Soft X-Ray Tomography Reveals Gradual Chromatin Compaction and Reorganization during Neurogenesis In Vivo

Gros, Mark A. Le; Clowney, E. Josephine; Magklara, Angeliki; Yen, Angela; Markenscoff-Papadimitriou, Eirene; Colquitt, Bradley M.; Myllys, Markko; Kellis, M; Lomvardas, Stavros; Larabell, Carolyn A.

doi:10.1016/j.celrep.2016.10.060

Cited by 88 publications

(74 citation statements)

References 67 publications

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“…hierarchical fashion during development, with cis interactions being detected first, trans interactions appearing in more differentiated stages and reaching maximum frequency in mOSNs. Interestingly, the gradual increase of compartmentalization is not restricted to OR clusters, since our HMM-based prediction of genomic compartments shows that the total number of distinct compartments increases with differentiation (Extended data Fig.4a, b) consistent with predictions made by soft X-ray tomography studies on these cells 16 .…”

supporting

confidence: 84%

Cell type-specific interchromosomal interactions as a mechanism for transcriptional diversity

Horta

Monahan

Bashkirova

et al. 2018

Preprint

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The eukaryotic genome is partitioned into topologically associated domains (TADs) that assemble into compartments of shared chromatin valance. This architecture is influenced by the physical constraints imposed by the DNA polymer, which restricts DNA interactions predominantly to genomic segments from the same chromosome. Here, we report a dramatic divergence from this pattern of nuclear organization that occurs during the differentiation and specification of mouse olfactory sensory neurons (OSNs). In situ HiC on FAC-sorted OSNs shows that olfactory receptor (OR) genes from numerous chromosomes make frequent, extensive, and highly specific interchromosomal contacts that strengthen with differentiation. Moreover, in terminally differentiated OSNs, >30 intergenic enhancers generate a multi-chromosomal hub that associates only with the single active OR from a pool of ~1400 genes. Our data reveal that interchromosomal interactions can form with remarkable stereotypy between like neurons, generating a regulatory landscape for stochastic, monogenic, and monoallelic gene expression.Mouse ORs are encoded by a family of ~1400 genes that are organized in 69 heterochromatic genomic clusters distributed across most chromosomes. Every mature OSN (mOSN) expresses one OR gene from one allele in a seemingly stochastic fashion 1-3 . Previous work suggested that repressive and activating interchromosomal interactions contribute to the singular OR expression 4-6 . However, these interactions have only been analyzed with the use of biased and low-throughput approaches (3C, 4C, capture HiC, and DNA FISH), which have either limited genomic resolution or restricted genomic coverage. Thus, it remains unknown how prevalent and specific these interactions are, and how they form in relationship to OSN differentiation and OR expression. Moreover, in situ HiC 7 , which reduces the occurrence of non-specific ligation events observed in dilution HiC, revealed that interchromosomal associations between non-repetitive, genic regions are extremely infrequent 8,9 , and only emerge upon depletion of cohesin complexes 10,11 . Thus, to explore the landscape of interchromosomal interactions in a biological system that likely depends on them, and to provide a conclusive answer into whether interchromosomal contacts actually occur with biologically meaningful frequency and specificity, we performed in situ HiC in distinct cell populations of the main olfactory epithelium (MOE).

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supporting

confidence: 84%

Cell type-specific interchromosomal interactions as a mechanism for transcriptional diversity

Horta

Monahan

Bashkirova

et al. 2018

Preprint

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“…Soft X-ray Tomography (SXT 41 ) will be used to visualize the 3D organization of chromatin in nuclei of cells in the native state (cryo-immobilized). SXT will be used to directly measure chromatin compaction, e.g.…”

Section: Research Plansmentioning

confidence: 99%

The 4D nucleome project

Dekker

Belmont

Guttman

et al. 2017

Nature

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Preface The 4D Nucleome Network aims to develop and apply approaches to map the structure and dynamics of the human and mouse genomes in space and time with the goal of gaining deeper mechanistic understanding of how the nucleus is organized and functions. The project will develop and benchmark experimental and computational approaches for measuring genome conformation and nuclear organization, and investigate how these contribute to gene regulation and other genome functions. Validated experimental approaches will be combined with biophysical modeling to generate quantitative models of spatial genome organization in different biological states, both in cell populations and in single cells.

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“…At the chromatin compartment level, our data indicates that heterochromatin has a substantially (more than 2-fold) higher DNA concentration compared to euchromatin, which potentially addresses a perplexing question of the differences in density between euchromatin and heterochromatin with some of the prior studies suggesting that euchromatin is considerably denser than euchromatin while others arguing that the two compartments may have comparable density 19,50,52 . In future studies, precise segmentation of chromatin compartments based on labeling histone markers using correlative 3D optical super resolution and electron microscopy will need to be performed to further improve the measurement of chromatin compartments.…”

Section: Discussionmentioning

confidence: 52%

“…A number of methods have been developed to analyze 3D chromatin structure, including chromatin conformation capture (e.g. Hi-C), neutron scattering, soft x-ray tomography (SXT), and super-resolution microscopy 17,18,19,20,21,22 . These techniques have provided critical insights into the principles of 3D chromatin structure.…”

Section: Introductionmentioning

confidence: 99%

Quantifying Three-dimensional Chromatin Organization Utilizing Scanning Transmission Electron Microscopy: ChromSTEM

Li¹,

Roth²,

Agrawal³

et al. 2019

Preprint

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Chromatin organization over a wide range of length scales plays a critical role in the regulation of gene expression and deciphering these processes requires high-resolution, three-dimensional, quantitative imaging of chromatin structure in vitro. Herein we introduce ChromSTEM, a method which utilizes high angle annular dark field imaging and tomography in scanning transmission electron microscopy in combination with DNA-specific staining for electron microscopy. We utilized ChromSTEM to quantify chromatin structure in cultured cells and tissue biopsies through local DNA distribution and the scaling behavior of chromatin polymer. We observed that chromatin is densely packed with an average volume concentration of over 30% with heterochromatin having a two-fold higher density compared to euchromatin. Chromatin was arranged into spatially well-defined nanoscale packing domains with fractal internal structure and genomic size between 100 and 400 kb, comparable to that of topologically associated domains. The packing domains varied in DNA concentration and fractal dimension and had one of the distinct states of chromatin packing with differential ratio of DNA content to the chromatin volume concentration. Finally, we observed a significant intercellular heterogeneity of chromatin organization even within a genetically uniform cell population, which demonstrates the imperative for high-throughput characterization of chromatin structure at the single cell level.

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Soft X-Ray Tomography Reveals Gradual Chromatin Compaction and Reorganization during Neurogenesis In Vivo

Cited by 88 publications

References 67 publications

Cell type-specific interchromosomal interactions as a mechanism for transcriptional diversity

Cell type-specific interchromosomal interactions as a mechanism for transcriptional diversity

The 4D nucleome project

Quantifying Three-dimensional Chromatin Organization Utilizing Scanning Transmission Electron Microscopy: ChromSTEM

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