Molecular Cell
Volume 74, Issue 1, 4 April 2019, Pages 212-222.e5
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Microscopy-Based Chromosome Conformation Capture Enables Simultaneous Visualization of Genome Organization and Transcription in Intact Organisms

https://doi.org/10.1016/j.molcel.2019.01.011Get rights and content
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Highlights

  • Hi-M simultaneously reveals 3D chromatin organization and transcriptional activity

  • Hi-M and Hi-C maps agree across several orders of magnitude

  • Chromatin is spatially compacted into TADs after the midblastula transition

  • TAD internal organization dramatically changes upon transcriptional activation

Summary

Eukaryotic chromosomes are organized in multiple scales, from nucleosomes to chromosome territories. Recently, genome-wide methods identified an intermediate level of chromosome organization, topologically associating domains (TADs), that play key roles in transcriptional regulation. However, these methods cannot directly examine the interplay between transcriptional activation and chromosome architecture while maintaining spatial information. Here we present a multiplexed, sequential imaging approach (Hi-M) that permits simultaneous detection of chromosome organization and transcription in single nuclei. This allowed us to unveil the changes in 3D chromatin organization occurring upon transcriptional activation and homologous chromosome unpairing during awakening of the zygotic genome in intact Drosophila embryos. Excitingly, the ability of Hi-M to explore the multi-scale chromosome architecture with spatial resolution at different stages of development or during the cell cycle will be key to understanding the mechanisms and consequences of the 4D organization of the genome.

Keywords

topologically associating domains
genome organization
genome architecture
Drosophila development
fluorescence microscopy
oligopaint
fluorescent in situ hybridization
transcriptional regulation
chromosome conformation capture
chromatin

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Present address: CIQUIBIC (CONICET) – Departamento de Química Biológica Ranwel Caputto, Facultad de Ciencias Químicas, Universidad Nacional de Córdoba, Haya de la Torre y Medina Allende, Ciudad Universitaria, 5000 Córdoba, Argentina

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