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Newly synthesized RNA Sequencing Characterizes Transcription Dynamics in Three Pluripotent States

Rui Shao, Banushree Kumar, Katja Lidschreiber, View ORCID ProfileMichael Lidschreiber, View ORCID ProfilePatrick Cramer, View ORCID ProfileSimon J. Elsässer
doi: https://doi.org/10.1101/2021.06.11.448016
Rui Shao
1Science for Life Laboratory, Department of Medical Biochemistry and Biophysics, Division of Genome Biology, Karolinska Institutet, Tomtebodavagen 23, 17165 Stockholm, Sweden
2Ming Wai Lau Centre for Reparative Medicine, Stockholm node, Karolinska Institutet, Solnavägen 9, 17165 Stockholm, Sweden
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Banushree Kumar
1Science for Life Laboratory, Department of Medical Biochemistry and Biophysics, Division of Genome Biology, Karolinska Institutet, Tomtebodavagen 23, 17165 Stockholm, Sweden
2Ming Wai Lau Centre for Reparative Medicine, Stockholm node, Karolinska Institutet, Solnavägen 9, 17165 Stockholm, Sweden
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Katja Lidschreiber
3Department of Biosciences and Nutrition, Karolinska Institutet, Neo, 141 83 Huddinge, Sweden
4Department of Molecular Biology, Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, 37077 Göttingen, Germany
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Michael Lidschreiber
3Department of Biosciences and Nutrition, Karolinska Institutet, Neo, 141 83 Huddinge, Sweden
4Department of Molecular Biology, Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, 37077 Göttingen, Germany
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Patrick Cramer
3Department of Biosciences and Nutrition, Karolinska Institutet, Neo, 141 83 Huddinge, Sweden
4Department of Molecular Biology, Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, 37077 Göttingen, Germany
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Simon J. Elsässer
1Science for Life Laboratory, Department of Medical Biochemistry and Biophysics, Division of Genome Biology, Karolinska Institutet, Tomtebodavagen 23, 17165 Stockholm, Sweden
2Ming Wai Lau Centre for Reparative Medicine, Stockholm node, Karolinska Institutet, Solnavägen 9, 17165 Stockholm, Sweden
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  • ORCID record for Simon J. Elsässer
  • For correspondence: simon.elsasser@scilifelab.se
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Abstract

Unique transcriptomes define naïve, primed and paused pluripotent states in mouse embryonic stem cells. Here we perform transient transcriptome sequencing (TT-seq) to de novo define and quantify coding and non-coding transcription units (TUs) in different pluripotent states. We observe a global reduction of RNA synthesis, total RNA amount and turnover rates in ground state naïve cells (2i) and paused pluripotency (mTORi). We demonstrate that elongation velocity can be reliably estimated from TT-seq nascent RNA and RNA polymerase II occupancy and observe a transcriptome-wide attenuation of elongation velocity in the two inhibitor-induced states. We also discover a relationship between elongation velocity and termination read-through distance. Our analysis suggests that steady-state transcriptomes in mouse ES cells are controlled predominantly on the level of RNA synthesis, and that signaling pathways governing different pluripotent states immediately control key parameters of transcription.

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Posted June 13, 2021.
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Newly synthesized RNA Sequencing Characterizes Transcription Dynamics in Three Pluripotent States
Rui Shao, Banushree Kumar, Katja Lidschreiber, Michael Lidschreiber, Patrick Cramer, Simon J. Elsässer
bioRxiv 2021.06.11.448016; doi: https://doi.org/10.1101/2021.06.11.448016
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Newly synthesized RNA Sequencing Characterizes Transcription Dynamics in Three Pluripotent States
Rui Shao, Banushree Kumar, Katja Lidschreiber, Michael Lidschreiber, Patrick Cramer, Simon J. Elsässer
bioRxiv 2021.06.11.448016; doi: https://doi.org/10.1101/2021.06.11.448016

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