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Cell. 2018 Jul 12;174(2):363-376.e16. doi: 10.1016/j.cell.2018.05.035. Epub 2018 Jun 7.

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

Author information

1
Division of Biology and Biological Engineering, Caltech, Pasadena, CA 91125, USA; UCLA-Caltech Medical Scientist Training Program, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA.
2
Division of Biology and Biological Engineering, Caltech, Pasadena, CA 91125, USA.
3
Department of Biochemistry and Molecular Biophysics, Caltech, Pasadena, CA 91125, USA.
4
UCLA-Caltech Medical Scientist Training Program, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA.
5
UC Riverside School of Medicine, University of Riverside, Riverside, CA 92521, USA.
6
Division of Biology and Biological Engineering, Caltech, Pasadena, CA 91125, USA. Electronic address: lcai@caltech.edu.

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.

KEYWORDS:

chromosome; intron; nascent transcriptome; oscillations; seqFISH; smFISH; transcription

PMID:
29887381
PMCID:
PMC6046268
DOI:
10.1016/j.cell.2018.05.035
[Indexed for MEDLINE]
Free PMC Article

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