Dynamics and Spatial Genomics of the Nascent Transcriptome by Intron seqFISH

• Published in: Cell Vol. 174; no. 2; pp. 363 - 376.e16
• Main Authors: Shah, Sheel, Takei, Yodai, Zhou, Wen, Lubeck, Eric, Yun, Jina, Eng, Chee-Huat Linus, Koulena, Noushin, Cronin, Christopher, Karp, Christoph, Liaw, Eric J., Amin, Mina, Cai, Long
• Format: Journal Article
• Language: English
• Published: United States Elsevier Inc 12-07-2018
• Subjects: Animals; Catalytic Domain; Cell Line; chromosome; Chromosomes - metabolism; Fibroblasts - cytology; Fibroblasts - metabolism; In Situ Hybridization, Fluorescence - methods; intron; Introns; Mice; Microscopy, Fluorescence; Microscopy, Video; Mouse Embryonic Stem Cells - cytology; Mouse Embryonic Stem Cells - metabolism; nascent transcriptome; oscillations; RNA Polymerase II - genetics; RNA Polymerase II - metabolism; RNA, Long Noncoding - genetics; RNA, Messenger - genetics; seqFISH; Single-Cell Analysis; smFISH; transcription; Transcriptome; intron; transcription; nascent transcriptome; chromosome; seqFISH; smFISH; oscillations
• ISSN: 0092-8674; 1097-4172
• DOI: 10.1016/j.cell.2018.05.035

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.
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•Intron seqFISH allows in situ visualization of nascent transcription in single cells•Single-cell nascent transcriptome can distinguish cell types and states•Transcriptionally active loci are positioned at the surface of chromosome territories•Nascent transcriptome oscillates with a 2-hr period asynchronously in many cells
Development of intron seqFISH allows in situ profiling and visualization of nascent transcription at the single-cell level, revealing spatial and temporal features of nascent transcriptome.