Detection of nascent RNA, single-copy DNA and protein localization by immunoFISH in mouse germ cells and preimplantation embryos

Nature Protocols

Volumn 6, Issue 3, 2011, Pages 270-284

  Namekawa, Satoshi H ^a,b,c   Lee, Jeannie T ^a,b  

^a HOWARD HUGHES MEDICAL INSTITUTE   (United States)

^b HARVARD MEDICAL SCHOOL   (United States)

^c UNIVERSITY OF CINCINNATI COLLEGE OF MEDICINE   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

EPITOPE;

ARTICLE; CELL PERMEABILIZATION; CHROMATIN STRUCTURE; CLINICAL PROTOCOL; DEVELOPMENTAL STAGE; DNA DETERMINATION; FLUORESCENCE IN SITU HYBRIDIZATION; GAMETE; GENE TARGETING; IMMUNOFLUORESCENCE; NONHUMAN; PREIMPLANTATION EMBRYO; PRIORITY JOURNAL; PROCESS DEVELOPMENT; PROCESS OPTIMIZATION; PROTEIN LOCALIZATION; RELIABILITY; RNA ANALYSIS; RNA TRANSCRIPTION; SENSITIVITY ANALYSIS; SPERMATOGENESIS; TISSUE FIXATION;

ANIMALS; BLASTOCYST; CHROMATIN; CHROMOSOMES; DNA; GERM CELLS; IMMUNOHISTOCHEMISTRY; IN SITU HYBRIDIZATION, FLUORESCENCE; MALE; MICE; REPETITIVE SEQUENCES, NUCLEIC ACID; RNA PRECURSORS; SENSITIVITY AND SPECIFICITY;

EID: 79952418478     PISSN: 17542189     EISSN: 17502799     Source Type: Journal    
DOI: 10.1038/nprot.2010.195     Document Type: Article

References (34)

1. Youngson, N.A. & Whitelaw, E. Transgenerational epigenetic effects. Annu. Rev. Genomics Hum. Genet. 9, 233-257 (2008).
2. Carrell, D.T. & Hammoud, S.S. The human sperm epigenome and its potential role in embryonic development Mol. Hum. Reprod. 16, 37-47 (2010).
3. Cooper, D.W. Directed genetic change model for X chromosome inactivation in eutherian mammals. Nature 230, 292-294 (1971).
4. Lyon, M.F. Imprinting and X chromosome inactivation In Results and Problems in Cell Differentiation (ed. Ohlsson, R.) 73-90 (Springer-Verlag, 1999).
5. McCarrey, J.R. X-chromosome inactivation during spermatogenesis: the original dosage compensation mechanism in mammals? In Gene Families: Studies of DNA, RNA, Enzymes, and Proteins (eds. Xue, G. et al.) 59-72 (World Scientifc Publishing Co., 2001).
6. Huynh, K.D. & Lee, J.T. Inheritance of a pre-inactivated paternal X chromosome in early mouse embryos. Nature 426, 857-862 (2003). (Pubitemid 38056873)
7. Huynh, K.D. & Lee, J.T. X-chromosome inactivation: a hypothesis linking ontogeny and phylogeny. Nat Rev. Genet. 6, 410-418 (2005). (Pubitemid 40577184)
8. Hammoud, S.S. et al. Distinctive chromatin in human sperm packages genes for embryo development. Nature 460, 473-478 (2009).
9. Arpanahi, A. et al. Endonuclease-sensitive regions of human spermatozoal chromatin are highly enriched in promoter and CTCF binding sequences. Genome Res. 19, 1338-1349 (2009).
10. Brykczynska, U. et al. Repressive and active histone methylation mark distinct promoters in human and mouse spermatozoa. Nat Struct. Mol. Biol. 17, 679-687 (2010).
11. Darzacq, X. et al. Imaging transcription in living cells. Annu. Rev. Biophys. 38, 173-196 (2009).
12. Clemson, C.M. et al. An architectural role for a nuclear noncoding RNA: NEAT1 RNA is essential for the structure of paraspeckles. Mol. Cell 33, 717-726 (2009).
13. Cremer, T. & Cremer, M. Chromosome territories. Cold Spring Harb. Perspect Biol. 2, a003889 (2010).
14. Zhao, R., Bodnar, M.S. & Spector, D.L. Nuclear neighborhoods and gene expression. Curr. Opin. Genet Dev. 19, 172-179 (2009).
15. Namekawa, S.H. et al. Postmeiotic sex chromatin in the male germline of mice. Curr. Biol. 16, 660-667 (2006).
16. Namekawa, S.H., Payer, B., Huynh, K.D., Jaenisch, R. & Lee, J.T. Two-step imprinted X inactivation: repeat versus genic silencing in the mouse. Mol. Cell Biol. 30, 3187-3205 (2010).
17. Turner, J.M., Mahadevaiah, S.K., Ellis, P.J., Mitchell, M.J. & Burgoyne, P.S. Pachytene asynapsis drives meiotic sex chromosome inactivation and leads to substantial postmeiotic repression in spermatids. Dev. Cell 10, 521-529 (2006).
18. Okamoto, I. et al. Evidence for de novo imprinted X-chromosome inactivation independent of meiotic inactivation in mice. Nature 438, 369-373 (2005). (Pubitemid 41643954)
19. Okamoto, I., Otte, A.P., Allis, C.D., Reinberg, D. & Heard, E. Epigenetic dynamics of imprinted X inactivation during early mouse development. Science 303, 644-649 (2004). (Pubitemid 38141624)
20. Panning, B. X inactivation in mouse ES cells: histone modifcations and FISH. Methods Enzymol. 376, 419-428 (2004). (Pubitemid 38200195)
21. Erwin, J.A. & Lee, J.T. Characterization of X-chromosome inactivation status in human pluripotent stem cells. Curr. Protoc Stem Cell Biol. chapter 1 Unit 1B 6 (2010).
22. Peters, A.H., Plug, A.W., van Vugt, M.J. & de Boer, P. A drying-down technique for the spreading of mammalian meiocytes from the male and female germline. Chromosome Res. 5, 66-68 (1997). (Pubitemid 27129985)
23. Barlow, A.L., Benson, F.E., West, S.C. & Hulten, M.A. Distribution of the Rad51 recombinase in human and mouse spermatocytes. EMBO J. 16, 5207-5215 (1997). (Pubitemid 27380129)
24. Hall, L.L. et al. An ectopic human XIST gene can induce chromosome inactivation in postdifferentiation human HT-1080 cells. Proc Natl. Acad. Sci. USA 99, 8677-8682 (2002). (Pubitemid 34693619)
25. Namekawa, S.H., VandeBerg, J.L, McCarrey, J.R. & Lee, J.T. Sex chromosome silencing in the marsupial male germ line. Proc Natl. Acad. Sci. USA 104, 9730-9735 (2007). (Pubitemid 47175335)
26. Greaves, I.K., Rangasamy, D., Devoy, M., Marshall Graves, J.A. & Tremethick, D.J. The X and Y chromosomes assemble into H2A.Z, containing facultative heterochromatin, following meiosis. Mol. Cell Biol. 26, 5394-5405 (2006). (Pubitemid 44036208)
27. Khalil, A.M., Boyar, F.Z. & Driscoll, D.J. Dynamic histone modifcations mark sex chromosome inactivation and reactivation during mammalian spermatogenesis. Proc Natl. Acad. Sci. USA 101, 16583-16587 (2004). (Pubitemid 39557756)
28. Okamoto, I. et al. Evaluating the role of inducible nitric oxide synthase using a novel and selective inducible nitric oxide synthase inhibitor in septic lung injury produced by cecal ligation and puncture. Am. J. Respir. Crit Care Med. 162 (2 Pt 1): 716-722 (2000). (Pubitemid 30647224)
29. Ohno, M., Aoki, N. & Sasaki, H. Allele-specifc detection of nascent transcripts by fuorescence in situ hybridization reveals temporal and culture-induced changes in Igf2 imprinting during pre-implantation mouse development. Genes Cells 6, 249-259 (2001). (Pubitemid 32273387)
30. Silva, J. et al. Establishment of histone h3 methylation on the inactive X chromosome requires transient recruitment of Eed-Enx1 polycomb group complexes. Dev. Cell 4, 481-495 (2003). (Pubitemid 36437556)
31. Patrat, C et al. Dynamic changes in paternal X-chromosome activity during imprinted X-chromosome inactivation in mice. Proc Natl. Acad. Sci. USA 106, 5198-5203 (2009).
32. Nagy, A., Gertsenstein, M., Vintersen, K. & Behringer, R. Manipulating the Mouse Embryo (Cold Spring Harbor Laboratory Press, 2003).
33. Beatty, B., Mai, S. & Squire, J. FISH. A Practical Approach (Oxford University Press, 2002).
34. Zhang, L.F., Huynh, K.D. & Lee, J.T. Perinucleolar targeting of the inactive X during S phase: evidence for a role in the maintenance of silencing. Cell 129, 693-706 (2007). (Pubitemid 46802377)