Genome-wide analysis of the biophysical properties of chromatin and nuclear proteins in living cells with Hi-D.
Cesar Augusto Valades-CruzRoman BarthMarwan AbdellahHaitham A ShabanPublished in: Nature protocols (2024)
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.
Keyphrases
- living cells
- single molecule
- high resolution
- genome wide
- atomic force microscopy
- dna methylation
- fluorescent probe
- gene expression
- high speed
- genome wide analysis
- transcription factor
- dna damage
- primary care
- healthcare
- circulating tumor
- copy number
- mass spectrometry
- lymph node
- physical activity
- molecular dynamics simulations
- electronic health record
- optical coherence tomography
- deep learning
- single cell
- high density
- tandem mass spectrometry
- oxidative stress
- circulating tumor cells
- density functional theory
- genetic diversity