Hi-D: nanoscale mapping of nuclear dynamics in single living cells

Abstract

Bulk chromatin motion has not been analyzed at high resolution. We present HiD , a method to quantitatively map dynamics of chromatin and abundant nuclear proteins for every pixel simultaneously over the entire nucleus from fluorescence image series. HiD combines reconstruction of chromatin motion and classification of local diffusion processes by Bayesian inference. We show that DNA dynamics in the nuclear interior are spatially partitioned into 0.3-3-μm domains in a mosaic-like pattern, uncoupled from chromatin compaction. This pattern was remodeled in response to transcriptional activity. HiD can be applied to any dense and bulk structures opening new perspectives towards understanding motion of nuclear molecules.

Coupling chromatin structure and dynamics by live super-resolution imaging

“…However, our data do not reveal a correlation between the anomalous exponent and the time-averaged chromatin density ( fig. S8), in line with our previous results using conventional microscopy (14). Overall, the spatial cross-correlation between chromatin structure and dynamics indicates that the NND between blobs and their mobility stand in a strong mutual, negative relationship.…”

“…Overall, the spatial cross-correlation between chromatin structure and dynamics indicates that the NND between blobs and their mobility stand in a strong mutual, negative relationship. This relationship, however, concerns chromatin density variations at the nanoscale, but not global spatial density variations such as in euchromatin or heterochromatin (14). These results support a model in which regions with high local chromatin density, i.e., larger blobs are more prevalent and are mobile, while small blobs are sparsely distributed and less mobile (Fig.…”

Dynamic nuclear structure emerges from chromatin crosslinks and motors

“…We then use the function below to compute the correlation function: From Ref. [6] we assume the correlation function follows C r (r) =…”

“…This material is ∼ 1 meter of DNA with proteins, forming chromatin, and it is packaged across multiple spatial scales to fit inside a ∼ 10 µm nucleus [1]. Chromatin is highly dynamic; for instance, correlated motion of micron-scale genomic regions over timescales of tens of seconds has been observed in mammalian cell nuclei [2][3][4][5][6]. This correlated motion diminishes both in the absence of ATP and by inhibition of the transcription motor RNA polymerase II, suggesting that motor activity plays a key role [2,3].…”

“…In the shell's center-of-mass frame, the correlation length is decreased, but still larger than in the hard shell simulations (see SM). Interestingly, experiments demonstrating large-scale correlated motion measure chromatin motion with an Eulerian specification (e.g., by particle image velocimetry) and do not subtract off the global center of mass [2,3,6]. However, one experiment noted that they observed drift of the nucleus on a frame-to-frame basis, but considered it negligible over the relevant time scales [3].…”