>MSH6|NM_000179|3'UTR
   1 ACTGACTACATTGGAAGCTTTGAGTTGACTTCTGACAAAGGTGGTAAATTCAGACAACATTATGATCTAATAAACTTTAT
  81 TTTTTAAAAATGAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
 161 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA

ID	Duplex structure	Position	Score	MFE
1	miRNA 3' gacUCUGUCAGGGUACUAGAc 5' ||||| ::||||||| Target 5' ttcAGACAACATTATGATCTa 3'	49 - 69	158.00	-13.60
2	miRNA 3' gacucugucaggguACU--AGAc 5' ||| ||| Target 5' tggaagctttgagtTGACTTCTg 3'	12 - 34	80.00	-5.70

Mutant ID	Mutant Position	Mutant Source
422862	1	ClinVar
525598	1	ClinVar
141250	2	ClinVar
628581	3	ClinVar
920052	3	ClinVar
186897	4	ClinVar
420211	4	ClinVar
918402	6	ClinVar
1172169	7	ClinVar
630635	9	ClinVar
378174	10	ClinVar
378969	11	ClinVar
629850	11	ClinVar
630443	11	ClinVar
627653	12	ClinVar
630458	14	ClinVar
234374	18	ClinVar
89151	20	ClinVar
921124	20	ClinVar
897353	35	ClinVar
495703	49	ClinVar
89155	86	ClinVar
COSM4778906	1	COSMIC
COSN30124044	39	COSMIC
COSN30155212	52	COSMIC
COSN30181248	57	COSMIC
COSN30648911	86	COSMIC
COSN30101286	93	COSMIC

Mutant ID	Mutant Position	Mutant Source
rs1064796051	1	dbSNP
rs587781604	2	dbSNP
rs752809310	3	dbSNP
rs766605075	3	dbSNP
rs1064794352	4	dbSNP
rs1451012329	4	dbSNP
rs786203308	4	dbSNP
rs1472954352	5	dbSNP
rs1162814122	6	dbSNP
rs758445380	7	dbSNP
rs371301277	10	dbSNP
rs757778351	11	dbSNP
rs757708396	12	dbSNP
rs1407543591	15	dbSNP
rs374743162	17	dbSNP
rs876661000	18	dbSNP
rs921851843	19	dbSNP
rs1431803657	20	dbSNP
rs587779200	20	dbSNP
rs754683604	20	dbSNP
rs1436363202	22	dbSNP
rs781241504	23	dbSNP
rs200412142	24	dbSNP
rs1354832431	25	dbSNP
rs756712244	27	dbSNP
rs1230548163	28	dbSNP
rs931895599	31	dbSNP
rs568272054	34	dbSNP
rs752652467	34	dbSNP
rs184571812	35	dbSNP
rs1432294473	37	dbSNP
rs755754032	37	dbSNP
rs771683883	37	dbSNP
rs368491299	38	dbSNP
rs777409019	49	dbSNP
rs772973603	50	dbSNP
rs1397050672	51	dbSNP
rs746634080	52	dbSNP
rs1247177755	54	dbSNP
rs1296025817	56	dbSNP
rs551144193	58	dbSNP
rs1216880840	59	dbSNP
rs1394797552	59	dbSNP
rs1298531996	60	dbSNP
rs1391130317	60	dbSNP
rs1337995746	63	dbSNP
rs569367018	63	dbSNP
rs1385671074	65	dbSNP
rs953470502	68	dbSNP
rs1367730855	69	dbSNP
rs1277049941	71	dbSNP
rs1398708138	76	dbSNP
rs587779201	76	dbSNP
rs1299259554	84	dbSNP
rs267608143	85	dbSNP
rs2020906	86	dbSNP
rs911906395	89	dbSNP
rs1284334358	94	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.