Transcription elongation by RNA polymerase II
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:
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of special interest
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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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Cited by (40)
Arabidopsis thaliana PRP40s are RNA polymerase II C-terminal domain-associating proteins
2009, Archives of Biochemistry and BiophysicsCitation Excerpt :The CTD is phosphorylated by TFIIH at Ser5 early in transcription elongation, but is dephosphorylated at Ser5 and hyper-phosphorylated at Ser2 during productive transcription elongation [5]. Studies of CTD functions in fungi and metazoans have illuminated the role of the CTD as a structurally plastic “landing pad” for proteins that regulate transcription and co-transcriptional mRNA processing [6]. The CTD is highly hydrophilic and unstructured in an aqueous solution [7].
Transcription elongation through a chromatin template
2007, BiochimieCitation Excerpt :Indeed, transcription on chromatin complex is slower in vitro than in vivo, and also slower than on naked DNA templates in vitro, probably because enhancement of pausing [18–20]. Elongation raises in fact many questions, some of the most puzzling being the way RNA polymerase progresses along chromatin template (reviewed in [21]), the subsequent fate of nucleosomes [22,23] and the need for numerous elongation factors (including ATP-dependent remodeling factors, histone chaperones and histone modification enzymes; see [24–26] for reviews and Fig. 2D) as well as topoisomerase activity [27–34] (see Fig. 2F). Also poorly documented is the question whether polymerase moves/rotates along DNA or DNA moves/rotates along a fixed polymerase [35].
Phasing RNA Polymerase II Using Intrinsically Bound Zn Atoms: An Updated Structural Model
2006, StructureCitation Excerpt :For the Pol II system, this limitation of phasing power worsens for cocrystals between the polymerase and associated factor(s), particularly for factors that represent greater than 20% of the total mass of Pol II (P.A.M. and J.F., unpublished data). As novel cocrystals of subassemblies are being produced for the Pol II machinery (which consists of 5–6 protein factors in its basal apparatus and several tens of factors in its various regulated complexes; Hartzog, 2003; Kornberg, 1999; Roeder, 1996; Shilatifard, 2004), this phasing problem will become a general rate-limiting step of crystallographic investigation. Therefore, strategies for generating experimental phases will be critical for solving various complex structures of Pol II and its regulatory factors.
P-TEFb-mediated phosphorylation of hSpt5 C-terminal repeats is critical for processive transcription elongation
2006, Molecular CellCitation Excerpt :These findings suggest that a postassembly step, perhaps transcription elongation, is rate limiting and important for transcriptional regulation. We and others have shown biochemically that transcription elongation is controlled both positively and negatively by a number of transcription elongation factors (reviewed in Conaway et al. [2000] and Hartzog [2003]). Among these, DSIF and NELF bind to RNA Pol II together and repress transcription elongation in the promoter-proximal region (Wada et al., 1998a; Yamaguchi et al., 1999a).