Transcription elongation by RNA polymerase II

https://doi.org/10.1016/S0959-437X(03)00024-8Get rights and content

Abstract

The elongation of transcripts by RNA polymerase II (RNAPII) is subject to regulation and requires the services of a host of accessory proteins. Although the biochemical mechanisms underlying elongation and its regulation remain obscure, recent progress sets the stage for rapid advancement in our understanding of this phase of transcription. High-resolution crystal structures will allow focused analyses of RNAPII in all its functional states. Several recent studies suggest specific roles for the C-terminal heptad repeats of the largest subunit of RNAPII in elongation. Proteomic approaches are being used to identify new transcription–elongation factors and to define interactions between elongation factors and RNAPII. Finally, a combination of genetic analysis and the localization of factors on transcribed chromatin is being used to confirm a role for factors in elongation.

Introduction

Viewed from the point of view of an RNA polymerase (RNAP), transcription is a cycle of distinct steps: promoter recruitment, initiation, escape, elongation and termination. Although most work on transcription has focused on promoter recruitment and initiation, interest in elongation has grown with the appreciation that it is regulated by and dependent upon accessory factors [1]. In this review, I summarize recent advances in our understanding of transcript elongation by RNAPII.

Section snippets

Structural studies of RNAPII

The multisubunit RNAPs of prokaryotes, eukaryotes and archaea share significant similarity among their core catalytic subunits [2]. High-resolution crystal structures of prokaryotic and eukaryotic RNAPs demonstrate that this homology extends to the structural organization of their catalytic domains. RNAPII is a large (∼550 kDa), highly conserved 12-subunit protein complex. Using a form of yeast RNAPII lacking the Rpb4 and Rpb7 subunits, Kornberg and colleagues were able obtain homogenous

The RNAPII CTD

A unique feature of RNAPII is the CTD, the set of heptapeptide repeats (Y1S2P3T4S5P6S7) found at the C terminus of the large subunit [15]. The CTD is found in all plants, animals and fungi, but in only a subset of other eukaryotes [16]. The CTD may be long — it consists of 26 repeats in yeast and 52 in humans — and therefore extend far from the main body of RNAPII [3••]. The CTD serves as a scaffold for a variety of accessory factors involved in the different phases of transcription and in the

CTD kinases and phosphatases

In yeast, the serine 5 position of the CTD heptad repeats is phosphorylated early in transcription and the CTD is also phosphorylated at serine 2 as RNAPII approaches the 3′ end of a gene [25]. Several protein kinases phosphorylate the CTD and regulate transcription [15]. Among these, positive transcription elongation factor b (P-TEFb) regulates elongation in vitro and in vivo, and is required for the function of the HIV Tat transactivator of elongation. The substrate specificity of P-TEFb has

Accessory factors for transcription elongation

A large and growing number of accessory factors have been found to modulate transcription elongation via several mechanisms. It is reasonable to expect that a bona fide elongation factor will associate with elongating RNAPII as well as with actively transcribed genes and will share genetic interactions with RNAPII and other elongation factors. In several cases, these predictions have now been tested.

Conclusions and perspectives

The determination of the structure of RNAPs has set the stage for the integration of biochemical and structural models of RNAP function and for the careful comparison of data derived from studies of prokaryotic, eukaryotic and archaeal multisubunit RNAPs. As the structures of additional functional states of RNAPII are solved, we will begin to see a moving picture of RNAPII in action. Co-crystallization of RNAPII with its accessory factors and continued biochemical investigation of elongation

Update

In a study by Fischbeck et al. [74], mutations in IWS1/SPN1 are isolated by virtue of their ability to genetically suppress an allele of the TATA binding protein (TBP) component of a general transcription initiation factor TFIID that is defective for some function that occurs after the recruitment of TBP to a promoter. This suggests that Iws1/Spn1 may have a role in initiation as well as in elongation.

Alén et al. [75] show that mutations in the gene encoding the Chd1 chromatin remodeling

References and recommended reading

Papers of particular interest, published within the annual period of review, have been highlighted as:

  • of special interest

  • ••

    of outstanding interest

Acknowledgements

I thank Craig Kaplan and Jennifer Armstrong for their comments on this manuscript. I apologize to colleagues whose work I have not cited due to space limitations. Work in my laboratory is supported by grant GM60479 from the National Institutes of Health and by the University of California Cancer Research Coordinating Committee.

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