Simultaneous live imaging of the transcription and nuclear position of specific genes

Nucleic Acids Research

Volumn 43, Issue 19, 2015, Pages e127-

  Ochiai, Hiroshi ^a   Sugawara, Takeshi ^a   Yamamoto, Takashi ^a  

^a HIROSHIMA UNIVERSITY   (Japan)

Author keywords

[No Author keywords available]

Indexed keywords

OCTAMER TRANSCRIPTION FACTOR 4; TRANSCRIPTION FACTOR NANOG; CAPSID PROTEIN; ENDONUCLEASE; GREEN FLUORESCENT PROTEIN; HOMEODOMAIN PROTEIN; HYBRID PROTEIN; NANOG PROTEIN, MOUSE;

ANIMAL CELL; ARTICLE; CONTROLLED STUDY; EMBRYO; GENE; GENE EXPRESSION REGULATION; GENE LOCATION; GENE TARGETING; GENETIC ASSOCIATION; GENETIC PROCEDURES; GENOME ANALYSIS; IMAGING AND DISPLAY; LIVE IMAGING; MOUSE; MOUSE EMBRYONIC STEM CELL; NANOG GENE; NONHUMAN; OCT4 GENE; PRIORITY JOURNAL; REAL TIME OBSERVATION OF LOCALIZATION AND EXPRESSION SYSTEM; SENSITIVITY ANALYSIS; TRANSACTIVATION; TRANSCRIPTION REGULATION; ANIMAL; C57BL MOUSE; CELL CULTURE; CELL NUCLEUS; EMBRYONIC STEM CELL; FLUORESCENCE IMAGING; FLUORESCENCE IN SITU HYBRIDIZATION; GENE EXPRESSION; GENETIC TRANSCRIPTION; GENETICS; METABOLISM; PLURIPOTENT STEM CELL; PROCEDURES;

ANIMALS; CAPSID PROTEINS; CELL NUCLEUS; CELLS, CULTURED; EMBRYONIC STEM CELLS; ENDONUCLEASES; GENE EXPRESSION; GREEN FLUORESCENT PROTEINS; HOMEODOMAIN PROTEINS; IN SITU HYBRIDIZATION, FLUORESCENCE; MICE; MICE, INBRED C57BL; NANOG HOMEOBOX PROTEIN; OPTICAL IMAGING; PLURIPOTENT STEM CELLS; RECOMBINANT FUSION PROTEINS; TRANSCRIPTION, GENETIC;

EID: 84959330720     PISSN: 03051048     EISSN: 13624962     Source Type: Journal    
DOI: 10.1093/nar/gkv624     Document Type: Article

References (51)

1. Dekker,J., Marti-Renom,M.A. and Mirny,L.A. (2013) Exploring the three-dimensional organization of genomes: interpreting chromatin interaction data. Nat. Rev. Genet., 14, 390-403.
2. Dixon,J.R., Selvaraj,S., Yue,F., Kim,A., Li,Y., Shen,Y., Hu,M., Liu,J.S. and Ren,B. (2012) Topological domains in mammalian genomes identified by analysis of chromatin interactions. Nature, 485, 376-380.
3. de Wit,E., Bouwman,B.A.M., Zhu,Y., Klous,P., Splinter,E., Verstegen,M.J.A.M., Krijger,P.H.L., Festuccia,N., Nora,E.P., Welling,M. et al. (2013) The pluripotent genome in three dimensions is shaped around pluripotency factors. Nature, 501, 227-231.
4. Phillips-Cremins,J.E., Sauria,M.E.G., Sanyal,A., Gerasimova,T.I., Lajoie,B.R., Bell,J.S.K., Ong,C.-T., Hookway,T.A., Guo,C., Sun,Y. et al. (2013) Architectural protein subclasses shape 3D organization of genomes during lineage commitment. Cell, 153, 1281-1295.
5. Schoenfelder,S., Sexton,T., Chakalova,L., Cope,N.F., Horton,A., Andrews,S., Kurukuti,S., Mitchell,J.A., Umlauf,D., Dimitrova,D.S. et al. (2010) Preferential associations between co-regulated genes reveal a transcriptional interactome in erythroid cells. Nat. Genet., 42, 53-61.
6. Noordermeer,D., de Wit,E., Klous,P., van de Werken,H., Simonis,M., Lopez-Jones,M., Eussen,B., de Klein,A., Singer,R.H. and de Laat,W. (2011) Variegated gene expression caused by cell-specific long-range DNA interactions. Nat. Cell Biol., 13, 944-951.
7. Nagano,T., Lubling,Y., Stevens,T.J., Schoenfelder,S., Yaffe,E., Dean,W., Laue,E.D., Tanay,A. and Fraser,P. (2014) Single-cell Hi-C reveals cell-to-cell variability in chromosome structure. Nature, 502, 59-64.
8. Giorgetti,L., Galupa,R., Nora,E.P., Piolot,T., Lam,F., Dekker,J., Tiana,G. and Heard,E. (2014) Predictive Polymer Modeling Reveals Coupled Fluctuations in Chromosome Conformation and Transcription. Cell, 157, 950-963.
9. Hocine,S., Raymond,P., Zenklusen,D., Chao,J.A. and Singer,R.H. (2012) Single-molecule analysis of gene expression using two-color RNA labeling in live yeast. Nat. Methods, 10, 119-121.
10. Chen,B., Gilbert,L.A., Cimini,B.A., Schnitzbauer,J., Zhang,W., Li,G.-W., Park,J., Blackburn,E.H., Weissman,J.S., Qi,L.S. et al. (2013) Dynamic imaging of genomic locin living human cells by an optimized CRISPR/Cas system. Cell, 155, 1479-1491.
11. Yusa,K., Rad,R., Takeda,J. and Bradley,A. (2009) Generation of transgene-free induced pluripotent mouse stem cells by the piggyBac transposon. Nat. Methods, 6, 363-369.
12. Shaner,N.C., Lambert,G.G., Chammas,A., Ni,Y., Cranfill,P.J., Baird,M.A., Sell,B.R., Allen,J.R., Day,R.N., Israelsson,M. et al. (2013) A bright monomeric green fluorescent protein derived from Branchiostoma lanceolatum. Nat. Methods, 10, 407-409.
13. Yusa,K., Zhou,L., Li,M.A., Bradley,A. and Craig,N.L. (2011) A hyperactive piggyBac transposase for mammalian applications. Proc. Natl. Acad. Sci. U.S.A., 108, 1531-1536.
14. Koike-Yusa,H., Li,Y., Tan,E.-P., Velasco-Herrera,M.D.C. and Yusa,K. (2014) Genome-wide recessive genetic screening in mammalian cells with a lentiviral CRISPR-guide RNA library. Nat. Biotechnol., 32, 267-273.
15. Ran,F.A., Hsu,P.D., Wright,J., Agarwala,V., Scott,D.A. and Zhang,F. (2013) Genome engineering using the CRISPR-Cas9 system. Nat. Protoc., 8, 2281-2308.
16. Cong,L., Ran,F.A., Cox,D., Lin,S., Barretto,R., Habib,N., Hsu,P.D., Wu,X., Jiang,W., Marraffini,L.A. et al. (2013) Multiplex genome engineering using CRISPR/Cas systems. Science, 339, 819-823.
17. Ochiai,H., Sugawara,T., Sakuma,T. and Yamamoto,T. (2014) Stochastic promoter activation affects Nanog expression variability in mouse embryonic stem cells. Sci. Rep., 4, 7125.
18. Matsuda,T. and Cepko,C.L. (2007) Controlled expression of transgenes introduced by in vivo electroporation. Proc. Natl. Acad. Sci. U.S.A., 104, 1027-1032.
19. Ochiai,H., Miyamoto,T., Kanai,A., Hosoba,K., Sakuma,T., Kudo,Y., Asami,K., Ogawa,A., Watanabe,A., Kajii,T. et al. (2014) TALEN-mediated single-base-pair editing identification of an intergenic mutation upstream of BUB1B as causative of PCS (MVA) syndrome. Proc. Natl. Acad. Sci. U.S.A., 111, 1461-1466.
20. Bolland,D.J., King,M.R., Reik,W., Corcoran,A.E. and Krueger,C. (2013) Robust 3D DNA FISH using directly labeled probes. J. Vis. Exp., doi:10.3791/50587.
21. Carpenter,A.E., Jones,T.R., Lamprecht,M.R., Clarke,C., Kang,I.H., Friman,O., Guertin,D.A., Chang,J.H., Lindquist,R.A., Moffat,J. et al. (2006) CellProfiler: image analysis software for identifying and quantifying cell phenotypes. Genome Biol., 7, R100.
22. Livak,K.J. and Schmittgen,T.D. (2001) Analysis of relative gene expression data using real-time quantitative PCR and the 2(-Delta Delta C(T)) Method. Methods, 25, 402-408.
23. Vazquez,J., Belmont,A.S. and Sedat,J.W. (2001) Multiple regimes of constrained chromosome motion are regulated in the interphase Drosophila nucleus. Curr. Biol., 11, 1227-1239.
24. Berg,H.C. (1993) Random Walks in Biology, Princeton University Press. Princeton, NJ.
25. Carmo-Fonseca,M., Platani,M. and Swedlow,J.R. (2002) Macromolecular mobility inside the cell nucleus. Trends Cell Biol., 12, 491-495.
26. Guenatri,M., Bailly,D., Maison,C. and Almouzni,G. (2004) Mouse centric and pericentric satellite repeats form distinct functional heterochromatin. J. Cell Biol., 166, 493-505.
27. 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.
28. Qi,L.S., Larson,M.H., Gilbert,L.A., Doudna,J.A., Weissman,J.S., Arkin,A.P. and Lim,W.A. (2013) Repurposing CRISPR as an RNA-guided platform for sequence-specific control of gene expression. Cell, 152, 1173-1183.
29. Miyanari,Y. and Torres-Padilla,M.-E. (2012) Control of ground-state pluripotency by allelic regulation of Nanog. Nature, 483, 470-473.
30. Singer,Z.S., Yong,J., Tischler,J., Hackett,J.A., Altinok,A., Surani,M.A., Cai,L. and Elowitz,M.B. (2014) Dynamic heterogeneity and DNA methylation in embryonic stem cells. Mol. Cell, 55, 319-331.
31. Cabal,G.G., Genovesio,A., Rodriguez-Navarro,S., Zimmer,C., Gadal,O., Lesne,A., Buc,H., Feuerbach-Fournier,F., Olivo-Marin,J.-C., Hurt,E.C. et al. (2006) SAGA interacting factors confine sub-diffusion of transcribed genes to the nuclear envelope. Nature, 441, 770-773.
32. Masui,O., Bonnet,I., Le Baccon,P., Brito,I., Pollex,T., Murphy,N., Hupé,P., Barillot,E., Belmont,A.S. and Heard,E. (2011) Live-cell chromosome dynamics and outcome of X chromosome pairing events during ES cell differentiation. Cell, 145, 447-458.
33. Kalmar,T., Lim,C., Hayward,P., Muñoz-Descalzo,S., Nichols,J., Garcia-Ojalvo,J. and Martinez-Arias,A. (2009) Regulated fluctuations in nanog expression mediate cell fate decisions in embryonic stem cells. PLoS Biol., 7, e1000149.
34. Chalut,K.J., Höpfler,M., Lautenschläger,F., Boyde,L., Chan,C.J., Ekpenyong,A., Martinez-Arias,A. and Guck,J. (2012) Chromatin decondensation and nuclear softening accompany nanog downregulation in embryonic stem cells. Biophys. J., 103, 2060-2070.
35. Pagliara,S., Franze,K., McClain,C.R., Wylde,G.W., Fisher,C.L., Franklin,R.J.M., Kabla,A.J., Keyser,U.F. and Chalut,K.J. (2014) Auxetic nuclei in embryonic stem cells exiting pluripotency. Nat. Mater., 13, 638-644.
36. Lawrence,J.B. and Singer,R.H. (1991) Spatial organization of nucleic acid sequences within cells. Semin. Cell Biol., 2, 83-101.
37. Clemson,C.M. and Lawrence,J.B. (1996) Multifunctional compartments in the nucleus: insights from DNA and RNA localization. J. Cell. Biochem., 62, 181-190.
38. Lindhout,B.I., Fransz,P., Tessadori,F., Meckel,T., Hooykaas,P.J.J. and van der Zaal,B.J. (2007) Live cell imaging of repetitive DNA sequences via GFP-tagged polydactyl zinc finger proteins. Nucleic Acids Res., 35, e107.
39. Miyanari,Y., Ziegler-Birling,C. and Torres-Padilla,M.-E. (2013) Live visualization of chromatin dynamics with fluorescent TALEs. Nat. Struct. Biol., 20, 1321-1324.
40. Thanisch,K., Schneider,K., Morbitzer,R., Solovei,I., Lahaye,T., Bultmann,S. and Leonhardt,H. (2014) Targeting and tracing of specific DNA sequences with dTALEs in living cells. Nucleic Acids Res., 42, e38.
41. Ma,H., Reyes-Gutierrez,P. and Pederson,T. (2013) Visualization of repetitive DNA sequences in human chromosomes with transcription activator-like effectors. Proc. Natl. Acad. Sci. U.S.A., 110, 21048-21053.
42. Ma,H., Naseri,A., Reyes-Gutierrez,P., Wolfe,S.A., Zhang,S. and Pederson,T. (2015) Multicolor CRISPR labeling of chromosomal loci in human cells. Proc. Natl. Acad .Sci. U.S.A., 112, 3002-3007.
43. Carroll,D. (2014) Genome engineering with targetable nucleases. Annu. Rev. Biochem., 83, 409-439.
44. Xiong,W., Goverdhana,S., Sciascia,S.A., Candolfi,M., Zirger,J.M., Barcia,C., Curtin,J.F., King,G.D., Jaita,G., Liu,C. et al. (2006) Regulatable gutless adenovirus vectors sustain inducible transgene expression in the brain in the presence of an immune response against adenoviruses. J. Virol., 80, 27-37.
45. Barde,I., Zanta-Boussif,M.A., Paisant,S., Leboeuf,M., Rameau,P., Delenda,C. and Danos,O. (2006) Efficient control of gene expression in the hematopoietic system using a single Tet-on inducible lentiviral vector. Mol. Ther., 13, 382-390.
46. Ying,Y., Yang,X., Zhao,K., Mao,J., Kuang,Y., Wang,Z., Sun,R. and Fei,J. (2015) The Krüppel-associated box repressor domain induces reversible and irreversible regulation of endogenous mouse genes by mediating different chromatin states. Nucleic Acids Res., 43, 1549-1561.
47. García-Cao,M., O'Sullivan,R., Peters,A.H.F.M., Jenuwein,T. and Blasco,M.A. (2004) Epigenetic regulation of telomere length in mammalian cells by the Suv39h1 and Suv39h2 histone methyltransferases. Nat. Genet., 36, 94-99.
48. Kuznetsova,I.S., Prusov,A.N., Enukashvily,N.I. and Podgornaya,O.I. (2005) New types of mouse centromeric satellite DNAs. Chromosome Res., 13, 9-25.
49. Tanenbaum,M.E., Gilbert,L.A., Qi,L.S., Weissman,J.S. and Vale,R.D. (2014) A protein-tagging system for signal amplification in gene expression and fluorescence imaging. Cell, 159, 635-646.
50. Urbanek,M.O., Galka-Marciniak,P., Olejniczak,M. and Krzyzosiak,W.J. (2014) RNA imaging in living cells - methods and applications. RNA Biol., 11, 1083-1095.
51. Das,S., Jena,S. and Levasseur,D.N. (2011) Alternative splicing produces Nanog protein variants with different capacities for self-renewal and pluripotency in embryonic stem cells. J. Biol. Chem., 286, 42690-42703.