Dynamics and Spatial Genomics of the Nascent Transcriptome by Intron seqFISH

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


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.

Publication types

  • Research Support, N.I.H., Extramural
  • Research Support, Non-U.S. Gov't

MeSH terms

  • Animals
  • Catalytic Domain
  • Cell Line
  • Chromosomes / metabolism
  • Fibroblasts / cytology
  • Fibroblasts / metabolism
  • In Situ Hybridization, Fluorescence / methods*
  • Introns
  • Mice
  • Microscopy, Fluorescence
  • Microscopy, Video
  • Mouse Embryonic Stem Cells / cytology
  • Mouse Embryonic Stem Cells / metabolism
  • RNA Polymerase II / genetics
  • RNA Polymerase II / metabolism
  • RNA, Long Noncoding / genetics
  • RNA, Messenger / genetics
  • Single-Cell Analysis
  • Transcriptome*


  • RNA, Long Noncoding
  • RNA, Messenger
  • RNA Polymerase II