Please use this identifier to cite or link to this item: https://doi.org/10.1038/srep42422
Title: Superresolution imaging of nanoscale chromosome contacts
Authors: Wang Y. 
Ratna P.
Shivashankar G.V. 
Keywords: immunoglobulin enhancer binding protein
phosphoprotein
protein binding
serum response factor
signal transducing adaptor protein
transcription factor
Yap protein, mouse
animal
cell line
cell nucleus
chromatin
chromatin immunoprecipitation
chromosome
fluorescence in situ hybridization
genetics
high throughput sequencing
human
metabolism
mouse
procedures
Adaptor Proteins, Signal Transducing
Animals
Cell Line
Cell Nucleus
Chromatin
Chromatin Immunoprecipitation
Chromosomes
High-Throughput Nucleotide Sequencing
Humans
In Situ Hybridization, Fluorescence
Mice
NF-kappa B
Phosphoproteins
Protein Binding
Serum Response Factor
Transcription Factors
Issue Date: 2017
Citation: Wang Y., Ratna P., Shivashankar G.V. (2017). Superresolution imaging of nanoscale chromosome contacts. Scientific Reports 7 : 42422. ScholarBank@NUS Repository. https://doi.org/10.1038/srep42422
Abstract: Co-expression of a specific group of genes requires physical associations among these genes, which form functional chromosomal contacts. While DNA fluorescence in situ hybridization (FISH) pinpoints the localization of genes within the 3D nuclear architecture, direct evidence of physical chromosomal contacts is still lacking. Here, we report a method for the direct visualization of transcription-dependent chromosomal contacts formed in two distinct mechanical states of cells. We prepared open chromatin spreads from isolated nuclei, ensuring 2D rendering of chromosome organization. Superresolution imaging of these chromatin spreads resolved the nanoscale organization of genome contacts. We optimized our imaging method using chromatin spreads from serum+/- cells. We then showed direct visualization of functional gene clusters targeted by YAP (Yes-associated protein) and SRF (Serum response factor) transcription factors. In addition, we showed the association of NF-?B bound gene clusters induced by TNF-? addition. Furthermore, EpiTect ChIP qPCR results showed that these nanoscale clusters were enriched with corresponding transcription factors. Taken together, our method provides a robust platform to directly visualize and study specific genome-wide chromosomal contacts. © 2017 The Author(s).
Source Title: Scientific Reports
URI: https://scholarbank.nus.edu.sg/handle/10635/173942
ISSN: 20452322
DOI: 10.1038/srep42422
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