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- Title
Precise measurements of chromatin diffusion dynamics by modeling using Gaussian processes.
- Authors
Oliveira, Guilherme M.; Oravecz, Attila; Kobi, Dominique; Maroquenne, Manon; Bystricky, Kerstin; Sexton, Tom; Molina, Nacho
- Abstract
The spatiotemporal organization of chromatin influences many nuclear processes: from chromosome segregation to transcriptional regulation. To get a deeper understanding of these processes, it is essential to go beyond static viewpoints of chromosome structures, to accurately characterize chromatin's diffusion properties. We present GP-FBM: a computational framework based on Gaussian processes and fractional Brownian motion to extract diffusion properties from stochastic trajectories of labeled chromatin loci. GP-FBM uses higher-order temporal correlations present in the data, therefore, outperforming existing methods. Furthermore, GP-FBM allows to interpolate incomplete trajectories and account for substrate movement when two or more particles are present. Using our method, we show that average chromatin diffusion properties are surprisingly similar in interphase and mitosis in mouse embryonic stem cells. We observe surprising heterogeneity in local chromatin dynamics, correlating with potential regulatory activity. We also present GP-Tool, a user-friendly graphical interface to facilitate usage of GP-FBM by the research community. Although much effort has been devoted to determine the 3D structure of chromatin, there is a need for new experimental and computational methods. Here the authors present GP-FBM to extract chromatin diffusion parameters with high precision and apply it to live-imaging of embryonic stem cells, revealing that the diffusive properties of mitotic and interphase chromatin do not differ significantly.
- Subjects
DIFFUSION measurements; GAUSSIAN processes; CHROMOSOME structure; WIENER processes; CHROMOSOME segregation; CHROMATIN; EMBRYONIC stem cells
- Publication
Nature Communications, 2021, Vol 12, Issue 1, p1
- ISSN
2041-1723
- Publication type
Academic Journal
- DOI
10.1038/s41467-021-26466-7