Binding of hnRNP H and U2AF65 to respective G-codes and a poly-uridine tract collaborate in the N50-5'ss selection of the REST N exon in H69 cells

PLoS ONE

Volumn 7, Issue 7, 2012, Pages

  Ortuño Pineda, Carlos ^a   Galindo Rosales, José Manuel ^a   Calderón Salinas, José Victor ^a   Villegas Sepúlveda, Nicolás ^a   Saucedo Cárdenas, Odila ^b,c   de Nova Ocampo, Mónica ^d   Valdés, Jesús ^a  

^a DEPARTAMENTO DE FÍSICA   (Mexico)

^b Medicina UANL   (Mexico)

^c INSTITUTO MEXICANO DEL SEGURO SOCIAL   (Mexico)

^d INSTITUTO POLITÉCNICO NACIONAL   (Mexico)

Author keywords

[No Author keywords available]

Indexed keywords

BETA GLOBIN; HETEROGENEOUS NUCLEAR RIBONUCLEOPROTEIN; HETEROGENEOUS NUCLEAR RIBONUCLEOPROTEIN H; NUCLEAR PROTEIN; PROTEIN U2AF65; RE1 SILENCING TRANSCRIPTION FACTOR; TRANSCRIPTION FACTOR; UNCLASSIFIED DRUG;

ARTICLE; CANCER CELL CULTURE; CONTROLLED STUDY; EXON SPLICING; GEL MOBILITY SHIFT ASSAY; GENE SILENCING; HUMAN; HUMAN CELL; IMMUNOPRECIPITATION; LUNG SMALL CELL CANCER; POLYURIDINE TRACT; PROTEIN CROSS LINKING; PROTEIN DOMAIN; PROTEIN EXPRESSION; PROTEIN RNA BINDING; PROTEIN TARGETING; REVERSE TRANSCRIPTION POLYMERASE CHAIN REACTION; RNA SPLICING; RNA STRUCTURE; TRANSCRIPTION REGULATION; WILD TYPE;

ALTERNATIVE SPLICING; BASE SEQUENCE; CELL LINE; EXONS; GENE EXPRESSION; GENE KNOCKDOWN TECHNIQUES; HETEROGENEOUS-NUCLEAR RIBONUCLEOPROTEIN GROUP F-H; HUMANS; MOLECULAR SEQUENCE DATA; NUCLEAR PROTEINS; POLY U; PROTEIN BINDING; PROTEIN INTERACTION DOMAINS AND MOTIFS; PROTEIN ISOFORMS; REPRESSOR PROTEINS; RIBONUCLEOPROTEIN, U1 SMALL NUCLEAR; RIBONUCLEOPROTEINS; RNA PRECURSORS; RNA SPLICE SITES; RNA, SMALL INTERFERING;

EID: 84863633016     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0040315     Document Type: Article

References (37)

1. Venables JP, (2004) Aberrant and alternative splicing in cancer. Cancer Res 64: 7647-7654.
2. Kirschbaum-Slager N, Lopes GM, Galante PA, Riggins GJ, de Souza SJ, (2004) Splicing factors are differentially expressed in tumors. Genet Mol Res 3: 512-520.
3. Coulson JM, Fiskerstrand CE, Woll PJ, Quinn JP, (1999) Arginine vasopressin promoter regulation is mediated by a neuron-restrictive silencer element in small cell lung cancer. Cancer Res 59: 5123-5127.
4. Coulson JM, Edgson JL, Woll PJ, Quinn JP, (2000) A splice variant of the neuron-restrictive silencer factor repressor is expressed in small cell lung cancer: a potential role in derepression of neuroendocrine genes and a useful clinical marker. Cancer Res 60: 1840-1844.
5. Palm K, Metsis M, Timmusk T, (1999) Neuron-specific splicing of zinc finger transcription factor REST/NRSF/XBR is frequent in neuroblastomas and conserved in human, mouse and rat. Brain Res Mol Brain Res 72: 30-39.
6. Palm K, Belluardo N, Metsis M, Timmusk T, (1998) Neuronal expression of zinc finger transcription factor REST/NRSF/XBR gene. J Neurosci 18: 1280-1296.
7. Singh R, Banerjee H, Green MR, (2000) Differential recognition of the polypyrimidine-tract by the general splicing factor U2AF65 and the splicing repressor sex-lethal. RNA 6: 901-911.
8. Sickmier EA, Frato KE, Shen H, Paranawithana SR, Green MR, et al. (2006) Structural basis for polypyrimidine tract recognition by the essential pre-mRNA splicing factor U2AF65. Mol Cell 23: 49-59.
9. Aznarez I, Barash Y, Shai O, He D, Zielenski J, et al. (2008) A systematic analysis of intronic sequences downstream of 5′ splice sites reveals a widespread role for U-rich motifs and TIA1/TIAL1 proteins in alternative splicing regulation. Genome Res 18: 1247-1258.
10. Le Guiner C, Lejeune F, Galiana D, Kister L, Breathnach R, et al. (2001) TIA-1 and TIAR activate splicing of alternative exons with weak 5′ splice sites followed by a U-rich stretch on their own pre-mRNAs. J Biol Chem 276: 40638-40646.
11. Forch P, Merendino L, Martinez C, Valcarcel J, (2003) U2 small nuclear ribonucleoprotein particle (snRNP) auxiliary factor of 65 kDa, U2AF65, can promote U1 snRNP recruitment to 5′ splice sites. Biochem J 372: 235-240.
12. Calarco JA, Superina S, O'Hanlon D, Gabut M, Raj B, et al. (2009) Regulation of vertebrate nervous system alternative splicing and development by an SR-related protein. Cell 138: 898-910.
13. Grabowski PJ, (2004) A molecular code for splicing silencing: configurations of guanosine-rich motifs. Biochem Soc Trans 32: 924-927.
14. Han K, Yeo G, An P, Burge CB, Grabowski PJ, (2005) A combinatorial code for splicing silencing: UAGG and GGGG motifs. PLoS Biol 3: e158.
15. Chou MY, Rooke N, Turck CW, Black DL, (1999) hnRNP H is a component of a splicing enhancer complex that activates a c-src alternative exon in neuronal cells. Mol Cell Biol 19: 69-77.
16. Wang E, Cambi F, (2009) Heterogeneous nuclear ribonucleoproteins H and F regulate the proteolipid protein/DM20 ratio by recruiting U1 small nuclear ribonucleoprotein through a complex array of G runs. J Biol Chem 284: 11194-11204.
17. Talukdar I, Sen S, Urbano R, Thompson J, Yates JR 3rd, et al (2011) hnRNP A1 and hnRNP F modulate the alternative splicing of exon 11 of the insulin receptor gene. PLoS One 6: e27869.
18. Zhu H, Hinman MN, Hasman RA, Mehta P, Lou H, (2008) Regulation of neuron-specific alternative splicing of neurofibromatosis type 1 pre-mRNA. Mol Cell Biol 28: 1240-1251.
19. Raj B, O'Hanlon D, Vessey JP, Pan Q, Ray D, et al. (2011) Cross-regulation between an alternative splicing activator and a transcription repressor controls neurogenesis. Mol Cell 43: 843-850.
20. Boehr DD, (2012) Promiscuity in protein-RNA interactions: Conformational ensembles facilitate molecular recognition in the spliceosome: Conformational diversity in U2AF(65) facilitates binding to diverse RNA sequences. Bioessays.
21. Magin A, Lietz M, Cibelli G, Thiel G, (2002) RE-1 silencing transcription factor-4 (REST4) is neither a transcriptional repressor nor a de-repressor. Neurochem Int 40: 195-202.
22. Lawinger P, Venugopal R, Guo ZS, Immaneni A, Sengupta D, et al. (2000) The neuronal repressor REST/NRSF is an essential regulator in medulloblastoma cells. Nat Med 6: 826-831.
23. Immaneni A, Lawinger P, Zhao Z, Lu W, Rastelli L, et al. (2000) REST-VP16 activates multiple neuronal differentiation genes in human NT2 cells. Nucleic Acids Res 28: 3403-3410.
24. Kuwabara T, Hsieh J, Nakashima K, Taira K, Gage FH, (2004) A small modulatory dsRNA specifies the fate of adult neural stem cells. Cell 116: 779-793.
25. Sun YM, Greenway DJ, Johnson R, Street M, Belyaev ND, et al. (2005) Distinct profiles of REST interactions with its target genes at different stages of neuronal development. Mol Biol Cell 16: 5630-5638.
26. Bruce AW, Donaldson IJ, Wood IC, Yerbury SA, Sadowski MI, et al. (2004) Genome-wide analysis of repressor element 1 silencing transcription factor/neuron-restrictive silencing factor (REST/NRSF) target genes. Proc Natl Acad Sci U S A 101: 10458-10463.
27. Chong JA, Tapia-Ramirez J, Kim S, Toledo-Aral JJ, Zheng Y, et al. (1995) REST: a mammalian silencer protein that restricts sodium channel gene expression to neurons. Cell 80: 949-957.
28. Ballas N, Grunseich C, Lu DD, Speh JC, Mandel G, (2005) REST and its corepressors mediate plasticity of neuronal gene chromatin throughout neurogenesis. Cell 121: 645-657.
29. Neumann SB, Seitz R, Gorzella A, Heister A, Doeberitz MK, et al. (2004) Relaxation of glycine receptor and onconeural gene transcription control in NRSF deficient small cell lung cancer cell lines. Brain Res Mol Brain Res 120: 173-181.
30. Eperon IC, Makarova OV, Mayeda A, Munroe SH, Caceres JF, et al. (2000) Selection of alternative 5′ splice sites: role of U1 snRNP and models for the antagonistic effects of SF2/ASF and hnRNP A1. Mol Cell Biol 20: 8303-8318.
31. Izquierdo JM, Majos N, Bonnal S, Martinez C, Castelo R, et al. (2005) Regulation of Fas alternative splicing by antagonistic effects of TIA-1 and PTB on exon definition. Mol Cell 19: 475-484.
32. Hoffman BE, Grabowski PJ, (1992) U1 snRNP targets an essential splicing factor, U2AF65, to the 3′ splice site by a network of interactions spanning the exon. Genes Dev 6: 2554-2568.
33. Expert-Bezancon A, Sureau A, Durosay P, Salesse R, Groeneveld H, et al. (2004) hnRNP A1 and the SR proteins ASF/SF2 and SC35 have antagonistic functions in splicing of beta-tropomyosin exon 6B. J Biol Chem 279: 38249-38259.
34. Tavanez JP, Madl T, Kooshapur H, Sattler M, Valcarcel J, (2012) hnRNP A1 Proofreads 3′ Splice Site Recognition by U2AF. Mol Cell 45: 314-329.
35. Dignam JD, (1990) Preparation of extracts from higher eukaryotes. Methods Enzymol 182: 194-203.
36. Del Gatto-Konczak F, Bourgeois CF, Le Guiner C, Kister L, Gesnel MC, et al. (2000) The RNA-binding protein TIA-1 is a novel mammalian splicing regulator acting through intron sequences adjacent to a 5′ splice site. Mol Cell Biol 20: 6287-6299.
37. Scheer JM, Ryan CA, (2001) A method for the quantitative recovery of proteins from polyacrylamide gels. Anal Biochem 298: 130-132.