Global Splicing Pattern Reversion during Somatic Cell Reprogramming

Cell Reports

Volumn 5, Issue 2, 2013, Pages 357-366

  Ohta, Sho ^a,b   Nishida, Eisuke ^b,c   Yamanaka, Shinya ^a,d,e   Yamamoto, Takuya ^a,d  

^a KYOTO UNIVERSITY   (Japan)

^b KYOTO UNIVERSITY   (Japan)

^c JAPAN SCIENCE AND TECHNOLOGY AGENCY   (Japan)

^d KYOTO UNIVERSITY   (Japan)

^e GLADSTONE INSTITUTE OF CARDIOVASCULAR DISEASE   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

RNA BINDING PROTEIN; SMALL INTERFERING RNA; MESSENGER RNA; NUCLEAR PROTEIN; RIBONUCLEOPROTEIN; SPLICING FACTOR U2AF; SRSF3 PROTEIN, MOUSE;

ANIMAL CELL; ARTICLE; CELL DIFFERENTIATION; CONTROLLED STUDY; GENE; GENE EXPRESSION REGULATION; GENE FUNCTION; GENE INTERACTION; GENE REGULATORY NETWORK; HIGH THROUGHPUT SEQUENCING; MOUSE; NONHUMAN; NUCLEAR REPROGRAMMING; NUCLEOTIDE SEQUENCE; PLURIPOTENT STEM CELL; PRIORITY JOURNAL; PROTEIN DETERMINATION; QUANTITATIVE STUDY; REVERSE TRANSCRIPTION POLYMERASE CHAIN REACTION; REVERTANT; RNA ANALYSIS; RNA SEQUENCE; RNA SPLICING; SOMATIC CELL; SRSF3 GENE; TESTIS; TISSUE DISTRIBUTION; U2AF1 GENE; UPREGULATION; ANIMAL; ANTAGONISTS AND INHIBITORS; CELL LINE; EXON; GENETICS; METABOLISM; RNA INTERFERENCE;

ANIMALS; CELL LINE; CELLULAR REPROGRAMMING; EXONS; GENE EXPRESSION REGULATION; INDUCED PLURIPOTENT STEM CELLS; MICE; NUCLEAR PROTEINS; RIBONUCLEOPROTEINS; RNA INTERFERENCE; RNA SPLICING; RNA, MESSENGER; RNA, SMALL INTERFERING; RNA-BINDING PROTEINS;

EID: 84887016186     PISSN: None     EISSN: 22111247     Source Type: Journal    
DOI: 10.1016/j.celrep.2013.09.016     Document Type: Article

References (23)

1. Atlasi Y., Mowla S.J., Ziaee S.A., Gokhale P.J., Andrews P.W. OCT4 spliced variants are differentially expressed in human pluripotent and nonpluripotent cells. Stem Cells 2008, 26:3068-3074.
2. Brambrink T., Foreman R., Welstead G.G., Lengner C.J., Wernig M., Suh H., Jaenisch R. Sequential expression of pluripotency markers during direct reprogramming of mouse somatic cells. Cell Stem Cell 2008, 2:151-159.
3. Chen T., Yuan D., Wei B., Jiang J., Kang J., Ling K., Gu Y., Li J., Xiao L., Pei G. E-cadherin-mediated cell-cell contact is critical for induced pluripotent stem cell generation. Stem Cells 2010, 28:1315-1325.
4. Cheong C.Y., Lufkin T. Alternative splicing in self-renewal of embryonic stem cells. Stem Cells Int. 2011, 2011:560261.
5. Cooper T.A., Wan L., Dreyfuss G. RNA and disease. Cell 2009, 136:777-793.
6. Fox-Walsh K.L., Dou Y., Lam B.J., Hung S.P., Baldi P.F., Hertel K.J. The architecture of pre-mRNAs affects mechanisms of splice-site pairing. Proc. Natl. Acad. Sci. USA 2005, 102:16176-16181.
7. Gabut M., Samavarchi-Tehrani P., Wang X., Slobodeniuc V., O'Hanlon D., Sung H.K., Alvarez M., Talukder S., Pan Q., Mazzoni E.O., et al. An alternative splicing switch regulates embryonic stem cell pluripotency and reprogramming. Cell 2011, 147:132-146.
8. Gopalakrishnan S., Van Emburgh B.O., Shan J., Su Z., Fields C.R., Vieweg J., Hamazaki T., Schwartz P.H., Terada N., Robertson K.D. 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, 7:1622-1634.
9. Han H., Irimia M., Ross P.J., Sung H.K., Alipanahi B., David L., Golipour A., Gabut M., Michael I.P., Nachman E.N., et al. MBNL proteins repress ES-cell-specific alternative splicing and reprogramming. Nature 2013, 498:241-245.
10. Lareau L.F., Inada M., Green R.E., Wengrod J.C., Brenner S.E. Unproductive splicing of SR genes associated with highly conserved and ultraconserved DNA elements. Nature 2007, 446:926-929.
11. Licatalosi D.D., Darnell R.B. RNA processing and its regulation: global insights into biological networks. Nat. Rev. Genet. 2010, 11:75-87.
12. Mikkelsen T.S., Hanna J., Zhang X., Ku M., Wernig M., Schorderet P., Bernstein B.E., Jaenisch R., Lander E.S., Meissner A. Dissecting direct reprogramming through integrative genomic analysis. Nature 2008, 454:49-55.
13. Ni J.Z., Grate L., Donohue J.P., Preston C., Nobida N., O'Brien G., Shiue L., Clark T.A., Blume J.E., Ares M. Ultraconserved elements are associated with homeostatic control of splicing regulators by alternative splicing and nonsense-mediated decay. Genes Dev. 2007, 21:708-718.
14. Nilsen T.W., Graveley B.R. Expansion of the eukaryotic proteome by alternative splicing. Nature 2010, 463:457-463.
15. Okita K., Ichisaka T., Yamanaka S. Generation of germline-competent induced pluripotent stem cells. Nature 2007, 448:313-317.
16. Pan Q., Shai O., Lee L.J., Frey B.J., Blencowe B.J. Deep surveying of alternative splicing complexity in the human transcriptome by high-throughput sequencing. Nat. Genet. 2008, 40:1413-1415.
17. Rao S., Zhen S., Roumiantsev S., McDonald L.T., Yuan G.C., Orkin S.H. Differential roles of Sall4 isoforms in embryonic stem cell pluripotency. Mol. Cell. Biol. 2010, 30:5364-5380.
18. Salomonis N., Schlieve C.R., Pereira L., Wahlquist C., Colas A., Zambon A.C., Vranizan K., Spindler M.J., Pico A.R., Cline M.S., et al. Alternative splicing regulates mouse embryonic stem cell pluripotency and differentiation. Proc. Natl. Acad. Sci. USA 2010, 107:10514-10519.
19. Stadtfeld M., Maherali N., Breault D.T., Hochedlinger K. Defining molecular cornerstones during fibroblast to iPS cell reprogramming in mouse. Cell Stem Cell 2008, 2:230-240.
20. Sterner D.A., Carlo T., Berget S.M. Architectural limits on split genes. Proc. Natl. Acad. Sci. USA 1996, 93:15081-15085.
21. Takahashi K., Yamanaka S. Induction of pluripotent stem cells from mouse embryonic and adult fibroblast cultures by defined factors. Cell 2006, 126:663-676.
22. Wang E.T., Sandberg R., Luo S., Khrebtukova I., Zhang L., Mayr C., Kingsmore S.F., Schroth G.P., Burge C.B. Alternative isoform regulation in human tissue transcriptomes. Nature 2008, 456:470-476.
23. Yeo G.W., Xu X., Liang T.Y., Muotri A.R., Carson C.T., Coufal N.G., Gage F.H. Alternative splicing events identified in human embryonic stem cells and neural progenitors. PLoS Comput. Biol. 2007, 3:1951-1967.