Super-resolution chromatin tracing reveals domains and cooperative interactions in single cells

Abstract

The spatial organization of chromatin is pivotal for regulating genome functions. We report an imaging method for tracing chromatin organization with kilobase- and nanometer-scale resolution, unveiling chromatin conformation across topologically associating domains (TADs) in thousands of individual cells. Our imaging data revealed TAD-like structures with globular conformation and sharp domain boundaries in single cells. The boundaries varied from cell to cell, occurring with non-zero probabilities at all genomic positions, but preferentially at CCCTC-binding factor (CTCF)- and cohesin-binding sites. Notably, cohesin depletion, which abolished TADs at the population-average level, did not diminish domain structures in single cells, but eliminated preferential TAD-like boundary positions. Moreover, we observed wide-spread, cooperative, multi-way chromatin interactions, which remained after cohesin depletion. These results provide critical insight into the mechanisms underlying chromatin domain and hub formation.

Nuclear compartmentalization, dynamics, and function of regulatory DNA sequences

“…Hi‐C and other recent methods, such as genome architecture mapping (GAM), split‐pool recognition of interactions by tag extension, and the recently described method of super‐resolution chromatin tracing have allowed the 3D modeling of a hierarchy of genome structures from the level of individual genes to TADs, CTs and entire 3D genomes (Figure D‐F). Most importantly, results of 1D mapping of structurally and functionally relevant proteins distributed along the linear DNA can be immediately integrated into such 3D models.…”

“…A given high‐resolution TAD is related to an average structure of millions of chromatin domains (CDs) with the same DNA sequence. Single cell Hi‐C can provide data on TADs, whose 3D structure can be more directly compared with the 3D structure of individual TADs studied by advanced microscopy, (for review, see References 70 and 73). The greatly reduced number of contacts, which can be identified within the nucleus of an individual cell, however, goes hand in hand with a loss of Hi‐C resolution.…”

Chromatin is frequently unknotted at the megabase scale

“…We analyse here chromosome tracings deposited by Bintu et al (29), The detailed description of the complex Oligopaint method of simultaneous tracing of selected genomic regions in chromosomes within thousands of fixed cells can be found in Bintu et al (29). Here we just briefly describe the principle of the method.…”

“…To probe the knottedness of chromatin at the smaller scale than these probed using single cell Hi-C approach one would need a method that can provide us with the spatial positions of chromatin intervals smaller than 100 kb. Very recently, an exciting new approach has emerged, combining Oligopaint chromatin labelling with high resolution optical imaging in order to determine the position of a series of consecutive loci (29,30). Using this approach, the centroid position of many sequential 30kb-large chromatin loci spanning a 2Mb long chromosomal region were determined with 50 nm accuracy (29).…”

“…Here, we use stochastic closure analysis to determine whether a genomic trajectory is knotted in the setting of realistic experimental noise. We use our method to look for knots in 4727 chromatin tracings generated by Bintu et al, (29) and which are publicly available at https://raw.githubusercontent.com/BogdanBintu/ChromatinImaging/master/Data/IMR90_chr21-28-30Mb.csv. We find that the true topology of the region could be inferred in 243 cases.…”