Hi-M: A Multiplex Oligopaint FISH Method to Capture Chromatin Conformations In Situ and Accompanying Open-Source...

Area of Science:

• Molecular Biology
• Genomics
• Cell Biology

Background:

• Understanding the relationship between 3D chromatin organization and gene transcription is crucial for deciphering cellular processes.
• Existing technologies often lack the ability to simultaneously capture both spatial genome architecture and transcriptional activity at a single-cell level.

Purpose of the Study:

• To introduce and provide a comprehensive guide for the innovative Hi-M technology.
• To enable simultaneous observation of three-dimensional (3D) chromatin structure and transcription in single cells.
• To detail the workflow from probe creation to data acquisition using open-source software.

Main Methods:

• The Hi-M (High-throughput Imaging of multi-omic loci) technology utilizes sequential tagging for 3D visualization and precise localization of genomic regions.
• RNA expression is simultaneously measured within individual cells.
• The process involves specific probe creation, sample preparation, labeling, and acquisition using the Qudi-HiM open-source software package that controls a robotic microscope.

Main Results:

• The study provides a detailed protocol for implementing the Hi-M technique.
• The Qudi-HiM software facilitates the entire acquisition procedure, ensuring precise data collection.
• This enables the simultaneous mapping of genomic loci and gene expression within single cells.

Conclusions:

• Hi-M is an innovative technology that bridges the gap between 3D genome organization and gene expression analysis in single cells.
• The provided guide and open-source software lower the barrier for researchers to adopt this powerful technique.
• This advancement is critical for a deeper understanding of genome regulation and cellular function.