RT Journal Article
SR Electronic
T1 Topokaryotyping demonstrates single cell variability and stress dependent variations in nuclear envelope associated domains
JF bioRxiv
FD Cold Spring Harbor Laboratory
SP 401539
DO 10.1101/401539
A1 Jurisic, Anamarija
A1 Robin, Chloe
A1 Tarlykov, Pavel
A1 Siggens, Lee
A1 Schoell, Brigitte
A1 Jauch, Anna
A1 Ekwal, Karl
A1 Sørensen, Claus Storgaard
A1 Lipinski, Marc
A1 Shoaib, Muhammad
A1 Ogryzko, Vasily
YR 2018
UL http://biorxiv.org/content/early/2018/08/27/401539.abstract
AB 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.