Review
Regulation of transcription elongation by phosphorylation

https://doi.org/10.1016/S0167-4781(02)00457-8Get rights and content

Abstract

The synthesis of mRNA by RNA polymerase II (RNAPII) is a multistep process that is regulated by different mechanisms. One important aspect of transcriptional regulation is phosphorylation of components of the transcription apparatus. The phosphorylation state of RNAPII carboxy-terminal domain (CTD) is controlled by a variety of protein kinases and at least one protein phosphatase. We discuss emerging genetic and biochemical evidence that points to a role of these factors not only in transcription initiation but also in elongation and possibly termination. In addition, we review phosporylation events involving some of the general transcription factors (GTFs) and other regulatory proteins. As an interesting example, we describe the modulation of transcription associated kinases and phosphatase by the HIV Tat protein. We focus on bringing together recent findings and propose a revised model for the RNAPII phosphorylation cycle.

Introduction

Specific and regulated initiation of transcription on protein coding genes requires the assembly of RNA polymerase II (RNAPII), the general transcription factors (GTFs) and the SRB/mediator complex at the promoter [1]. After productive initiation, transcription proceeds into elongation mode and this is accompanied by a partial disassembly of the initiation complex and the formation of an elongation complex that consists of a different set of factors. After transcription termination, the RNAPII enzyme is recycled and transcription reinitiation can occur.

The purpose of this review is to discuss phosphorylation events that occur at various stages of the transcription cycle with a specific emphasis on transcription elongation. One major target of kinases and at least one phosphatase is the RNAPII enzyme itself and we will discuss in detail the various aspects of RNAPII phosphorylation. Strong evidence for the involvement in transcription elongation of some of the transcription-associated kinases and phosphatase(s) comes from genetic studies in yeast. Although much less well characterized, a large number of general transcription initiation and elongation factors, as well as upstream factors that influence the activity of the core transcription complex, are also phosphorylated. We have listed the important phosphoproteins generally involved in transcription by RNAPII and the enzymes that modify them in Table 1 and will discuss them in detail in the course of this review. Finally, we will describe the human immunodeficency virus (HIV)–Tat transcription system, which is a good example for the role of phosphorylation in RNAPII-mediated gene expression.

Section snippets

Phosphorylation of the RNAPII carboxy-terminal domain (CTD) as a regulatory mechanism

Two major forms of RNAPII are found in cells, either hyperphosphorylated (RNAPIIO) or hypophosphorylated (RNAPIIA) on the CTD of its largest subunit [2]. Minor forms of RNAPII with intermediate phosphorylation have been observed under some circumstances and may have specialized roles [3].

The CTD is unique to RNAPII and is not found on either RNAPI or RNAPIII, the two other nuclear RNAPs that otherwise share extensive homology with RNAPII [4]. The CTD consists of heptapeptide repeats with a

Genetic evidence for roles of CTD kinases and CTD phosphatase in transcription elongation

Additional evidence for the involvement of the various transcription-related kinases and phosphatases in transcription elongation comes from genetic experiments in yeast. This complex genetic network is summarized in Table 2. Most of the genetic interactions identified so far are synthetic phenotypes, generally considered a hallmark of overlapping or redundant function [102]. Importantly, a few cases have been described in which the combination of mutated alleles in two different genes leads to

Other phosphorylation events involving the general initiation and elongation factors

Aside from the CTD of RNAPII, a number of factors that are involved in the transcription process are also phosphorylated and therefore might be critical targets for regulatory phosphorylation events. As well as the CTD kinases mentioned above, other phosphorylation targets are the general transcription factors TBP, a central subunit of the TFIID complex, the large subunit of TFIIE and the large subunit of TFIIF. The elongation factors DSIF, Tat-SF1, TFIIS and the coactivator/termination factor

Modulation of transcription associated kinases and phosphatase by the HIV Tat protein

The HIV Tat protein was one of the first eukaryotic regulators shown to enhance elongation by RNAPII. Tat stimulates the transcription of HIV DNA through an interaction with the transactivation response element (TAR) located near the 5′ end of the nascent RNA transcript. In the absence of Tat, predominantly short abortive transcripts are produced, whereas the presence of Tat results in enhanced elongation for RNAPII [141], [142], [143]. Activation of the HIV promoter by Tat requires the CTD in

A revised scenario for RNAPII CTD phosphorylation during the transcription cycle

Since nonspecific promoter-independent transcription in vitro by purified RNAPII is not influenced by phosphorylation of the CTD or the CTD kinase inhibitor DRB, CTD phosphorylation most likely influences only the association of other proteins with the transcription complex [53]. Whereas RNAPII holoenzyme has a hypophosphorylated CTD, it is thought that the phosphorylation of the CTD that occurs at the transition from initiation to elongation probably leads to dissociation of the SRB/mediator

Acknowledgements

We thank J. Archambault and N. Krogan for helpful discussions. M.S.K. was supported by a Human Frontier Science Program Fellowship, and also thanks are due to J. Rine for support. This work was supported by a grant to J.G. from the National Cancer Institute of Canada with funds from the Canadian Cancer Society.

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