Microscopy-Based Chromosome Conformation Capture Enables Simultaneous Visualization of Genome Organization and Transcription in Intact Organisms
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Abstract
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.
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Hi-M combines visualisation of chromatin interactions and transcription in single cells.
“Hi-M is one such technique that combines visualisation of chromatin interactions and transcription in single cells [501, 504].”
From Transcriptional enhancers and their communication with gene promoters (2021) · cites this paper as [501]
Advances in super-resolution imaging enable visualisation of multiple interacting loci to the resolution of a few kilobases in single cells.
“advances in super-resolution imaging (reviewed in [500]) now enable the visualisation of multiple interacting loci to the resolution of a few kilobases in single cells [448, 501–503].”
From Transcriptional enhancers and their communication with gene promoters (2021) · cites this paper as [501]
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Self-citation
- Authors
- Cardozo Gizzi, A. M., Cattoni, D. I., Fiche, J.-B., Espinola, S. M., Gurgo, J., Messina, O., Houbron, C., Ogiyama, Y., Papadopoulos, G. L., Cavalli, G., Lagha, M., & Nollmann, M.
- Affiliations
- Centre National de la Recherche Scientifique (FR)
- ORCID
- Venue
- Molecular Cell
- Publisher
- Elsevier BV
- Published
- 2019-04
- Volume
- 74
- Issue
- 1
- Pages
- 212-222.e5
- ISSN
- 1097-2765 (ISSN-L)
- OpenAlex
- W2895567766
- Cited by
- 258
- References
- 59
- Citations by year
- 2026: 17 · 2025: 31 · 2024: 39 · 2023: 31 · 2022: 29 · 2021: 52 · 2020: 38 · 2019: 20 · 2018: 1
- FWCI
- 10.67
- Type
- journal article
- Language
- en
- Open access
- bronze
- doi.org
- Licence
- Locations
- Molecular Cell (publishedVersion)
- SSRN Electronic Journal (publishedVersion)
- bioRxiv (Cold Spring Harbor Laboratory) (acceptedVersion)
- PubMed (publishedVersion)
- HAL (submittedVersion)
- CONICET Digital (CONICET) (submittedVersion, cc-by-nc-sa)
- Funders
- European Research Council (724429)
- Labex EpiGenMed (ANR-10-LABX-12-01)
- French National Research Agency (ANR-10-INBS-04)
- ERC SyncDev
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Chromatin Dynamics
- Life Sciences › Agricultural and Biological Sciences › Plant Science › Chromosomal and Genetic Variations
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Nuclear Structure and Function
- Keywords
- chromosome conformation capture, topologically associating domains, 3D genome organization, transcriptional activation, zygotic genome activation, Drosophila embryo, chromosome territories
- MeSH terms
- Animals, Cell Cycle, Chromatin, Drosophila melanogaster, Microscopy, Fluorescence, RNA, Transcription, Genetic, Transcriptional Activation, Genome, In Situ Hybridization, Fluorescence, Gene Expression Regulation, Developmental, Chromatin Assembly and Disassembly, Chromosomes, Insect, Single-Cell Analysis, High-Throughput Nucleotide Sequencing
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