Quantitative approaches for investigating the spatial context of gene expression

Lee, J. H. (March 2017) Quantitative approaches for investigating the spatial context of gene expression. Wiley Interdiscip Rev Syst Biol Med, 9 (2). ISSN 1939-005X (Electronic)1939-005X (Linking)

URL: https://www.ncbi.nlm.nih.gov/pubmed/28001340
DOI: 10.1002/wsbm.1369


The spatial information associated with gene expression is important for elucidating the context-dependent transcriptional regulation during development. Recently, high-resolution sampling approaches, such as RNA tomography or single-cell RNA-seq combined with fluorescence in situ hybridization (FISH), have provided indirect ways to view global gene expression patterns in three dimensions. Now in situ sequencing technologies, such as fluorescent in situ sequencing (FISSEQ), are attempting to visualize the genetic signature directly in microscope images. This article will examine the basic principle of modern in situ and single-cell genetic methods, hurdles in quantifying intrinsic and extrinsic forces that influence cell decision-making, and technological requirements for making a visual map of gene regulation, form, and function. Successfully addressing these challenges will be essential for investigating the functional evolution of regulatory sequences during growth, development, and cancer progression. For further resources related to this article, please visit the WIREs website.

Item Type: Paper
Subjects: Investigative techniques and equipment
bioinformatics > genomics and proteomics > genetics & nucleic acid processing > DNA, RNA structure, function, modification > genes, structure and function > gene expression
CSHL Authors:
Communities: CSHL Cancer Center Program > Cancer Genetics
CSHL labs > Lee lab
Northwell Health
CSHL Cancer Center Program > Cancer Genetics and Genomics Program
Depositing User: Matt Covey
Date: March 2017
Date Deposited: 04 Jan 2017 15:36
Last Modified: 05 Nov 2020 21:34
PMCID: PMC5315614
Related URLs:
URI: https://repository.cshl.edu/id/eprint/33953

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