Advances in Chromatin Imaging at Kilobase-Scale Resolution

Abstract

HighlightsMicroscopy now allows the measurement of the polymeric structure of chromatin in intact, fixed nuclei, with a resolution of a few kilobases.Multiway contact interactions and physical separation of domains can be probed directly.Structural information can be combined with measurements of nascent transcription, nuclear position, cellular position, and cellular morphology.Single-cell imaging validates many of the features previously identified by bulk, proximity-based approaches, and challenges existing models of chromatin structure.In situ super-resolution imaging offers new potential for multiomic single-cell analyses.

The rich inner life of the cell nucleus: dynamic organization, active flows, and emergent rheology

“…Moreover, HiC identified functional sequence elements, e.g., CTCF, involved in the maintenance of genome folding (Dixon et al 2012 ; Nuebler et al 2018 ). Optical and electron microscopy revealed that chromatin density distribution inside human nuclei is quite heterogeneous (Ou et al 2017 ; Boettiger and Murphy 2020 ; Boopathi et al 2020 ) with major chromatin compartments being euchromatin and heterochromatin (Solovei et al 2016 ; Bonev and Cavalli 2016 ; Van Steensel and Belmont 2017 ). The former represents loosely packed transcriptionally active chromatin, whereas the latter corresponds to more condensed chromatin that houses predominantly silenced genes.…”

Toward understanding the dynamic state of 3D genome

“…This dynamics-based perspective can be used to amend the conventional perspective of the 3D genome organization. Recent advances in super-resolution chromatin imaging of fixed cells have revealed the physical 3D conformations of labeled chromatin domains in a few hundred kb sizes [53] , [54] . Furthermore, super-resolution chromatin tracing reveals TAD-like structures, which are separated globules in single cells, and the sum of the contacts in the 3D conformations is consistent with population-averaged Hi-C data [55] , [56] .…”

“…Although TADs have often been depicted as distinct, separate globules in schematic figures ( Fig. 6A ), it is unclear what is a structural feature of TADs in microscope observations [54] . Interestingly, the snapshots by cryo-electron microscopy (EM) [57] , [58] and EM tomography [59] techniques reveal not distinct chromatin globules but rather irregularly folded chromatin fibers.…”

Navigating the crowd: visualizing coordination between genome dynamics, structure, and transcription

“…However, all sequencing-based methods are by nature invasive and thus make microscopy-based single-cell time course experiments a necessity to understand the dynamic behavior of chromatin. For a comprehensive comparison between different imaging techniques used to studying genome organization and transcription, we refer the reader to recent reviews [8][9][10][11]. In addition, imaging techniques can be multiplexed for simultaneous visualization of a multitude of chromatin constituents and are amenable to highthroughput analysis of genome organization at kilobase resolution [10].…”

“…For a comprehensive comparison between different imaging techniques used to studying genome organization and transcription, we refer the reader to recent reviews [8][9][10][11]. In addition, imaging techniques can be multiplexed for simultaneous visualization of a multitude of chromatin constituents and are amenable to highthroughput analysis of genome organization at kilobase resolution [10]. While super resolution imaging-based approaches are often performed in fixed cells, time-resolved wholechromatin imaging recently revealed that chromatin moves in a spatially and temporally correlated manner at a nanoscale resolution [12,13].…”