Transcriptomics

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Unique nascent transcriptomes define naïve, primed and paused embryonic pluripotent states.


ABSTRACT: Unique transcriptomes define naïve, primed and paused embryonic pluripotent states. Here we perform calibrated transient transcription 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 (2i) and paused pluripotency (mTORi). We demonstrate that elongation speed can be reliably estimated from TT-seq nascent RNA and RNA Polymerase II occupancy levels, and observe a transcriptome-wide attenuation of elongation speeds in these two inhibitor-induced states. Comparing closely related transcriptional states with different elongation speeds, we also discover a relationship between elongation speed and termination read-through distance. Our analysis suggests that steady-state transcriptomes in mouse ESC cells are controlled predominantly on the level of RNA synthesis and signaling pathways governing different pluripotent states directly control key parameters of transcription.

ORGANISM(S): Mus musculus

PROVIDER: GSE168378 | GEO | 2021/07/28

REPOSITORIES: GEO

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