758559	28	dbSNP
rs1232602759	31	dbSNP
rs759685033	33	dbSNP
rs1327237864	37	dbSNP
rs1486480273	41	dbSNP
rs534946362	42	dbSNP
rs376338894	43	dbSNP
rs1241024823	44	dbSNP
rs1484586861	48	dbSNP
rs781276935	51	dbSNP
rs148465200	56	dbSNP
rs1311364860	64	dbSNP
rs1298948650	65	dbSNP
rs886056618	71	dbSNP
rs1367870197	73	dbSNP
rs1319232386	75	dbSNP
rs6119971	76	dbSNP
rs1390290147	85	dbSNP
rs1161975103	87	dbSNP
rs911106592	89	dbSNP
rs886056619	91	dbSNP
rs1016613687	97	dbSNP
rs576264538	102	dbSNP
rs1435071897	104	dbSNP
rs1395909561	110	dbSNP
rs542048406	113	dbSNP
rs563626929	114	dbSNP
rs575732121	116	dbSNP
rs1040865447	128	dbSNP
rs192157352	129	dbSNP
rs1482902057	138	dbSNP
rs1253952734	142	dbSNP
rs922450886	149	dbSNP
rs773948076	154	dbSNP
rs1348394526	155	dbSNP
rs1296413124	161	dbSNP
rs930023997	165	dbSNP
rs1320680621	178	dbSNP
rs184681543	180	dbSNP
rs747690585	181	dbSNP
rs886056620	184	dbSNP
rs1301669706	185	dbSNP
rs1467900396	201	dbSNP
rs528486207	207	dbSNP
rs1376490119	211	dbSNP
rs1012392452	218	dbSNP
rs1005437024	226	dbSNP
rs188514897	232	dbSNP
rs886056621	240	dbSNP
rs904067433	246	dbSNP
rs1193994359	250	dbSNP
rs1001115655	253	dbSNP
rs896816709	272	dbSNP
rs1253981171	279	dbSNP
rs993898376	284	dbSNP
rs1277287354	285	dbSNP
rs112260885	289	dbSNP
rs3215552	289	dbSNP
rs879033036	289	dbSNP
rs886056622	289	dbSNP
rs1024509449	291	dbSNP
rs1181367778	299	dbSNP
rs971588407	300	dbSNP
rs1200116195	301	dbSNP
rs1275975572	302	dbSNP
rs1441341016	303	dbSNP
rs562055636	308	dbSNP
rs752491436	308	dbSNP
rs1231478620	310	dbSNP
rs1239747700	311	dbSNP
rs1474691931	312	dbSNP
rs1002133930	313	dbSNP
rs1307838874	318	dbSNP
rs529402730	319	dbSNP
rs1372655857	321	dbSNP
rs537329540	321	dbSNP
rs1168769752	322	dbSNP
rs985224466	323	dbSNP
rs1366836875	332	dbSNP
rs771746763	333	dbSNP
rs1475512765	345	dbSNP
rs551204821	353	dbSNP
rs957582734	358	dbSNP
rs1483948172	359	dbSNP
rs990421675	364	dbSNP
rs913199669	367	dbSNP
rs1273267689	371	dbSNP
rs1208914742	374	dbSNP
rs967813672	375	dbSNP
rs1266717676	394	dbSNP
rs866382306	395	dbSNP
rs962556851	402	dbSNP
rs1356661536	406	dbSNP
rs1288051097	414	dbSNP
rs1408372779	418	dbSNP
rs1336192813	429	dbSNP
rs1329753074	430	dbSNP
rs1386470829	441	dbSNP
rs976188338	443	dbSNP
rs6058896	444	dbSNP
rs918536979	448	dbSNP
rs1411128355	450	dbSNP
rs929945135	454	dbSNP
rs1473430539	459	dbSNP
rs760431194	460	dbSNP
rs1449550045	461	dbSNP
rs992188469	461	dbSNP
rs1049520963	469	dbSNP
rs1340891679	473	dbSNP
rs1220168540	479	dbSNP
rs6088011	499	dbSNP
rs911072169	508	dbSNP
rs1280537697	511	dbSNP
rs1353261250	511	dbSNP
rs1343792327	529	dbSNP
rs941242270	530	dbSNP
rs1280091482	533	dbSNP
rs142670571	543	dbSNP
rs1487624953	549	dbSNP
rs1038259465	556	dbSNP
rs151015070	561	dbSNP
rs1402395268	562	dbSNP
rs541372379	568	dbSNP
rs1171790964	574	dbSNP
rs1476805964	576	dbSNP
rs1378993471	577	dbSNP
rs886056623	578	dbSNP
rs1045467733	581	dbSNP
rs906977406	584	dbSNP
rs1197636734	587	dbSNP
rs1207331584	589	dbSNP
rs1377304480	594	dbSNP
rs1053096580	603	dbSNP
rs1285321190	604	dbSNP
rs1001300333	609	dbSNP
rs1305858720	611	dbSNP
rs1010286765	612	dbSNP
rs1034494977	617	dbSNP
rs893314078	621	dbSNP
rs1029336436	627	dbSNP
rs1011825272	629	dbSNP
rs1432732565	631	dbSNP
rs1345733317	632	dbSNP
rs1333498082	637	dbSNP
rs1020586270	654	dbSNP
rs967384538	655	dbSNP
rs570434284	661	dbSNP
rs1387743262	662	dbSNP
rs559488718	663	dbSNP
rs1187777654	676	dbSNP
rs962502425	677	dbSNP
rs1401642390	678	dbSNP
rs973953860	682	dbSNP
rs1030343599	683	dbSNP
rs1330195428	701	dbSNP
rs534618647	703	dbSNP
rs953563076	709	dbSNP
rs1282936013	712	dbSNP
rs1211812298	721	dbSNP
rs1436727555	725	dbSNP
rs986181247	725	dbSNP
rs1216393391	726	dbSNP
rs1362832662	730	dbSNP
rs911019937	731	dbSNP
rs941232412	732	dbSNP
rs972336742	741	dbSNP
rs553256979	748	dbSNP
rs886056624	755	dbSNP
rs951338752	756	dbSNP
rs574832388	758	dbSNP
rs1313294601	761	dbSNP
rs1276170724	763	dbSNP
rs372489697	764	dbSNP
rs535281176	764	dbSNP
rs1172170021	766	dbSNP
rs1410007076	769	dbSNP
rs992530145	778	dbSNP
rs1181735401	785	dbSNP
rs557153882	792	dbSNP
rs948071020	802	dbSNP
rs1189118380	807	dbSNP
rs777071671	824	dbSNP
rs759991354	827	dbSNP
rs2424932	828	dbSNP
rs753244931	833	dbSNP
rs1226497317	838	dbSNP
rs1336862548	845	dbSNP
rs1293894325	847	dbSNP
rs1055584238	848	dbSNP
rs1408984551	854	dbSNP
rs758453155	861	dbSNP
rs1299500958	873	dbSNP
rs1442510401	893	dbSNP
rs116329759	896	dbSNP
rs1162090874	900	dbSNP
rs1460287719	919	dbSNP
rs577546719	923	dbSNP
rs1052483504	924	dbSNP
rs764293630	931	dbSNP
rs1006536554	933	dbSNP
rs1159278627	937	dbSNP
rs1246135239	939	dbSNP
rs55901282	943	dbSNP
rs1469930705	947	dbSNP
rs903403430	957	dbSNP
rs997795381	959	dbSNP
rs561047184	966	dbSNP
rs1025478551	982	dbSNP
rs1223925719	983	dbSNP
rs115698306	989	dbSNP
rs531564507	997	dbSNP
rs1291491612	1000	dbSNP
rs1442463561	1011	dbSNP
rs1161291472	1013	dbSNP
rs1327141181	1014	dbSNP
rs986171474	1016	dbSNP
rs1016343169	1042	dbSNP
rs1362385042	1046	dbSNP
rs1013497085	1053	dbSNP
rs550022433	1062	dbSNP
rs886056625	1062	dbSNP
rs1424719380	1068	dbSNP
rs757507215	1069	dbSNP
rs540238718	1070	dbSNP
rs1374130888	1071	dbSNP
rs973907652	1071	dbSNP
rs779656204	1077	dbSNP
rs879315947	1083	dbSNP
rs1379817059	1086	dbSNP
rs1262207984	1092	dbSNP
rs929861416	1095	dbSNP
rs1216226408	1096	dbSNP
rs1311462499	1097	dbSNP
rs15475	1104	dbSNP
rs1408947452	1107	dbSNP
rs928257057	1118	dbSNP
rs562043447	1119	dbSNP
rs181314156	1123	dbSNP
rs1296273025	1126	dbSNP
rs1434927264	1128	dbSNP
rs1383455211	1132	dbSNP
rs756101113	1133	dbSNP
rs749116948	1134	dbSNP
rs1171954367	1141	dbSNP
rs1455768418	1142	dbSNP
rs947131338	1148	dbSNP
rs1211944247	1169	dbSNP
rs1042253844	1173	dbSNP
rs933517850	1174	dbSNP
rs1052004594	1176	dbSNP
rs903353686	1182	dbSNP
rs766251644	1193	dbSNP
rs544465929	1195	dbSNP
rs1457450674	1196	dbSNP
rs942343495	1214	dbSNP
rs998141402	1215	dbSNP
rs368437593	1221	dbSNP
rs1273210450	1225	dbSNP
rs1240074989	1227	dbSNP
rs889112595	1229	dbSNP
rs1007539274	1231	dbSNP
rs1016290514	1232	dbSNP
rs1298344933	1240	dbSNP
rs963402827	1245	dbSNP
rs1378845312	1262	dbSNP
rs34168690	1262	dbSNP
rs1311445611	1267	dbSNP
rs993616853	1271	dbSNP
rs1436751690	1284	dbSNP
rs1376273329	1285	dbSNP
rs1168272483	1290	dbSNP
rs1460505861	1291	dbSNP
rs1420863217	1299	dbSNP
rs995264863	1307	dbSNP
rs1185319287	1310	dbSNP
rs1189816281	1311	dbSNP
rs1190885393	1311	dbSNP
rs398088406	1311	dbSNP
rs73904044	1312	dbSNP
rs1250574500	1313	dbSNP
rs1193766072	1320	dbSNP
rs754924547	1333	dbSNP
rs1473013665	1334	dbSNP
rs1251414249	1336	dbSNP
rs532308734	1337	dbSNP
rs951256129	1341	dbSNP
rs1334779905	1345	dbSNP
rs981760099	1347	dbSNP
rs928558406	1350	dbSNP
rs1351360741	1351	dbSNP
rs1356552644	1351	dbSNP
rs563126581	1351	dbSNP
rs1328414807	1352	dbSNP
rs991123501	1354	dbSNP
rs1389914400	1357	dbSNP
rs1398682376	1358	dbSNP
rs1168572743	1367	dbSNP
rs1457295557	1370	dbSNP
rs1415564962	1373	dbSNP
rs1464752853	1376	dbSNP
rs374112122	1376	dbSNP
rs1002171741	1383	dbSNP
rs1032344505	1385	dbSNP
rs755161320	1386	dbSNP
rs547367297	1406	dbSNP
rs761348229	1407	dbSNP
rs914001435	1415	dbSNP
rs1041474891	1416	dbSNP
rs1208708583	1419	dbSNP
rs1466800255	1424	dbSNP
rs1394870953	1428	dbSNP
rs954878531	1429	dbSNP
rs1235733375	1441	dbSNP
rs1312652054	1444	dbSNP
rs370255086	1445	dbSNP
rs1279372443	1454	dbSNP

- RNA (New York, N.Y.), 2008

MicroRNAs (miRNAs) are small noncoding RNA molecules of 20-24 nucleotides that regulate gene expression. In animals, miRNAs form imperfect interactions with sequences in the 3' Untranslated region (3'UTR) of mRNAs, causing translational inhibition and mRNA decay. In contrast, plant miRNAs mostly associate with protein coding regions. Here we show that human miR-148 represses DNA methyltransferase 3b (Dnmt3b) gene expression through a region in its coding sequence. This region is evolutionary conserved and present in the Dnmt3b splice variants Dnmt3b1, Dnmt3b2, and Dnmt3b4, but not in the abundantly expressed Dnmt3b3. Whereas overexpression of miR-148 results in decreased DNMT3b1 expression, short-hairpin RNA-mediated miR-148 repression leads to an increase in DNMT3b1 expression. Interestingly, mutating the putative miR-148 target site in Dnmt3b1 abolishes regulation by miR-148. Moreover, endogenous Dnmt3b3 mRNA, which lacks the putative miR-148 target site, is resistant to miR-148-mediated regulation. Thus, our results demonstrate that the coding sequence of Dnmt3b mediates regulation by the miR-148 family. More generally, we provide evidence that coding regions of human genes can be targeted by miRNAs, and that such a mechanism might play a role in determining the relative abundance of different splice variants.

- Stem cells and development, 2010

MicroRNAs (miRNAs), important regulators of cellular processes, show specific expression signatures in different blood cell lineages and stages of hematopoietic stem cell (HSC) differentiation, indicating their role in the control of hematopoiesis. Because neonatal blood displays various features of immaturity, we might expect differential miRNA regulation. Herein, we determined miRNA expression profiles of umbilical cord blood (UCB) cell lineages and compared them to those of bone marrow (BM) and peripheral blood (PB) cell counterparts. Further, we determined mRNA expression profiles using whole-genome microarrays. An approach combining bioinformatic prediction of miRNA targets with mRNA expression profiling was used to search for putative targets of miRNAs with potential functions in UCB. We pointed out several differentially expressed miRNAs and associated their expression with the target transcript levels. miR-148a expression was suppressed in HSCs and its level inversely correlated with the previously verified target, DNA methyltransferase 3B, suggesting dependence of de novo DNA methylation in HSCs on miR-148a. Prolonged cell survival of UCB HSCs may be associated with low expression of miR-143 and miR-145 and up-regulation of their downstream targets (high expression of c-MYC and miR-17-92 and following repression of TGFBR2). In HSCs, we monitored significant up-regulation of eight miRNAs, which were previously verified as regulators of HOX genes. Further, miR-146b may be associated with immaturity of neonatal immune system because it is strongly up-regulated in UCB granulocytes and T lymphocytes compared to PB cell counterparts. Comparative analysis revealed 13 miRNAs significantly altered between UCB and BM CD34(+) cells. In UCB CD34(+) cells, we monitored up-regulation of miR-520h, promoting differentiation of HSCs into progenitor cells, and reduction of miR-214, whose expression might support HSC survival. In conclusion, UCB cells show specific miRNA expression patterns, indicating different regulation in these cells.