Biopolym. Cell. 2015; 31(1):72-79.
http://dx.doi.org/10.7124/bc.0008CF
Methods
Topokaryotyping – a proposal for a novel approach to study nuclear organization
1Jurisic A., 1Robin C., 1Ogryzko V.
  1. CNRS UMR 8126, Universit Paris-Sud 11, Institut Gustave Roussy
    114, rue Edouard Vaillant, Villejuif, France, 94805

Abstract

Gene positioning in the nucleus plays an important role in gene activity and genome stability, both in norm and pathology. We propose a new principle for the analysis of the large scale chromatin organization at the single-cell level, termed Topokaryotyping. It is based on coexpression in cells of (i) biotin ligase BirA targeted to a particular intranuclear domain (via its fusion with a protein-marker of this domain) together with (ii) BAP-histone fusion. The application of biotin pulse chase followed by (i) generation of mitotic spreads, (ii) detection of the biotin label and (iii) karyotyping technique to identify the chromosomes should provide information on the association of particular chromosome regions with the nuclear domain under study. We discuss potential advantages of the proposed approach as compared to other methods to study genome topology in the nucleus.
Keywords: chromatin, single-cell analysis, biotinylation, nucleus, genome topology, epigenetics
Full text: (PDF, in English)

References

[1] Saade E, Ogryzko VV. Epigenetics: What it is about? Biopolym Cell. 2014;30(1):3–9.
[2] Cremer T, Cremer M, Dietzel S, M?ller S, Solovei I, Fakan S. Chromosome territories--a functional nuclear landscape. Curr Opin Cell Biol. 2006;18(3):307-16.
[3] Misteli T. Beyond the sequence: cellular organization of genome function. Cell. 2007;128(4):787-800.
[4] Schneider R, Grosschedl R. Dynamics and interplay of nuclear architecture, genome organization, and gene expression. Genes Dev. 2007;21(23):3027-43.
[5] Takizawa T, Meaburn KJ, Misteli T. The meaning of gene positioning. Cell. 2008;135(1):9-13.
[6] Parada L, Misteli T. Chromosome positioning in the interphase nucleus. Trends Cell Biol. 2002;12(9):425-32.
[7] Takizawa T, Gudla PR, Guo L, Lockett S, Misteli T. Allele-specific nuclear positioning of the monoallelically expressed astrocyte marker GFAP. Genes Dev. 2008;22(4):489-98.
[8] Foster HA, Bridger JM. The genome and the nucleus: a marriage made by evolution. Genome organisation and nuclear architecture. Chromosoma. 2005;114(4):212-29.
[9] Borden J, Manuelidis L. Movement of the X chromosome in epilepsy. Science. 1988;242(4886):1687-91.
[10] Meaburn KJ, Cabuy E, Bonne G, Levy N, Morris GE, Novelli G, Kill IR, Bridger JM. Primary laminopathy fibroblasts display altered genome organization and apoptosis. Aging Cell. 2007;6(2):139-53.
[11] Zink D, Fischer AH, Nickerson JA. Nuclear structure in cancer cells. Nat Rev Cancer. 2004;4(9):677-87.
[12] Cremer M, K?pper K, Wagler B, Wizelman L, von Hase J, Weiland Y, Kreja L, Diebold J, Speicher MR, Cremer T. Inheritance of gene density-related higher order chromatin arrangements in normal and tumor cell nuclei. J Cell Biol. 2003;162(5):809-20.
[13] Meaburn KJ, Gudla PR, Khan S, Lockett SJ, Misteli T. Disease-specific gene repositioning in breast cancer. J Cell Biol. 2009;187(6):801-12.
[14] Wiech T, Stein S, Lachenmaier V, Schmitt E, Schwarz-Finsterle J, Wiech E, Hildenbrand G, Werner M, Hausmann M. Spatial allelic imbalance of BCL2 genes and chromosome 18 territories in nonneoplastic and neoplastic cervical squamous epithelium. Eur Biophys J. 2009;38(6):793-806.
[15] Sklyar IV, Iarovaia OV, Lipinski M, Vassetzky YS. Translocations affecting human immunoglobulin heavy chain locus. Biopolym Cell. 2014;30(2):90–5.
[16] Solomon MJ, Larsen PL, Varshavsky A. Mapping protein-DNA interactions in vivo with formaldehyde: evidence that histone H4 is retained on a highly transcribed gene. Cell. 1988;53(6):937-47.
[17] Weinmann AS, Farnham PJ. Identification of unknown target genes of human transcription factors using chromatin immunoprecipitation. Methods. 2002;26(1):37-47.
[18] van Steensel B, Henikoff S. Identification of in vivo DNA targets of chromatin proteins using tethered dam methyltransferase. Nat Biotechnol. 2000;18(4):424-8.
[19] Dekker J, Rippe K, Dekker M, Kleckner N. Capturing chromosome conformation. Science. 2002;295(5558):1306-11.
[20] Dostie J, Richmond TA, Arnaout RA, Selzer RR, Lee WL, Honan TA, Rubio ED, Krumm A, Lamb J, Nusbaum C, Green RD, Dekker J. Chromosome Conformation Capture Carbon Copy (5C): a massively parallel solution for mapping interactions between genomic elements. Genome Res. 2006;16(10):1299-309.
[21] Lieberman-Aiden E, van Berkum NL, Williams L, Imakaev M, Ragoczy T, Telling A, Amit I, Lajoie BR, Sabo PJ, Dorschner MO, Sandstrom R, Bernstein B, Bender MA, Groudine M, Gnirke A, Stamatoyannopoulos J, Mirny LA, Lander ES, Dekker J. Comprehensive mapping of long-range interactions reveals folding principles of the human genome. Science. 2009;326(5950):289-93.
[22] Simonis M, Klous P, Splinter E, Moshkin Y, Willemsen R, de Wit E, van Steensel B, de Laat W. Nuclear organization of active and inactive chromatin domains uncovered by chromosome conformation capture-on-chip (4C). Nat Genet. 2006;38(11):1348-54.
[23] Rao SS, Huntley MH, Durand NC, Stamenova EK, Bochkov ID, Robinson JT, Sanborn AL, Machol I, Omer AD, Lander ES, Aiden EL. A 3D map of the human genome at kilobase resolution reveals principles of chromatin looping. Cell. 2014;159(7):1665-80.
[24] Medema JP. Cancer stem cells: the challenges ahead. Nat Cell Biol. 2013;15(4):338-44.
[25] Langer-Safer PR, Levine M, Ward DC. Immunological method for mapping genes on Drosophila polytene chromosomes. Proc Natl Acad Sci U S A. 1982;79(14):4381-5.
[26] Ried T, Schr?ck E, Ning Y, Wienberg J. Chromosome painting: a useful art. Hum Mol Genet. 1998;7(10):1619-26.
[27] Sharma AK, Sharma A. Chromosome painting - principles, strategies and scope. Methods Cell Sci. 2001;23(1-3):1-5.
[28] Padilla-Nash HM, Barenboim-Stapleton L, Difilippantonio MJ, Ried T. Spectral karyotyping analysis of human and mouse chromosomes. Nat Protoc. 2006;1(6):3129-42.
[29] Geigl JB, Uhrig S, Speicher MR. Multiplex-fluorescence in situ hybridization for chromosome karyotyping. Nat Protoc. 2006;1(3):1172-84.
[30] Carroll D. Genome engineering with zinc-finger nucleases. Genetics. 2011;188(4):773-82.
[31] Urnov FD, Rebar EJ, Holmes MC, Zhang HS, Gregory PD. Genome editing with engineered zinc finger nucleases. Nat Rev Genet. 2010;11(9):636-46.
[32] Sanjana NE, Cong L, Zhou Y, Cunniff MM, Feng G, Zhang F. A transcription activator-like effector toolbox for genome engineering. Nat Protoc. 2012;7(1):171-92.
[33] Mali P, Esvelt KM, Church GM. Cas9 as a versatile tool for engineering biology. Nat Methods. 2013;10(10):957-63.
[34] Viens A, Mechold U, Lehrmann H, Harel-Bellan A, Ogryzko V. Use of protein biotinylation in vivo for chromatin immunoprecipitation. Anal Biochem. 2004;325(1):68-76.
[35] de Boer E, Rodriguez P, Bonte E, Krijgsveld J, Katsantoni E, Heck A, Grosveld F, Strouboulis J. Efficient biotinylation and single-step purification of tagged transcription factors in mammalian cells and transgenic mice. Proc Natl Acad Sci U S A. 2003;100(13):7480-5.
[36] Viens A, Harper F, Pichard E, Comisso M, Pierron G, Ogryzko V. Use of protein biotinylation in vivo for immunoelectron microscopic localization of a specific protein isoform. J Histochem Cytochem. 2008;56(10):911-9.
[37] Mechold U, Gilbert C, Ogryzko V. Codon optimization of the BirA enzyme gene leads to higher expression and an improved efficiency of biotinylation of target proteins in mammalian cells. J Biotechnol. 2005;116(3):245-9.
[38] Roux KJ, Kim DI, Raida M, Burke B. A promiscuous biotin ligase fusion protein identifies proximal and interacting proteins in mammalian cells. J Cell Biol. 2012;196(6):801-10.
[39] Fern?ndez-Su?rez M, Chen TS, Ting AY. Protein-protein interaction detection in vitro and in cells by proximity biotinylation. J Am Chem Soc. 2008;130(29):9251-3.
[40] Kulyyassov A, Shoaib M, Pichugin A, Kannouche P, Ramanculov E, Lipinski M, Ogryzko V. PUB-MS: a mass spectrometry-based method to monitor protein-protein proximity in vivo. J Proteome Res. 2011;10(10):4416-27.
[41] Shoaib M, Kulyyassov A, Robin C, Winczura K, Tarlykov P, Despas E, Kannouche P, Ramanculov E, Lipinski M, Ogryzko V. PUB-NChIP--"in vivo biotinylation" approach to study chromatin in proximity to a protein of interest. Genome Res. 2013;23(2):331-40.
[42] Blower MD, Sullivan BA, Karpen GH. Conserved organization of centromeric chromatin in flies and humans. Dev Cell. 2002;2(3):319-30.
[43] Uttamapinant C, White KA, Baruah H, Thompson S, Fern?ndez-Su?rez M, Puthenveetil S, Ting AY. A fluorophore ligase for site-specific protein labeling inside living cells. Proc Natl Acad Sci U S A. 2010;107(24):10914-9.