RNA polymerase II pausing in development: orchestrating transcription

Abstract

The coordinated regulation of transcriptional networks underpins cellular identity and developmental progression. RNA polymerase II promoter-proximal pausing (Pol II pausing) is a prevalent mechanism by which cells can control and synchronize transcription. Pol II pausing regulates the productive elongation step of transcription at key genes downstream of a variety of signalling pathways, such as FGF and Nodal. Recent advances in our understanding of the Pol II pausing machinery and its role in transcription call for an assessment of these findings within the context of development. In this review, we discuss our current understanding of the molecular basis of Pol II pausing and its function during organismal development. By critically assessing the tools used to study this process we conclude that combining recently developed genomics approaches with refined perturbation systems has the potential to expand our understanding of Pol II pausing mechanistically and functionally in the context of development and beyond.

Keywords: Pol II pausing; development; embryonic stem cells; transcription.

Figure 1.

Stepwise activation of mammalian transcription. (a) Illustration of three steps leading to active gene transcription along with key complexes involved and example profile of nascent transcription levels along the gene body. (b) Illustration of pausing index, a commonly used metric to determine degree of Pol II pausing at a particular gene.

Figure 2.

Paused Pol II interacts with its environment. (a) Loss of NELF results in a destabilized paused complex and consequently can lead to the establishment of a repressive chromatin landscape downstream. (b) Pol II pausing can interact with the PIC upstream and the chromatin landscape downstream through various histone modifiers to maintain or repress gene expression.

Figure 3.

Points of interaction points between cellular signalling pathways and transcription. (a) Signalling cascades can regulate transcription at the level of PIC assembly, enforcement of Pol II pausing or pause-release. (b) Pol II pausing at inactive promoters downstream of signalling pathways can protect chromatin accessibility.

Figure 4.

Proposed model showing how dynamic signalling activity can feed into paused Pol II to encode distinct cell fates. In models where a progenitor is specified to either cell fate A or cell fate B by different levels and/or dynamics of signalling activity, pausing can ‘prime’ the cell fate A gene network. A short temporal pulse of signalling can thus lead to pause-release and activation of gene network A and cell fate A specification. Mutual inhibition of opposing cell fate gene networks allows gene network A to repress cell fate B. Sustained signalling activity is required for sufficient induction of gene network B and establishment of cell fate B.

Figure 5.

A model for synchronous induction of gene expression downstream of a signal mediated by Pol II pausing. Paused Pol II complexes at direct signalling target genes synchronously progress to productive elongation upon the inducing signal. Target genes lacking paused Pol II may have varying dynamics of transcriptional activation due to differences in chromatin accessibility and requirement of PIC assembly resulting in asynchronous induction. Different colours of nascent RNA tracks represent different target genes.

Figure 6.

Proposed model outlining the contribution of Pol II pausing at promoters and enhancers to overall regulation of gene expression. Pol II pausing occurs at gene promoters as well as enhancers in mES cells. At highly expressed genes, paused Pol II is short lived at both promoters and enhancers and has a rapid turnover. In this case, Pol II pausing can be a rate-limiting step for gene expression. However, at minimally expressed genes Pol II pausing may serve necessary roles in preserving expression where it is has a longer half-life. In the absence of Pol II pausing, TF residence time at enhancers can be drastically reduced leading to destabilization and dissociation of the transcriptional complex. Similarly, the transcriptional complex is destabilized at the gene promoter leading to downregulation of expression.