RNA-binding protein Rbm47 binds to Nanog in mouse embryonic stem cells

Molecular Biology Reports

Volumn 40, Issue 7, 2013, Pages 4391-4396

  Yeganeh, Meghdad ^a   Seyedjafari, Ehsan ^a   Kamrani, Farnaz Akbari ^b   Ghaemi, Nasser ^a  

^a UNIVERSITY OF TEHRAN   (Iran)

^b TEHRAN UNIVERSITY OF MEDICAL SCIENCES   (Iran)

Author keywords

Embryonic stem cell; Rbm47; RIP; RNA binding protein

Indexed keywords

EPITOPE; OCTAMER TRANSCRIPTION FACTOR 4; PROTEIN RBM47; RNA BINDING PROTEIN; SMALL NUCLEAR RIBONUCLEOPROTEIN; SMALL NUCLEAR RIBONUCLEOPROTEIN 70; TRANSCRIPTION FACTOR NANOG; TRANSCRIPTION FACTOR SOX2; UNCLASSIFIED DRUG; HOMEODOMAIN PROTEIN; NANOG PROTEIN, MOUSE; PROTEIN BINDING; RBM47 PROTEIN, MOUSE; TRANSCRIPTION FACTOR SOX;

ANIMAL CELL; ARTICLE; CONTROLLED STUDY; EMBRYONIC STEM CELL; GENE; GENE OVEREXPRESSION; IMMUNOPRECIPITATION; MOUSE; NANOG GENE; NONHUMAN; OCT4 GENE; PROTEIN PROTEIN INTERACTION; PROTEIN TARGETING; RBM47 GENE; REVERSE TRANSCRIPTION POLYMERASE CHAIN REACTION; SOX2 GENE; WESTERN BLOTTING; ANIMAL; GENE EXPRESSION; GENE EXPRESSION REGULATION; GENE ORDER; GENE VECTOR; GENETICS; METABOLISM;

ANIMALS; EMBRYONIC STEM CELLS; GENE EXPRESSION; GENE EXPRESSION REGULATION; GENE ORDER; GENETIC VECTORS; HOMEODOMAIN PROTEINS; MICE; OCTAMER TRANSCRIPTION FACTOR-3; PROTEIN BINDING; RNA-BINDING PROTEINS; SOXB1 TRANSCRIPTION FACTORS;

EID: 84879411409     PISSN: 03014851     EISSN: 15734978     Source Type: Journal    
DOI: 10.1007/s11033-013-2528-0     Document Type: Article

References (53)

1. Kolios G, Moodley Y (2013) Introduction to stem cells and regenerative medicine. Respiration 85:3-10
2. Ilic D, Polak JM (2011) Stem cells in regenerative medicine: introduction. Br Med Bull 98:117-126
3. Barker RA (2012) Stem cells and neurodegenerative diseases: Where is it all going? Regen Med 7:26-31
4. Yokote S, Yokoo T (2012) Stem cells in kidney regeneration. Curr Med Chem 19:6009-6017
5. Abdelwahid E, Siminiak T, Guarita-Souza LC, Teixeira de Carvalho KA, Gallo P et al (2011) Stem cell therapy in heart diseases: a review of selected new perspectives, practical considerations and clinical applications. Curr Cardiol Rev 7:201-212
6. Yeo JC, Ng HH (2012) The transcriptional regulation of pluripotency. Cell Res 23:20-32
7. Heinrich EM, Dimmeler S (2012) MicroRNAs and stem cells: control of pluripotency, reprogramming, and lineage commitment. Circ Res 110:1014-1022
8. Huo JS, Zambidis ET (2012) Pivots of pluripotency: the roles of non-coding RNA in regulating embryonic and induced pluripotent stem cells. Biochim Biophys Acta 1830:2385-2394
9. Chen X, Vega VB, Ng HH (2008) Transcriptional regulatory networks in embryonic stem cells. Cold Spring Harb Symp Quant Biol 73:203-209
10. Orkin SH, Wang J, Kim J, Chu J, Rao S et al (2008) The transcriptional network controlling pluripotency in ES cells. Cold Spring Harb Symp Quant Biol 73:195-202
11. Orphanides G, Reinberg D (2002) A unified theory of gene expression. Cell 108:439-451
12. Sanchez-Diaz P, Penalva LO (2006) Post-transcription meets post-genomic: the saga of RNA binding proteins in a new era. RNA Biol 3:101-109
13. Tenenbaum SA, Christiansen J, Nielsen H (2011) The post-transcriptional operon. Methods Mol Biol 703:237-245
14. Hogan DJ, Riordan DP, Gerber AP, Herschlag D, Brown PO (2008) Diverse RNA-binding proteins interact with functionally related sets of RNAs, suggesting an extensive regulatory system. PLoS Biol 6:e255
15. Janga SC, Mittal N (2011) Construction, structure and dynamics of post-transcriptional regulatory network directed by RNA-binding proteins. Adv Exp Med Biol 722:103-117
16. Tenenbaum SA, Lager PJ, Carson CC, Keene JD (2002) Ribonomics: identifying mRNA subsets in mRNP complexes using antibodies to RNA-binding proteins and genomic arrays. Methods 26:191-198
17. Penalva LO, Tenenbaum SA, Keene JD (2004) Gene expression analysis of messenger RNP complexes. Methods Mol Biol 257:125-134
18. Milek M, Wyler E, Landthaler M (2012) Transcriptome-wide analysis of protein-RNA interactions using high-throughput sequencing. Semin Cell Dev Biol 23:206-212
19. Zhao J, Ohsumi TK, Kung JT, Ogawa Y, Grau DJ et al (2010) Genome-wide identification of polycomb-associated RNAs by RIP-seq. Mol Cell 40:939-953
20. Keene JD, Komisarow JM, Friedersdorf MB (2006) RIP-Chip: the isolation and identification of mRNAs, microRNAs and protein components of ribonucleoprotein complexes from cell extracts. Nat Protoc 1:302-307
21. Zhu R, Iacovino M, Mahen E, Kyba M, Matin A (2011) Transcripts that associate with the RNA binding protein, DEAD-END (DND1), in embryonic stem (ES) cells. BMC Mol Biol 12:37
22. Darnell RB (2010) HITS-CLIP: panoramic views of protein-RNA regulation in living cells. Wiley Interdiscip Rev RNA 1:266-286
23. Ascano M, Hafner M, Cekan P, Gerstberger S, Tuschl T (2012) Identification of RNA-protein interaction networks using PAR-CLIP. Wiley Interdiscip Rev RNA 3:159-177
24. Niranjanakumari S, Lasda E, Brazas R, Garcia-Blanco MA (2002) Reversible cross-linking combined with immunoprecipitation to study RNA-protein interactions in vivo. Methods 26:182-190
25. Mitsui K, Tokuzawa Y, Itoh H, Segawa K, Murakami M et al (2003) The homeoprotein Nanog is required for maintenance of pluripotency in mouse epiblast and ES cells. Cell 113:631-642
26. Legendre JB, Campbell ZT, Kroll-Conner P, Anderson P, Kimble J et al (2012) RNA targets and specificity of Staufen, a double-stranded RNA-binding protein in C. elegans. J Biol Chem 288:2532-2545
27. Mitchell SF, Jain S, She M, Parker R (2012) Global analysis of yeast mRNPs. Nat Struct Mol Biol 20:127-133
28. Sephton CF, Cenik C, Kucukural A, Dammer EB, Cenik B et al (2011) Identification of neuronal RNA targets of TDP-43-containing ribonucleoprotein complexes. J Biol Chem 286:1204-1215
29. Narva E, Rahkonen N, Emani MR, Lund R, Pursiheimo JP et al (2012) RNA-binding protein L1TD1 interacts with LIN28 via RNA and is required for human embryonic stem cell self-renewal and cancer cell proliferation. Stem Cells 30:452-460
30. Elatmani H, Dormoy-Raclet V, Dubus P, Dautry F, Chazaud C et al (2011) The RNA-binding protein Unr prevents mouse embryonic stem cells differentiation toward the primitive endoderm lineage. Stem Cells 29:1504-1516
31. Wuebben EL, Mallanna SK, Cox JL, Rizzino A (2012) Musashi2 is required for the self-renewal and pluripotency of embryonic stem cells. PLoS ONE 7:e34827
32. Park JM, Kohn MJ, Bruinsma MW, Vech C, Intine RV et al (2006) The multifunctional RNA-binding protein La is required for mouse development and for the establishment of embryonic stem cells. Mol Cell Biol 26:1445-1451
33. Hong IS, Kang KS (2013) The effects of hedgehog on the RNA-binding protein Msi1 in the proliferation and apoptosis of mesenchymal stem cells. PLoS ONE 8:e56496
34. Niu C, Zhang J, Breslin P, Onciu M, Ma Z et al (2009) c-Myc is a target of RNA-binding motif protein 15 in the regulation of adult hematopoietic stem cell and megakaryocyte development. Blood 114:2087-2096
35. Salton M, Elkon R, Borodina T, Davydov A, Yaspo ML et al (2011) Matrin 3 binds and stabilizes mRNA. PLoS ONE 6:e23882
36. Calaluce R, Gubin MM, Davis JW, Magee JD, Chen J et al (2010) The RNA binding protein HuR differentially regulates unique subsets of mRNAs in estrogen receptor negative and estrogen receptor positive breast cancer. BMC Cancer 10:126
37. Ule J, Jensen K, Mele A, Darnell RB (2005) CLIP: a method for identifying protein-RNA interaction sites in living cells. Methods 37:376-386
38. Konig J, Zarnack K, Rot G, Curk T, Kayikci M et al (2011) iCLIP - transcriptome-wide mapping of protein-RNA interactions with individual nucleotide resolution. J Vis Exp 50:e2638
39. Ule J, Jensen KB, Ruggiu M, Mele A, Ule A et al (2003) CLIP identifies Nova-regulated RNA networks in the brain. Science 302:1212-1215
40. Iruarrizaga-Lejarreta M, Varela-Rey M, Lozano JJ, Fernandez-Ramos D, Rodriguez-Ezpeleta N et al (2012) The RNA-binding protein human antigen R controls global changes in gene expression during Schwann cell development. J Neurosci 32:4944-4958
41. Apponi LH, Corbett AH, Pavlath GK (2011) RNA-binding proteins and gene regulation in myogenesis. Trends Pharmacol Sci 32:652-658
42. Cilley CD, Williamson JR (1999) PACE analysis of RNA-peptide interactions. Methods Mol Biol 118:129-141
43. Gao FB, Carson CC, Levine T, Keene JD (1994) Selection of a subset of mRNAs from combinatorial 3′ untranslated region libraries using neuronal RNA-binding protein Hel-N1. Proc Natl Acad Sci USA 91:11207-11211
44. SenGupta DJ, Zhang B, Kraemer B, Pochart P, Fields S et al (1996) A three-hybrid system to detect RNA-protein interactions in vivo. Proc Natl Acad Sci USA 93:8496-8501
45. Bernstein DS, Buter N, Stumpf C, Wickens M (2002) Analyzing mRNA-protein complexes using a yeast three-hybrid system. Methods 26:123-141
46. Tenenbaum SA, Carson CC, Lager PJ, Keene JD (2000) Identifying mRNA subsets in messenger ribonucleoprotein complexes by using cDNA arrays. Proc Natl Acad Sci USA 97:14085-14090
47. Tenenbaum SA, Carson CC, Atasoy U, Keene JD (2003) Genome-wide regulatory analysis using en masse nuclear run-ons and ribonomic profiling with autoimmune sera. Gene 317:79-87
48. Eystathioy T, Chan EK, Tenenbaum SA, Keene JD, Griffith K et al (2002) A phosphorylated cytoplasmic autoantigen, GW182, associates with a unique population of human mRNAs within novel cytoplasmic speckles. Mol Biol Cell 13:1338-1351
49. Kaneko S, Manley JL (2005) The mammalian RNA polymerase II C-terminal domain interacts with RNA to suppress transcription-coupled 3′ end formation. Mol Cell 20:91-103
50. Kim KK, Kim YC, Adelstein RS, Kawamoto S (2011) Fox-3 and PSF interact to activate neural cell-specific alternative splicing. Nucleic Acids Res 39:3064-3078
51. Liao TL, Wu CY, Su WC, Jeng KS, Lai MM (2010) Ubiquitination and deubiquitination of NP protein regulates influenza A virus RNA replication. EMBO J 29:3879-3890
52. Danilin S, Sourbier C, Thomas L, Lindner V, Rothhut S et al (2010) Role of the RNA-binding protein HuR in human renal cell carcinoma. Carcinogenesis 31:1018-1026
53. Anko ML, Morales L, Henry I, Beyer A, Neugebauer KM (2010) Global analysis reveals SRp20- and SRp75-specific mRNPs in cycling and neural cells. Nat Struct Mol Biol 17:962-970