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  • Dynamics and Spatial Genomics of the Nascent Transcriptome by Intron seqFISH.

Dynamics and Spatial Genomics of the Nascent Transcriptome by Intron seqFISH.

Cell (2018-06-12)
Sheel Shah, Yodai Takei, Wen Zhou, Eric Lubeck, Jina Yun, Chee-Huat Linus Eng, Noushin Koulena, Christopher Cronin, Christoph Karp, Eric J Liaw, Mina Amin, Long Cai
ABSTRACT

Visualization of the transcriptome and the nuclear organization in situ has been challenging for single-cell analysis. Here, we demonstrate a multiplexed single-molecule in situ method, intron seqFISH, that allows imaging of 10,421 genes at their nascent transcription active sites in single cells, followed by mRNA and lncRNA seqFISH and immunofluorescence. This nascent transcriptome-profiling method can identify different cell types and states with mouse embryonic stem cells and fibroblasts. The nascent sites of RNA synthesis tend to be localized on the surfaces of chromosome territories, and their organization in individual cells is highly variable. Surprisingly, the global nascent transcription oscillated asynchronously in individual cells with a period of 2 hr in mouse embryonic stem cells, as well as in fibroblasts. Together, spatial genomics of the nascent transcriptome by intron seqFISH reveals nuclear organizational principles and fast dynamics in single cells that are otherwise obscured.

MATERIALS
Product Number
Brand
Product Description

Sigma-Aldrich
Triton X-100 solution, BioUltra, for molecular biology, ~10% in H2O
Sigma-Aldrich
Triton X-100, laboratory grade
Sigma-Aldrich
Dextran sulfate sodium salt from Leuconostoc spp., for molecular biology, average Mw >500,000 (dextran starting material), contains 0.5-2% phosphate buffer