Visualization of DNA methylation and histone modifications in living cells

Current Opinion in Cell Biology

Volumn 22, Issue 3, 2010, Pages 412-418

  Kimura, Hiroshi ^a   Hayashi Takanaka, Yoko ^a   Yamagata, Kazuo ^b  

^a OSAKA UNIVERSITY   (Japan)

^b RIKEN KOBE INSTITUTE   (Japan)

Author keywords

[No Author keywords available]

Indexed keywords

DNA; DNA METHYLTRANSFERASE; HISTONE; HISTONE H3; METHYL CPG BINDING PROTEIN; METHYL CPG BINDING PROTEIN 1; UNCLASSIFIED DRUG;

ACETYLATION; ANTIBODY SPECIFICITY; ANTIGEN BINDING; DEMETHYLATION; DNA METHYLATION; ENZYME ACTIVITY; EPIGENETICS; FLUORESCENCE RESONANCE ENERGY TRANSFER; HUMAN; PRIORITY JOURNAL; PROTEIN LOCALIZATION; PROTEIN MODIFICATION; PROTEIN PHOSPHORYLATION; REVIEW; ZYGOTE; ANIMAL; CELL SURVIVAL; METABOLISM; PROTEIN PROCESSING;

ANIMALS; CELL SURVIVAL; DNA METHYLATION; FLUORESCENCE RESONANCE ENERGY TRANSFER; HISTONES; HUMANS; PROTEIN PROCESSING, POST-TRANSLATIONAL; ZYGOTE;

EID: 77954814488     PISSN: 09550674     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.ceb.2010.02.004     Document Type: Review

References (51)

1. Luger K. Structure and dynamic behavior of nucleosomes. Curr Opin Genet Dev 2003, 13:127-135.
2. Kouzarides T. Chromatin modifications and their function. Cell 2007, 128:693-705.
3. van Attikum H., Gasser S.M. Crosstalk between histone modifications during the DNA damage response. Trends Cell Biol 2009, 19:207-217.
4. Clayton A.L., Hazzalin C.A., Mahadevan L.C. Enhanced histone acetylation and transcription: a dynamic perspective. Mol Cell 2006, 23:289-296.
5. Wang Z., Schones D.E., Zhao K. Characterization of human epigenomes. Curr Opin Genet Dev 2009, 19:127-134.
6. Klose R.J., Bird A.P. Genomic DNA methylation: the mark and its mediators. Trends Biochem Sci 2006, 31:89-97.
7. Morgan H.D., Santos F., Green K., Dean W., Reik W. Epigenetic reprogramming in mammals. Hum Mol Genet 2005, 14(Spec No 1):R47-R58.
8. Seki Y., Yamaji M., Yabuta Y., Sano M., Shigeta M., Matsui Y., Saga Y., Tachibana M., Shinkai Y., Saitou M. Cellular dynamics associated with the genome-wide epigenetic reprogramming in migrating primordial germ cells in mice. Development 2007, 134:2627-2638.
9. Giepmans B.N., Adams S.R., Ellisman M.H., Tsien R.Y. The fluorescent toolbox for assessing protein location and function. Science 2006, 312:217-224.
10. Chalfie M. GFP: lighting up life. Proc Natl Acad Sci U S A 2009, 106:10073-10080.
11. Kanda T., Sullivan K.F., Wahl G.M. Histone-GFP fusion protein enables sensitive analysis of chromosome dynamics in living mammalian cells. Curr Biol 1998, 8:377-385.
12. Parada L.A., Roix J.J., Misteli T. An uncertainty principle in chromosome positioning. Trends Cell Biol 2003, 13:393-396.
13. Kimura H., Cook P.R. Kinetics of core histones in living human cells: little exchange of H3 and H4 and some rapid exchange of H2B. J Cell Biol 2001, 153:1341-1353.
14. Kimura H. Histone dynamics in living cells revealed by photobleaching. DNA Repair (Amst) 2005, 4:939-950.
15. Esteller M. Cancer epigenomics: DNA methylomes and histone-modification maps. Nat Rev Genet 2007, 8:286-298.
16. Yamagata K., Yamazaki T., Yamashita M., Hara Y., Ogonuki N., Ogura A. Noninvasive visualization of molecular events in the mammalian zygote. Genesis 2005, 43:71-79.
17. Yamazaki T., Yamagata K., Baba T. Time-lapse and retrospective analysis of DNA methylation in mouse preimplantation embryos by live cell imaging. Dev Biol 2007, 304:409-419.
18. Kobayakawa S., Miike K., Nakao M., Abe K. Dynamic changes in the epigenomic state and nuclear organization of differentiating mouse embryonic stem cells. Genes Cells 2007, 12:447-460.
19. Yamagata K., Yamazaki T., Miki H., Ogonuki N., Inoue K., Ogura A., Baba T. Centromeric DNA hypomethylation as an epigenetic signature discriminates between germ and somatic cell lineages. Dev Biol 2007, 312:419-426.
20. Ohki I., Shimotake N., Fujita N., Jee J., Ikegami T., Nakao M., Shirakawa M. Solution structure of the methyl-CpG binding domain of human MBD1 in complex with methylated DNA. Cell 2001, 105:487-497.
21. Tsumura A., Hayakawa T., Kumaki Y., Takebayashi S., Sakaue M., Matsuoka C., Shimotohno K., Ishikawa F., Li E., Ueda H.R., et al. Maintenance of self-renewal ability of mouse embryonic stem cells in the absence of DNA methyltransferases Dnmt1, Dnmt3a and Dnmt3b. Genes Cells 2006, 11:805-814.
22. Wakayama T. Production of cloned mice and ES cells from adult somatic cells by nuclear transfer: how to improve cloning efficiency?. J Reprod Dev 2007, 53:13-26.
23. Okada Y., Yamagata K., Hong K., Wakayama T., Zhang Y. A role for the elongator complex in zygotic paternal genome demethylation. Nature 2010, 463:554-558.
24. Schermelleh L., Spada F., Easwaran H.P., Zolghadr K., Margot J.B., Cardoso M.C., Leonhardt H. Trapped in action: direct visualization of DNA methyltransferase activity in living cells. Nat Methods 2005, 2:751-756.
25. 2+ based on green fluorescent proteins and calmodulin. Nature 1997, 388:882-887.
26. VanEngelenburg S.B., Palmer A.E. Fluorescent biosensors of protein function. Curr Opin Chem Biol 2008, 12:60-65.
27. Aye-Han N.N., Ni Q., Zhang J. Fluorescent biosensors for real-time tracking of post-translational modification dynamics. Curr Opin Chem Biol 2009, 13:392-397.
28. Lin C.W., Ting A.Y. A genetically encoded fluorescent reporter of histone phosphorylation in living cells. Angew Chem Int Ed Engl 2004, 43:2940-2943.
29. Goto H., Tomono Y., Ajiro K., Kosako H., Fujita M., Sakurai M., Okawa K., Iwamatsu A., Okigaki T., Takahashi T., et al. Identification of a novel phosphorylation site on histone H3 coupled with mitotic chromosome condensation. J Biol Chem 1999, 274:25543-25549.
30. Lin C.W., Jao C.Y., Ting A.Y. Genetically encoded fluorescent reporters of histone methylation in living cells. J Am Chem Soc 2004, 126:5982-5983.
31. Brehm A., Tufteland K.R., Aasland R., Becker P.B. The many colours of chromodomains. Bioessays 2004, 26:133-140.
32. Sasaki K., Ito T., Nishino N., Khochbin S., Yoshida M. Real-time imaging of histone H4 hyperacetylation in living cells. Proc Natl Acad Sci U S A 2009, 106:16257-16262.
33. Pivot-Pajot C., Caron C., Govin J., Vion A., Rousseaux S., Khochbin S. Acetylation-dependent chromatin reorganization by BRDT, a testis-specific bromodomain-containing protein. Mol Cell Biol 2003, 23:5354-5365.
34. Llères D., James J., Swift S., Norman D.G., Lamond A.I. Quantitative analysis of chromatin compaction in living cells using FLIM-FRET. J Cell Biol 2009, 187:481-496.
35. Kanno T., Kanno Y., Siegel R.M., Jang M.K., Lenardo M.J., Ozato K. Selective recognition of acetylated histones by bromodomain proteins visualized in living cells. Mol Cell 2004, 13:33-43.
36. Hu C.D., Chinenov Y., Kerppola T.K. Visualization of interactions among bZIP and Rel family proteins in living cells using bimolecular fluorescence complementation. Mol Cell 2002, 9:789-798.
37. Vincenz C., Kerppola T.K. Different polycomb group CBX family proteins associate with distinct regions of chromatin using nonhomologous protein sequences. Proc Natl Acad Sci U S A 2008, 105:16572-16577.
38. Hayashi-Takanaka Y., Yamagata K., Nozaki N., Kimura H. Visualizing histone modifications in living cells: spatiotemporal dynamics of H3 phosphorylation during interphase. J Cell Biol 2009, 187:781-790.
39. Einck L., Bustin M. Inhibition of transcription in somatic cells by microinjection of antibodies to chromosomal proteins. Proc Natl Acad Sci U S A 1983, 80:6735-6739.
40. Johansen K.M., Johansen J. Regulation of chromatin structure by histone H3S10 phosphorylation. Chromosome Res 2006, 14:393-404.
41. Cowell I.G., Aucott R., Mahadevaiah S.K., Burgoyne P.S., Huskisson N., Bongiorni S., Prantera G., Fanti L., Pimpinelli S., Wu R., et al. Heterochromatin, HP1 and methylation at lysine 9 of histone H3 in animals. Chromosoma 2002, 111:22-36.
42. Santos F., Peters A.H., Otte A.P., Reik W., Dean W. Dynamic chromatin modifications characterise the first cell cycle in mouse embryos. Dev Biol 2005, 280:225-236.
43. Hendzel M.J., Wei Y., Mancini M.A., Van Hooser A., Ranalli T., Brinkley B.R., Bazett-Jones D.P., Allis C.D. Mitosis-specific phosphorylation of histone H3 initiates primarily within pericentromeric heterochromatin during G2 and spreads in an ordered fashion coincident with mitotic chromosome condensation. Chromosoma 1997, 106:348-360.
44. McNeil P.L. Incorporation of macromolecules into living cells. Methods Cell Biol 1989, 29:153-173.
45. Andersen D.C., Reilly D.E. Production technologies for monoclonal antibodies and their fragments. Curr Opin Biotechnol 2004, 15:456-462.
46. Hochedlinger K., Plath K. Epigenetic reprogramming and induced pluripotency. Development 2009, 136:509-523.
47. Hamon M.A., Cossart P. Histone modifications and chromatin remodeling during bacterial infections. Cell Host Microbe 2008, 4:100-109.
48. Pantry S.N., Medveczky P.G. Epigenetic regulation of Kaposi's sarcoma-associated herpesvirus replication. Semin Cancer Biol 2009, 19:153-157.
49. Allen M.D., DiPilato L.M., Rahdar M., Ren Y.R., Chong C., Liu J.O., Zhang J. Reading dynamic kinase activity in living cells for high-throughput screening. ACS Chem Biol 2006, 1:371-376.
50. Cortez C.C., Jones P.A. Chromatin, cancer and drug therapies. Mutat Res 2008, 647:44-51.
51. Dahl J.A., Reiner A.H., Collas P. Fast genomic μChIP-chip from 1,000 cells. Genome Biol 2009, 10:R13.