Microscopy-based chromosome conformation capture enables simultaneous visualization of genome organization and transcription in intact organisms

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. Cardozo Gizzi et al. developed Hi-M, a multiplexed imaging-based approach to detect 3D chromatin folding in single cells within intact Drosophila embryos. The ability of Hi-M to detect the spatial organization of cells enabled measurement of changes in TAD organization during early embryogenesis and upon transcriptional activation.Fil: Cardozo Gizzi, Andres Mauricio. Instituto Universitario de Ciencias Biomédicas de Córdoba; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentina. Université Montpellier II; FranciaFil: Cattoni, Diego Ignacio. Université Montpellier II; Francia. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Houssay. Instituto de Química y Físico-Química Biológicas "Prof. Alejandro C. Paladini". Universidad de Buenos Aires. Facultad de Farmacia y Bioquímica. Instituto de Química y Físico-Química Biológicas; ArgentinaFil: Fiche, Jean-Bernard. Centre de Biochimie Structurale; FranciaFil: Espínola, Sergio Martín. Centre de Biochimie Structurale; FranciaFil: Gurgo, Julián Roberto. Centre de Biochimie Structurale; FranciaFil: Messina, Olivier. Centre de Biochimie Structurale; FranciaFil: Houbron, Christophe. Centre de Biochimie Structurale; FranciaFil: Ogiyama, Yuki. Institute Of Human Genetics; FranciaFil: Papadopoulos, Giorgio L.. Institute Of Human Genetics; FranciaFil: Cavalli, Giacomo. Institut de Génétique Humaine, Cnrs Umr 9002; Francia. Institute Of Human Genetics; FranciaFil: Lagha, Mounia. Institut de Génétique Moléculaire de Montpellier; FranciaFil: Nollmann, Marcelo. Centre de Biochimie Structurale; Franci