Hi-M imaging of chromatin architecture in adult Drosophila brain cryosections
Abstract
Hi-M combines fluorescence in situ hybridization (FISH), automated microfluidics, sequential imaging, and computational chromatin tracing to measure the three-dimensional organization of selected genomic regions in single cells. This chapter describes a Hi-M workflow adapted for cryosections of adult Drosophila melanogaster brains, enabling chromatin tracing while preserving tissue architecture and cell identity. The protocol covers Oligopaint library design and amplification, fixation, brain dissection, cryoprotection, cryosectioning, sequential RNA-FISH for cell-type identification, sequential DNA-FISH labeling, automated acquisition, and chromatin trace reconstruction. We also provide practical guidance for experimental design, sample preparation, tissue handling, image acquisition, and data analysis, highlighting critical steps that influence tissue integrity, hybridization efficiency, image registration, barcode detection, and chromatin trace reconstruction. The workflow is readily adaptable to different genomic loci and cell types, providing a robust approach for studying 3D genome organization in intact adult tissues.
Related
- Chromatin states coordinate diurnal gene expression in the Drosophila retina
- Centrosome maintains the integrity of and repairs mature olfactory cilia in adult Drosophila
- The complete gustatory connectome of adult Drosophila reveals how taste guides feeding, foraging, and social behavior
- Epigenome Alterations and 3D Chromatin Architecture Remodeling in Inflammatory Macrophage Activation under Diabetic Conditions
- Mitochondrial genetic effects mediate the response to stress through development, but not adult metabolic rate in Drosophila melanogaster
BibTeX
@misc{youhanna2026imaging,
title = {{Hi-M imaging of chromatin architecture in adult Drosophila brain cryosections}},
author = {Christel Elkhoury Youhanna and Julie Garona and Marie Schaeffer and Christophe Houbron and Jean-Bernard Fiche and Olivier Messina and Marcelo Nollmann},
howpublished = {arXiv},
year = {2026},
month = sep,
doi = {10.48550/arxiv.2609.08776},
eprint = {2609.08776},
archivePrefix = {arXiv},
url = {https://arxiv.org/abs/2609.08776},
}
RIS
TY - UNPB
TI - Hi-M imaging of chromatin architecture in adult Drosophila brain cryosections
AU - Christel Elkhoury Youhanna
AU - Julie Garona
AU - Marie Schaeffer
AU - Christophe Houbron
AU - Jean-Bernard Fiche
AU - Olivier Messina
AU - Marcelo Nollmann
PY - 2026
DA - 2026/09/08
PB - arXiv
DO - 10.48550/arxiv.2609.08776
UR - https://arxiv.org/abs/2609.08776
AB - Hi-M combines fluorescence in situ hybridization (FISH), automated microfluidics, sequential imaging, and computational chromatin tracing to measure the three-dimensional organization of selected genomic regions in single cells. This chapter describes a Hi-M workflow adapted for cryosections of adult Drosophila melanogaster brains, enabling chromatin tracing while preserving tissue architecture and cell identity. The protocol covers Oligopaint library design and amplification, fixation, brain dissection, cryoprotection, cryosectioning, sequential RNA-FISH for cell-type identification, sequential DNA-FISH labeling, automated acquisition, and chromatin trace reconstruction. We also provide practical guidance for experimental design, sample preparation, tissue handling, image acquisition, and data analysis, highlighting critical steps that influence tissue integrity, hybridization efficiency, image registration, barcode detection, and chromatin trace reconstruction. The workflow is readily adaptable to different genomic loci and cell types, providing a robust approach for studying 3D genome organization in intact adult tissues.
ER -