ES cell differentiation system recapitulates the establishment of imprinted gene expression in a cell-type-specific manner

Human Molecular Genetics

Volumn 21, Issue 6, 2012, Pages 1391-1401

  Kohama, Chihiro ^a   Kato, Hidemasa ^a,b   Numata, Koji ^c   Hirose, Michiko ^d   Takemasa, Tohru ^a   Ogura, Atsuo ^d   Kiyosawa, Hidenori ^e,f  

^a UNIVERSITY OF TSUKUBA   (Japan)

^b SAITAMA MEDICAL UNIVERSITY   (Japan)

^c Technology and Development Team for Mammalian Cellular Dynamics   (Japan)

^d RIKEN BIORESOURCE CENTER   (Japan)

^e UNIVERSITY OF TOKYO   (Japan)

^f NATIONAL INSTITUTE OF GENETICS   (Japan)

Author keywords

[No Author keywords available]

Indexed keywords

ALLELE; ARTICLE; CELL MATURATION; EMBRYONIC STEM CELL; FEMALE; GENE EXPRESSION; GENE LOCUS; GENETIC ANALYSIS; GENOME IMPRINTING; HYBRID CELL; IN VITRO STUDY; MALE; MOUSE; NERVE CELL DIFFERENTIATION; NERVE FIBER GROWTH; NONHUMAN; PRIORITY JOURNAL; TRANSCRIPTION REGULATION; UPREGULATION;

ALLELES; ANIMALS; CELL DIFFERENTIATION; EMBRYONIC STEM CELLS; FEMALE; GENE EXPRESSION REGULATION, DEVELOPMENTAL; GENOMIC IMPRINTING; MALE; MICE; MICE, INBRED C57BL; NEURONS; POLYMORPHISM, SINGLE NUCLEOTIDE; REAL-TIME POLYMERASE CHAIN REACTION; REVERSE TRANSCRIPTASE POLYMERASE CHAIN REACTION; RNA, MESSENGER; RNA, UNTRANSLATED; UBIQUITIN-PROTEIN LIGASES;

MUS; MUS MUSCULUS;

EID: 84857679041     PISSN: 09646906     EISSN: 14602083     Source Type: Journal    
DOI: 10.1093/hmg/ddr577     Document Type: Article

References (36)

1. Reik, W. (2007) Stability and flexibility of epigenetic gene regulation in mammalian development. Nature, 447, 425-432.
2. Sasaki, H. and Matsui, Y. (2008) Epigenetic events in mammalian germ-cell development: reprogramming and beyond. Nat. Rev. Genet., 9, 129-140.
3. Loi, P., Beaujean, N., Khochbin, S., Fulka, J. and Ptak, G. (2008) Asymmetric nuclear reprogramming in somatic cell nuclear transfer? Bioessays, 30, 66-74.
4. Koerner, M.V. and Barlow, D.P. (2010) Genomic imprinting-an epigenetic gene-regulatory model. Curr. Opin. Genet. Dev., 20, 164-170.
5. Gregg, C., Zhang, J., Weissbourd, B., Luo, S., Schroth, G.P., Haig, D. and Dulac, C. (2010) High-resolution analysis of parent-of-origin allelic expression in the mouse brain. Science, 329, 643-648.
6. Gregg, C., Zhang, J., Butler, J.E., Haig, D. and Dulac, C. (2010) Sex-specific parent-of-origin allelic expression in the mouse brain. Science, 329, 682-685.
7. Humpherys, D., Eggan, K., Akutsu, H., Hochedlinger, K., Rideout, W.M. III, Biniszkiewicz, D., Yanagimachi, R. and Jaenisch, R. (2001) Epigenetic instability in ES cells and cloned mice. Science, 293, 95-97.
8. Rougeulle, C., Glatt, H. and Lalande, M. (1997) The Angelman syndrome candidate gene, UBE3A/E6-AP, is imprinted in brain. Nat. Genet., 17, 14-15.
9. Vu, T.H. and Hoffman, A.R. (1997) Imprinting of the Angelman syndrome gene, UBE3A, is restricted to brain. Nat. Genet., 17, 12-13.
10. Albrecht, U., Sutcliffe, J.S., Cattanach, B.M., Beechey, C.V., Armstrong, D., Eichele, G. and Beaudet, A.L. (1997) Imprinted expression of the murine Angelman syndrome gene, Ube3a, in hippocampal and Purkinje neurons. Nat. Genet., 17, 75-78.
11. Muhle, R., Trentacoste, S.V. and Rapin, I. (2004) The genetics of autism. Pediatrics, 113, e472-e486.
12. Rougeulle, C., Cardoso, C., Fontes, M., Colleaux, L. and Lalande, M. (1998) An imprinted antisense RNA overlaps UBE3A and a second maternally expressed transcript. Nat. Genet., 19, 15-16.
13. Chamberlain, S.J. and Brannan, C.I. (2001) The Prader-Willi syndrome imprinting center activates the paternally expressed murine Ube3a antisense transcript but represses paternal Ube3a. Genomics, 73, 316-322.
14. Yamasaki, K., Joh, K., Ohta, T., Masuzaki, H., Ishimaru, T., Mukai, T., Niikawa, N., Ogawa, M., Wagstaff, J. and Kishino, T. (2003) Neurons but not glial cells show reciprocal imprinting of sense and antisense transcripts of Ube3a. Hum. Mol. Genet., 12, 837-847.
15. Landers, M., Bancescu, D.L., Le Meur, E., Rougeulle, C., Glatt-Deeley, H., Brannan, C., Muscatelli, F. and Lalande, M. (2004) Regulation of the large (approximately 1000 kb) imprinted murine Ube3a antisense transcript by alternative exons upstream of Snurf/Snrpn. Nucleic Acids Res., 32, 3480-3492.
16. Le Meur, E., Watrin, F., Landers, M., Sturny, R., Lalande, M. and Muscatelli, F. (2005) Dynamic developmental regulation of the large non-coding RNA associated with the mouse 7C imprinted chromosomal region. Dev. Biol., 286, 587-600.
17. Bouhon, I.A., Kato, H., Chandran, S. and Allen, N.D. (2005) Neural differentiation of mouse embryonic stem cells in chemically defined medium. Brain Res. Bull., 68, 62-75.
18. Bouhon, I.A., Joannides, A., Kato, H., Chandran, S. and Allen, N.D. (2006) Embryonic stem cell-derived neural progenitors display temporal restriction to neural patterning. Stem Cells, 24, 1908-1913.
19. Moriwaki, K., Miyashita, N., Mita, A., Gotoh, H., Tsuchiya, K., Kato, H., Mekada, K., Noro, C., Oota, S., Yoshiki, A., Obata, Y., Yonekawa, H. and Shiroishi, T. (2009) Unique inbred strain MSM/Ms established from the Japanese wild mouse. Exp. Anim., 58, 123-134.
20. Numata, K., Kohama, C., Abe, K. and Kiyosawa, H. (2011) Highly parallel SNP genotyping reveals high-resolution landscape of mono-allelic Ube3a expression associated with locus-wide antisense transcription. Nucleic Acids Res., 39, 2649-2657.
21. Qian, X., Goderie, S.K., Shen, Q., Stern, J.H. and Temple, S. (1998) Intrinsic programs of patterned cell lineages in isolated vertebrate CNS ventricular zone cells. Development, 125, 3143-3152.
22. Ying, Q.L., Wray, J., Nichols, J., Batlle-Morera, L., Doble, B., Woodgett, J., Cohen, P. and Smith, A. (2008) The ground state of embryonic stem cell self-renewal. Nature, 453, 519-523.
23. Reik, W. and Walter, J. (2001) Genomic imprinting: parental influence on the genome. Nat. Rev. Genet., 2, 21-32.
24. Runte, M., Hüttenhofer, A., Gross, S., Kiefmann, M., Horsthemke, B. and Buiting, O. (2011) The IC-SNURF-SNRPN transcript serves as a host for multiple small nucleolar RNA species and as an antisense RNA for UBE3A. Hum. Mol. Genet., 10, 2687-2700.
25. Batlle-Morera, L., Smith, A. and Nichols, J. (2008) Parameters influencing derivation of embryonic stem cells from murine embryos. Genesis, 46, 758-767.
26. Waterston, R.H., Lindblad-Toh, K., Birney, E., Rogers, J., Abril, J.F., Agarwal, P., Agarwala, R., Ainscough, R., Alexandersson, M., An, P. et al., Mouse Genome Sequencing Consortium (2002) Initial sequencing and comparative analysis of the mouse genome. Nature, 420, 520-562.
27. Gagneur, J., Sinh, A., Perocchi, F., Bourgon, R., Huber, W. and Steinmetz, L.M. (2009) Genome-wide allele- and strand-specific expression profiling. Mol. Syst. Biol., 5, 274.
28. Watanabe, K., Kato, H., Abe, K. and Kiyosawa, H. (2010) Genome-wide analysis of expression modes and DNA methylation status at sense-antisense transcript loci in mouse. Genomics, 96, 333-341.
29. Stadtfeld, M., Apostolou, E., Akutsu, H., Fukuda, A., Follett, P., Natesan, S., Kono, T., Shioda, T. and Hochedlinger, K. (2010) Aberrant silencing of imprinted genes on chromosome 12qF1 in mouse induced pluripotent stem cells. Nature, 465, 175-181.
30. Braem, C., Recolin, B., Rancourt, R.C., Angiolini, C., Barthe's, P., Branchu, P., Court, F., Cathala, G., Ferguson-Smith, A.C. and Forné, T. (2008) Genomic matrix attachment region and chromosome conformation capture quantitative real time PCR assays identify novel putative regulatory elements at the imprinted Dlk1/Gtl2 locus. J. Biol. Chem., 283, 18612-18620.
31. Su, W.Y., Xiong, H. and Fang, J.Y. (2010) Natural antisense transcripts regulate gene expression in an epigenetic manner. Biochem. Biophys. Res. Commun., 396, 177-181.
32. Beisel, C. and Paro, R. (2011) Silencing chromatin: comparing modes and mechanisms. Nat. Rev. Genet., 12, 123-135.
33. Latos, P.A., Stricker, S.H., Steenpass, L., Pauler, F.M., Huang, R., Senergin, B.H., Regha, K., Koerner, M.V., Warczok, K.E., Unger, C. and Barlow, D.P. (2009) An in vitro ES cell imprinting model shows that imprinted expression of the Igf2r gene arises from an allele-specific expression bias. Development, 136, 437-448.
34. Chamberlain, S.J., Chen, P.F., Ng, K.Y., Bourgois-Rocha, F., Lemtiri-Chlieh, F., Levine, E.S. and Lalande, M. (2010) Induced pluripotent stem cell models of the genomic imprinting disorders Angelman and Prader-Willi syndromes. Proc. Natl Acad. Sci. USA, 107, 17668-17673.
35. Hikichi, T., Kohda, T., Kaneko-Ishino, T. and Ishino, F. (2003) Imprinting regulation of the murine Meg1/Grb10 and human GRB10 genes; roles of brain-specific promoters and mouse-specific CTCF-binding sites. Nucleic Acids Res., 31, 1398-1406.
36. Smyth, G.K. (2005) Limma: linear models for microarray data. In Robert Gentleman, V.J.C., Huber, W., Irizarry, R.A. and Dudoit, S. (eds), Bioinformatics and Computational Biology Solutions using R and Bioconductor. Springer, New York, pp. 397-420.