Alternative splicing in stem cell self-renewal and differentiation

Advances in Experimental Medicine and Biology

Volumn 695, Issue , 2010, Pages 92-104

  Nelles, David A ^b   Yeo, Gene W ^a  

^a UNIVERSITY OF CALIFORNIA   (United States)

^b NONE

Author keywords

[No Author keywords available]

Indexed keywords

CASPASE 3; DNA METHYLTRANSFERASE 3B; FIBROBLAST GROWTH FACTOR 4; OCTAMER TRANSCRIPTION FACTOR 2; OCTAMER TRANSCRIPTION FACTOR 4; PROTEIN KINASE C DELTA; RNA BINDING PROTEIN; SERINE ARGININE RICH PROTEIN; SOMATOMEDIN C; VASCULOTROPIN A; MESSENGER RNA; RNA PRECURSOR;

ALTERNATIVE RNA SPLICING; ARTICLE; BINDING AFFINITY; CELL DIFFERENTIATION; CELL LINEAGE; CELL RENEWAL; CHROMATIN IMMUNOPRECIPITATION; DNA METHYLATION; DOWN REGULATION; EMBRYONIC STEM CELL; EXON; GENE EXPRESSION REGULATION; GENETIC TRANSCRIPTION; HIGH THROUGHPUT SEQUENCING; HUMAN; INTRON; MESENCHYMAL STEM CELL; NONHUMAN; PRIORITY JOURNAL; PROMOTER REGION; PROTEIN BINDING; PROTEIN DOMAIN; SIGNAL TRANSDUCTION; STEM CELL; UPREGULATION; CELL SELF-RENEWAL; GENETICS; METABOLISM;

ALTERNATIVE SPLICING; CELL SELF RENEWAL; EXONS; HUMANS; INTRONS; RNA PRECURSORS; RNA, MESSENGER;

EID: 79959730734     PISSN: 00652598     EISSN: None     Source Type: Book Series    
DOI: 10.1007/978-1-4419-7037-4_7     Document Type: Article

References (58)

1. Brandenberger R, Wei H, Zhang S et al. Transcriptome characterization elucidates signaling networks that control human ES cell growth and differentiation. Nat Biotechnol 2004; 22(6):707-716. (Pubitemid 38702827)
2. Brandenberger R, Khrebtukova I, Thies RS et al. MPSS profiling of human embryonic stem cells. BMC Dev Biol 2004; 4:10.
3. Miura T, Luo Y, Khrebtukova I et al. Monitoring early differentiation events in human embryonic stem cells by massively parallel signature sequencing and expressed sequence tag scan. Stem Cells Dev 2004; 13(6):694-715. (Pubitemid 40052646)
4. Bhattacharya B, Cai J, Luo Y et al. Comparison of the gene expression profile of undifferentiated human embryonic stem cell lines and differentiating embryoid bodies. BMC Dev Biol 2005; 5:22.
5. Jurica MS, Moore MJ. Pre-mRNA splicing: awash in a sea of proteins. Mol Cell 2003; 12(1):5-14. (Pubitemid 36945033)
6. Nilsen TW. The spliceosome: the most complex macromolecular machine in the cell? Bioessays 2003; 25(12):1147-1149. (Pubitemid 37499313)
7. Matlin AJ, Clark F, Smith CW. Understanding alternative splicing: towards a cellular code. Nat Rev Mol Cell Biol 2005; 6(5):386-398. (Pubitemid 40637856)
8. Martinez-Contreras R, Cloutier P, Shkreta L et al. hnRNP proteins and splicing control. Adv Exp Med Biol 2007;623:123-147.
9. Blencowe BJ. Alternative splicing: new insights from global analyses. Cell 2006; 126(l):37-47. (Pubitemid 44040990)
10. Wang ET, Sandberg R, Luo S et al. Alternative isoform regulation in human tissue transcriptomes. Nature 2008;456(7221):470-476. (Pubitemid 352759009)
11. Pritsker M, Doniger TT, Kramer LC et al. Diversification of stem cell molecular repertoire by alternative splicing. Proc Natl Acad Sci USA 2005; 102(40):14290-14295. (Pubitemid 41429691)
12. Takahashi K, Tanabe K, Ohnuki M et al. Induction of pluripotent stem cells from adult human fibroblasts by defined factors. Cell 2007; 131(5):861~872. (Pubitemid 350138099)
13. Yu J, Vodyanik MA, Smuga-Otto K et al. Induced pluripotent stem cell lines derived from human somatic cells. Science 2007; 318(5858): 1917-1920.
14. Lowry WE, Richter L, Yachechko R et al. Generation of human induced pluripotent stem cells from dermal fibroblasts. Proc Natl Acad Sci USA 2008; 105(8):2883-2888. (Pubitemid 351723638)
15. Tai MH, Chang CC, Kiupel M et al. Oct4 expression in adult human stem cells: evidence in support of the stem cell theory of carcinogenesis. Carcinogenesis 2005; 26(2):495-502.
16. Zangrossi S, Marabese M, Broggini M et al. Oct-4 expression in adult human differentiated cells challenges its role as a pure stem cell marker. Stem Cells 2007; 25(7): 1675-1680. (Pubitemid 47121844)
17. Atlasi Y, Mowla SJ, Ziaee SA et al. OCT4 spliced variants are differentially expressed in human pluripotent and nonpluripotent cells. Stem Cells 2008; 26(12):3068-3074.
18. Cauffman G, Liebaers I, Van Steirteghem A et al. POU5F1 isoforms show different expression patterns in human embryonic stem cells and preimplantation embryos. Stem Cells 2006; 24(12):2685-2691. (Pubitemid 46053006)
19. Lee J, Kim HK, Rho JY et al. The human OCT-4 isoforms differ in their ability to confer self-renewal. J Biol Chem 2006; 281(44):33554-33565. (Pubitemid 46036736)
20. He X, Treacy MN, Simmons DM et al. Expression of a large family of POU-domain regulatory genes in mammalian brain development. Nature 1989; 340(6228):35-41.
21. Theodorou E, Dalembert G, Heffelfinger C et al. A high throughput embryonic stem cell screen identifies Oct-2 as a bifunctional regulator of neuronal differentiation. Genes Dev 2009; 23(5):575-588.
22. Wang L, Wang J, Sun S et al. A novel DNMT3B subfamily, DeltaDNMT3B, is the predominant form of DNMT3B in nonsmall cell lung cancer. Int J Oncol 2006; 29(l):201-207.
23. Ostler KR, Davis EM, Payne SL et al. Cancer cells express aberrant DNMT3B transcripts encoding truncated proteins. Oncogene 2007; 26(38):5553-5563. (Pubitemid 47267842)
24. Gopalakrishnan S, Van Emburgh BO, Shan J et al. A novel DNMT3B splice variant expressed in tumor and pluripotent cells modulates genomic DNA methylation patterns and displays altered DNA binding. Mol Cancer Res 2009; 7(10): 1622-1634.
25. Margot JB, Ehrenhofer-Murray AE, Leonhardt H. Interactions within the mammalian DNA methyltransferase family. BMC Mol Biol 2003; 4:7.
26. Brodie C, Blumberg PM. Regulation of cell apoptosis by protein kinase c delta. Apoptosis 2003; 8(l):19-27. (Pubitemid 36133134)
27. Peluso JJ, Pappalardo A, Fernandez G. Basic fibroblast growth factor maintains calcium homeostasis and granulosa cell viability by stimulating calcium efflux via a PKC delta-dependent pathway. Endocrinology 2001; 142(10):4203-4211. (Pubitemid 32907046)
28. Zrachia A, Dobroslav M, Blass M et al. Infection of glioma cells with Sindbis virus induces selective activation and tyrosine phosphorylation of protein kinase C delta. Implications for Sindbis virus-induced apoptosis. J Biol Chem 2002; 277(26):23693-23701. (Pubitemid 34952209)
29. Kilpatrick LE, Lee JY, Haines KM et al. A role for PKC-delta and PI 3-kinase in TNF-alpha-mediated antiapoptotic signaling in the human neutrophil. Am J Physiol Cell Physiol 2002; 283(l):C48-57. (Pubitemid 34670547)
30. Sitailo LA, Tibudan SS, Denning MF. Bax activation and induction of apoptosis in human keratinocytes by the protein kinase C delta catalytic domain. J Invest Dermatol 2004; 123(3):434-443. (Pubitemid 39095610)
31. Sakurai Y, Onishi Y, Tanimoto Y, Kizaki H. Novel protein kinase C delta isoform insensitive to caspase-3. Biol Pharm Bull. Sep 2001;24(9):973-977. (Pubitemid 32894113)
32. Patel NA, Song SS, Cooper DR. PKCdelta alternatively spliced isoforms modulate cellular apoptosis in retinoic acid-induced differentiation of human NT2 cells and mouse embryonic stem cells. Gene Expr 2006; 13(2): 73-84. (Pubitemid 44491087)
33. Dvorak P, Dvorakova D, Koskova S et al. Expression and potential role of fibroblast growth factor 2 and its receptors in human embryonic stem cells. Stem Cells 2005; 23(8): 1200-1211. (Pubitemid 41377735)
34. Li J, Wang G, Wang C et al. MEK/ERK signaling contributes to the maintenance of human embryonic stem cell self-renewal. Differentiation 2007; 75(4):299-307. (Pubitemid 46434953)
35. Mayshar Y, Rom E, Chumakov I et al. Fibroblast growth factor 4 and its novel splice isoform have opposing effects on the maintenance of human embryonic stem cell self-renewal. Stem Cells 2008; 26(3):767-774.
36. Hill M, Goldspink G. Expression and splicing of the insulin-like growth factor gene in rodent muscle is associated with muscle satellite (stem) cell activation following local tissue damage. J Physiol 2003; 549(Pt 2):409-418. (Pubitemid 36701754)
37. Ates K, Yang SY, Orrell RW et al. The IGF-I splice variant MGF increases progenitor cells in ALS, dystrophic and normal muscle. FEBS Lett 2007; 581(14):2727-2732. (Pubitemid 46829121)
38. Gnecchi M, He H, Liang OD et al. Paracrine action accounts for marked protection of ischemic heart by Akt-modified mesenchymal stem cells. Nat Med 2005; 11(4):367-368. (Pubitemid 40562318)
39. Tang YL, Zhao Q, Qin X et al. Paracrine action enhances the effects of autologous mesenchymal stem cell transplantation on vascular regeneration in rat model of myocardial infarction. Ann Thorac Surg 2005; 80(l):229-236; discussion 236-227.
40. Lin H, Shabbir A, Molnar M et al. Adenoviral expression of vascular endothelial growth factor splice variants differentially regulate bone marrow-derived mesenchymal stem cells. J Cell Physiol 2008; 216(2):458-468. (Pubitemid 351898474)
41. Yang Z, Sui Y, Xiong S et al. Switched alternative splicing of oncogene CoAA during embryonal carcinoma stem cell differentiation. Nucleic Acids Res 2007; 35(6): 1919-1932. (Pubitemid 47061660)
42. Brooks YS, Wang G, Yang Z et al. Functional pre-mRNA trans-splicing of coactivator CoAA and corepressor RBM4 during stem/progenitor cell differentiation. J Biol Chem 2009; 284(27):18033-18046.
43. Yeakley JM, Fan JB, Doucet D et al. Profiling alternative splicing on fiber-optic arrays. Nat Biotechnol 2002; 20(4):353-358. (Pubitemid 34286328)
44. Johnson JM, Castle J, Garrett-Engele P et al. Genome-wide survey of human alternative premRNA splicing with exon junction microarrays. Science 2003; 302(5653):2141-2144. (Pubitemid 38017950)
45. Pan Q, Shai O, Misquitta C et al. Revealing global regulatory features of mammalian alternative splicing using a quantitative microarray platform. Mol Cell 2004; 16(6):929-941. (Pubitemid 40018403)
46. Yeo GW, Xu X, Liang TY et al. Alternative splicing events identified in human embryonic stem cells and neural progenitors. PLoS Comput Biol 2007; 3(10): 1951-1967. (Pubitemid 350043410)
47. Salomonis N, Nelson B, Vranizan K et al. Alternative splicing in the differentiation of human embryonic stem cells into cardiac precursors. PLoS Comput Biol 2009; 5(11):el000553.
48. Cloonan N, Forrest AR, Kolle G et al. Stem cell transcript ome profiling via massive-scale mRNA sequencing. Nat Methods 2008; 5(7):613-619. (Pubitemid 351911866)
49. Ule J, Jensen KB, Ruggiu M et al. CLIP identifies Nova-regulated RNA networks in the brain. Science 2003;302(5648):1212-1215. (Pubitemid 37421026)
50. Yeo GW, Coufal NG, Liang TY et al. An RNA code for the FOX2 splicing regulator revealed by mapping RNA-protein interactions in stem cells. Nat Struct Mol Biol 2009; 16(2): 130-137.
51. Ashiya M, Grabowski PJ. A neuron-specific splicing switch mediated by an array of premRNA repressor sites: evidence of a regulatory role for the polypyrimidine tract binding protein and a brain-specific PTB counterpart. RNA 1997; 3(9):996-1015. (Pubitemid 27371735)
52. Boutz PL, Stoilov P, Li Q et al. A posttranscriptional regulatory switch in polypyrimidine tract-binding proteins reprograms alternative splicing in developing neurons. Genes Dev 2007; 21(13): 1636-1652. (Pubitemid 47026368)
53. Makeyev EV, Zhang J, Carrasco MA et al. The MicroRNA miR-124 promotes neuronal differentiation by triggering brain-specific alternative premRNA splicing. Mol Cell 2007; 27(3):435-448. (Pubitemid 47126944)
54. Spellman R, Llorian M, Smith CW. Crossregulation and functional redundancy between the splicing regulator PTB and its paralogs nPTB and ROD1. Mol Cell 2007; 27(3):420-434. (Pubitemid 47126939)
55. Shibayama M, Ohno S, Osaka T et al. Polypyrimidine tract-binding protein is essential for early mouse development and embryonic stem cell proliferation. FEBS J 2009; 276(22):6658-6668.
56. Matter N, Herrlich P, Konig H. Signal-dependent regulation of splicing via phosphorylation of Sam68. Nature 2002; 420(6916):691-695. (Pubitemid 36764503)
57. Moritz S, Lehmann S, Faissner A et al. An induction gene trap screen in neural stem cells reveals an instructive function of the niche and identifies the splicing regulator sam68 as a tenascin-C-regulated target gene. Stem Cells 2008; 26(9):2321-2331.
58. Chawla G, Lin CH, Han A et al. Sam68 regulates a set of alternatively spliced exons during neurogenesis. Mol Cell Biol 2009; 29(1):201-213.