De Novo Gene Expression Reconstruction in Space

Lee, Je H. (July 2017) De Novo Gene Expression Reconstruction in Space. Trends in Molecular Medicine, 23 (7). pp. 583-593. ISSN 1471-4914

DOI: 10.1016/j.molmed.2017.05.004


The biological function of a gene often depends on spatial context, and an atlas of transcriptional regulation could be instrumental in defining functional elements across the genome. Despite recent advances in single-cell RNA sequencing and in situ RNA imaging, fundamental barriers limit the speed, genome-wide coverage, and resolution of de novo transcriptome assembly in space. Here, I discuss potential next-generation approaches for the de novo assembly of the transcriptome in space, and propose more efficient methods of detecting long-range spatial variations in gene expression. Finally, I discuss future in situ sequencing chemistries for visualizing biological pathways and processes in tissues so that genomics technologies might be more easily applied to conditions of human health and disease.

Item Type: Paper
Uncontrolled Keywords: gene expression atlas single cell RNA sequencing multiplex single-molecule FISH in situ sequencing FISSEQ
Subjects: bioinformatics > genomics and proteomics > genetics & nucleic acid processing > DNA, RNA structure, function, modification > genes, structure and function > gene expression
Investigative techniques and equipment > assays > RNA-seq
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: July 2017
Date Deposited: 05 Jun 2017 20:31
Last Modified: 05 Nov 2020 21:34
PMCID: PMC5514424
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