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Dynamics and spatial genomics of the nascent transcriptome in single mESCs by intron seqFISH

Shah, Sheel and Takei, Yodai and Zhou, Wen and Lubeck, Eric and Yun, Jina and Koulena, Noushin and Liaw, Eric J. and Amin, Mina and Cai, Long (2018) Dynamics and spatial genomics of the nascent transcriptome in single mESCs by intron seqFISH. . (Unpublished) https://resolver.caltech.edu/CaltechAUTHORS:20181030-084635585

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Abstract

Recent single cell experiments have revealed significant heterogeneities at the levels of transcription, DNA methylation and chromosome organization in individual cells. However, existing method of profiling mRNAs effectively averages transcriptional dynamics over many hours due to hours-long life time of most mRNAs. To capture the instantaneous activity of the transcriptome that reflects the rapid regulatory changes in cells, we imaged up to 10,421 nascent transcription active sites (TAS) in single mouse embryonic stem cells using seqFISH followed by multiple rounds of single molecule FISH and immunofluorescence. We observed that nascent transcription active sites appear to be distributed on the surface of individual chromosome territories and are dispersed throughout the nucleus. In addition, there are significant variability in the number of active transcription sites in single cells, representing globally more active to quiescent states. These states interconverted on the time scale of 2 hours as determined by a single cell pulse-chase experiment. Thus, transcriptome level seqFISH experiments provide an unprecedented spatial and dynamic view of chromosome organization and global nascent transcription activity in single cells.


Item Type:Report or Paper (Discussion Paper)
Related URLs:
URLURL TypeDescription
https://doi.org/10.1101/339234DOIDiscussion Paper
ORCID:
AuthorORCID
Lubeck, Eric0000-0002-5457-0258
Cai, Long0000-0002-7154-5361
Additional Information:The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY-NC-ND 4.0 International license. bioRxiv preprint first posted online Jun. 5, 2018.
Record Number:CaltechAUTHORS:20181030-084635585
Persistent URL:https://resolver.caltech.edu/CaltechAUTHORS:20181030-084635585
Official Citation:Dynamics and spatial genomics of the nascent transcriptome in single mESCs by intron seqFISH. Sheel Shah, Yodai Takei, Wen Zhou, Eric Lubeck, Jina Yun, Noushin Koulena, Eric J. Liaw, Mina Amin, Long Cai. bioRxiv 339234; doi: https://doi.org/10.1101/339234
Usage Policy:No commercial reproduction, distribution, display or performance rights in this work are provided.
ID Code:90491
Collection:CaltechAUTHORS
Deposited By: Tony Diaz
Deposited On:30 Oct 2018 17:01
Last Modified:03 Oct 2019 20:25

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