Genome-wide analysis of the biophysical properties of chromatin and nuclear proteins in living cells with Hi-D.
Details
Serval ID
serval:BIB_EC86BF4494A6
Type
Article: article from journal or magazin.
Collection
Publications
Institution
Title
Genome-wide analysis of the biophysical properties of chromatin and nuclear proteins in living cells with Hi-D.
Journal
Nature protocols
ISSN
1750-2799 (Electronic)
ISSN-L
1750-2799
Publication state
Published
Issued date
01/2025
Peer-reviewed
Oui
Volume
20
Number
1
Pages
163-179
Language
english
Notes
Publication types: Journal Article ; Review
Publication Status: ppublish
Publication Status: ppublish
Abstract
To understand the dynamic nature of the genome, the localization and rearrangement of DNA and DNA-binding proteins must be analyzed across the entire nucleus of single living cells. Recently, we developed a computational light microscopy technique, called high-resolution diffusion (Hi-D) mapping, which can accurately detect, classify and map diffusion dynamics and biophysical parameters such as the diffusion constant, the anomalous exponent, drift velocity and model physical diffusion from the data at a high spatial resolution across the genome in living cells. Hi-D combines dense optical flow to detect and track local chromatin and nuclear protein motion genome-wide and Bayesian inference to characterize this local movement at nanoscale resolution. Here we present the Python implementation of Hi-D, with an option for parallelizing the calculations to run on multicore central processing units (CPUs). The functionality of Hi-D is presented to the users via user-friendly documented Python notebooks. Hi-D reduces the analysis time to less than 1 h using a multicore CPU with a single compute node. We also present different applications of Hi-D for live-imaging of DNA, histone H2B and RNA polymerase II sequences acquired with spinning disk confocal and super-resolution structured illumination microscopy.
Keywords
Humans, Bayes Theorem, Chromatin/metabolism, Diffusion, DNA/metabolism, DNA/genetics, DNA/chemistry, Nuclear Proteins/metabolism, Nuclear Proteins/genetics, RNA Polymerase II/metabolism
Pubmed
Web of science
Create date
09/09/2024 13:50
Last modification date
21/01/2025 15:25