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Topokaryotyping demonstrates single cell variability and stress dependent variations in nuclear envelope associated domains

Anamarija Jurisic, Chloe Robin, Pavel Tarlykov, Lee Siggens, Brigitte Schoell, Anna Jauch, Karl Ekwal, Claus Storgaard Sørensen, Marc Lipinski, Muhammad Shoaib, Vasily Ogryzko
doi: https://doi.org/10.1101/401539
Anamarija Jurisic
1UMR8126, Université Paris-Sud 11, CNRS, Institut de Cancérologie Gustave Roussy, 94805 Villejuif, France
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Chloe Robin
1UMR8126, Université Paris-Sud 11, CNRS, Institut de Cancérologie Gustave Roussy, 94805 Villejuif, France
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Pavel Tarlykov
2National Center for Biotechnology, 01000, Astana, Kazakhstan
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Lee Siggens
3Department of Biosciences and Nutrition, NOVUM, Karolinska Institutet, Huddinge, 141 83, Sweden
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Brigitte Schoell
4Institute of Human Genetics, University of Heidelberg, D-69120, Heidelberg, Germany
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Anna Jauch
4Institute of Human Genetics, University of Heidelberg, D-69120, Heidelberg, Germany
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Karl Ekwal
3Department of Biosciences and Nutrition, NOVUM, Karolinska Institutet, Huddinge, 141 83, Sweden
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Claus Storgaard Sørensen
5Biotech Research and Innovation Centre (BRIC), Faculty of Health and Medical Sciences, University of Copenhagen, Ole Maaløes Vej 5, 2200, Copenhagen N, Denmark
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Marc Lipinski
1UMR8126, Université Paris-Sud 11, CNRS, Institut de Cancérologie Gustave Roussy, 94805 Villejuif, France
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Muhammad Shoaib
1UMR8126, Université Paris-Sud 11, CNRS, Institut de Cancérologie Gustave Roussy, 94805 Villejuif, France
5Biotech Research and Innovation Centre (BRIC), Faculty of Health and Medical Sciences, University of Copenhagen, Ole Maaløes Vej 5, 2200, Copenhagen N, Denmark
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  • For correspondence: muhammad.shoaib@bric.ku.dk
Vasily Ogryzko
1UMR8126, Université Paris-Sud 11, CNRS, Institut de Cancérologie Gustave Roussy, 94805 Villejuif, France
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ABSTRACT

Analysis of large-scale interphase genome positioning with reference to a nuclear landmark has recently been studied using sequencing-based single cell approaches. However, these approaches are dependent upon technically challenging, time consuming and costly high throughput sequencing technologies, requiring specialized bioinformatics tools and expertise. Here, we propose a novel, affordable and robust microscopy-based single cell approach, termed Topokaryotyping, to analyze and reconstruct the interphase positioning of genomic loci relative to a given nuclear landmark, detectable as banding pattern on mitotic chromosomes. This is accomplished by proximity-dependent histone labeling, where biotin ligase BirA fused to nuclear envelope marker Emerin was coexpressed together with Biotin Acceptor Peptide (BAP)-histone fusion followed by (i) biotin labeling, (ii) generation of mitotic spreads, (iii) detection of the biotin label on mitotic chromosomes and (iv) their identification by karyotyping. Using Topokaryotyping, we identified both cooperativity and stochasticity in the positioning of emerin-associated chromatin domains in individual cells. Furthermore, the chromosome-banding pattern showed dynamic changes in emerin-associated domains upon physical and radiological stress. In summary, Topokaryotyping is a sensitive and reliable technique to quantitatively analyze spatial positioning of genomic regions interacting with a given nuclear landmark at the single cell level in various experimental conditions.

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Posted August 27, 2018.
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Topokaryotyping demonstrates single cell variability and stress dependent variations in nuclear envelope associated domains
Anamarija Jurisic, Chloe Robin, Pavel Tarlykov, Lee Siggens, Brigitte Schoell, Anna Jauch, Karl Ekwal, Claus Storgaard Sørensen, Marc Lipinski, Muhammad Shoaib, Vasily Ogryzko
bioRxiv 401539; doi: https://doi.org/10.1101/401539
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Topokaryotyping demonstrates single cell variability and stress dependent variations in nuclear envelope associated domains
Anamarija Jurisic, Chloe Robin, Pavel Tarlykov, Lee Siggens, Brigitte Schoell, Anna Jauch, Karl Ekwal, Claus Storgaard Sørensen, Marc Lipinski, Muhammad Shoaib, Vasily Ogryzko
bioRxiv 401539; doi: https://doi.org/10.1101/401539

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