Transcription Pausing Regulates Mouse Embryonic Stem Cell Differentiation [GRO-seq]

The pluripotency of embryonic stem cells (ESCs) relies on appropriate responsiveness to developmental cues. Promoter-proximal pausing of RNA polymerase II (Pol II) has been suggested to play a role in keeping genes poised for future activation. To identify the role of Pol II pausing in regulating ESC pluripotency, we have generated mouse ESCs carrying a mutation in the pause-inducing factor SPT5. Consistent with previous in vitro studies showing the pausing deficiency of this mutant SPT5, our genomic analysis reveals genome-wide reduction of paused Pol II in mutant mESCs. Furthermore, we find that genes differentially regulated by mutant SPT5 correlates with distinct chromatin states. Functionally, this pausing-deficient SPT5 disrupts ESC differentiation without affecting self-renewal. Thus, our study uncovers an important role of Pol II pausing in regulating ESC differentiation and also suggests that Pol II pausing can both positively and negatively influence transcription depending on the local chromatin environment.

Dataset features

Information

Specifications

Application:	GRO-seq analysis
Number of samples:	7
Release date:	Dec 8 2017
Last update date:	Nov 20 2018
Access:	Public
Genes:	PDE6D, SUPT5H
Taxon:	Mus musculus
Dataset link	Transcription Pausing Regulates Mouse Embryonic Stem Cell Differentiation [GRO-seq]

Experimental Protocol

using Gro-seq to analyze transcription in wild-type and Spt5 mutant (Spt5V1008D) ESCs

Repositories

GEO

GSE99747

ENA

SRP108750

BioProject

PRJNA389560

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Contact

Xiaoying Bai