ArticleNature protocols2020
Direct and simultaneous observation of transcription and chromosome architecture in single cells with Hi-M.
Article in Nature protocols, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 17 papers.
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Who cites it
17 citing papers in PubMed, 35 citations in OpenAlex.
- A boundary-defining protein facilitates megabase-scale regulatory chromosomal loop formation inGenes & development · 2025Article
- A guide to studying 3D genome structure and dynamics in the kidney.Nature reviews. Nephrology · 2025Review
- Oligopaint FISH to Study Chromosomal Architecture and Structural Variations.Methods in molecular biology (Clifton, N.J.) · 2025Article
- Multiple allelic configurations govern long-range Shh enhancer-promoter communication in the embryonic forebrain.Molecular cell · 2024Article
- A PRE loop at the dac locus acts as a topological chromatin structure that restricts and specifies enhancer-promoter communication.Nature structural & molecular biology · 2024Article
- pyHiM: a new open-source, multi-platform software package for spatial genomics based on multiplexed DNA-FISH imaging.Genome biology · 2024Article
- Hi-M: A Multiplex Oligopaint FISH Method to Capture Chromatin Conformations In Situ and Accompanying Open-Source Acquisition Software.Methods in molecular biology (Clifton, N.J.) · 2024Article
- 3D chromatin interactions involving Drosophila insulators are infrequent but preferential and arise before TADs and transcription.Nature communications · 2023Article
- Simultaneous profiling of chromatin architecture and transcription in single cells.Nature structural & molecular biology · 2023Article
- Multiple parameters shape the 3D chromatin structure of single nuclei at the doc locus in Drosophila.Nature communications · 2022Article
- Image Observation Study on Improving the Effectiveness of Muscle Strength Training for Sprinters.Scanning · 2022Observational
- Qudi-HiM: an open-source acquisition software package for highly multiplexed sequential and combinatorial optical imaging.Open research Europe · 2022Article
- Transcriptional enhancers and their communication with gene promoters.Cellular and molecular life sciences : CMLS · 2021Review
- Chromatin Organization and Function inCells · 2021Review
- Single-cell imaging of genome organization and dynamics.Molecular systems biology · 2021Review
- Cis-regulatory chromatin loops arise before TADs and gene activation, and are independent of cell fate during early Drosophila development.Nature genetics · 2021Article
- Tracing DNA paths and RNA profiles in cultured cells and tissues with ORCA.Nature protocols · 2021Article
Corrections and comments
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Authors and funding
7 authors at 1 institution in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Simultaneous observation of 3D chromatin organization and transcription at the single-cell level and with high spatial resolution may hold the key to unveiling the mechanisms regulating embryonic development, cell differentiation and even disease. We recently developed Hi-M, a technology that enables the sequential labeling, 3D imaging and localization of multiple genomic DNA loci, together with RNA expression, in single cells within whole, intact Drosophila embryos. Importantly, Hi-M enables simultaneous detection of RNA expression and chromosome organization without requiring sample unmounting and primary probe rehybridization. Here, we provide a step-by-step protocol describing the design of probes, the preparation of samples, the stable immobilization of embryos in microfluidic chambers, and the complete procedure for image acquisition. The combined RNA/DNA fluorescence in situ hybridization procedure takes 4-5 d, including embryo collection. In addition, we describe image analysis software to segment nuclei, detect genomic spots, correct for drift and produce Hi-M matrices. A typical Hi-M experiment takes 1-2 d to complete all rounds of labeling and imaging and 4 additional days for image analysis. This technology can be easily expanded to investigate cell differentiation in cultured cells or organization of chromatin within complex tissues.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.