Quantitative approaches for investigating the spatial context of gene expression

Area of Science:

• Systems Biology
• Genomics
• Developmental Biology

Background:

• Spatial gene expression provides context for transcriptional regulation during development.
• High-resolution methods like RNA tomography and single-cell RNA-seq with FISH offer indirect 3D views.
• In situ sequencing technologies aim for direct visualization of genetic signatures.

Purpose of the Study:

• To examine principles of modern in situ and single-cell genetic methods.
• To identify challenges in quantifying forces influencing cell decision-making.
• To outline technological needs for a visual gene regulation map.

Main Methods:

• Review of in situ sequencing technologies (e.g., FISSEQ).
• Discussion of single-cell RNA sequencing (scRNA-seq) combined with Fluorescence In Situ Hybridization (FISH).
• Exploration of RNA tomography for spatial gene expression analysis.

Main Results:

• In situ sequencing enables direct visualization of genetic signatures in microscope images.
• Challenges exist in quantifying intrinsic and extrinsic factors affecting cell fate.
• Technological advancements are needed for comprehensive gene regulation mapping.

Conclusions:

• Direct visualization of gene expression is advancing through in situ sequencing.
• Overcoming quantification hurdles is key for understanding cell decision-making.
• Developing visual maps of gene regulation is essential for studying evolution during development and disease.