RT Journal Article
SR Electronic
T1 Newly synthesized RNA Sequencing Characterizes Transcription Dynamics in Three Pluripotent States
JF bioRxiv
FD Cold Spring Harbor Laboratory
SP 2021.06.11.448016
DO 10.1101/2021.06.11.448016
A1 Rui Shao
A1 Banushree Kumar
A1 Katja Lidschreiber
A1 Michael Lidschreiber
A1 Patrick Cramer
A1 Simon J. Elsässer
YR 2021
UL http://biorxiv.org/content/early/2021/06/13/2021.06.11.448016.abstract
AB 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.