Pol II waiting in the starting gates: Regulating the transition from transcription initiation into productive elongation

Laboratory of Molecular Carcinogenesis, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, NC 27709, USA.
Biochimica et Biophysica Acta (Impact Factor: 4.66). 11/2010; 1809(1):34-45. DOI: 10.1016/j.bbagrm.2010.11.001
Source: PubMed


Proper regulation of gene expression is essential for the differentiation, development and survival of all cells and organisms. Recent work demonstrates that transcription of many genes, including key developmental and stimulus-responsive genes, is regulated after the initiation step, by pausing of RNA polymerase II during elongation through the promoter-proximal region. Thus, there is great interest in better understanding the events that follow transcription initiation and the ways in which the efficiency of early elongation can be modulated to impact expression of these highly regulated genes. Here we describe our current understanding of the steps involved in the transition from an unstable initially transcribing complex into a highly stable and processive elongation complex. We also discuss the interplay between factors that affect early transcript elongation and the potential physiological consequences for genes that are regulated through transcriptional pausing.

Download full-text


Available from: Sergei Nechaev, Aug 10, 2014
  • Source
    • "This ordering of functions suggests that distinct CDKs govern discrete " phases " of the transcription cycle through unique sets of substrates, analogous to the way different CDK/cyclin complexes act on targets specific to DNA synthesis (S) phase or mitosis. The canonical function of P-TEFb is to overcome promoter-proximal Pol II pausing induced by the DRB sensitivity-inducing factor (DSIF; a heterodimer of Spt4 and Spt5) and the negative elongation factor (NELF) (Nechaev and Adelman 2011), recruitment of which depends on Cdk7 (Glover-Cutter et al. 2009; Larochelle et al. 2012). The exact molecular mechanism underlying this switch remains to be determined, but, in vitro, Cdk9 phosphorylates both DSIF and NELF (Kim and Sharp 2001; Fujinaga et al. 2004) in addition to the Ser2, Thr4, Ser5, and Ser7 residues of the Pol II CTD (Ramanathan et al. 2001; Glover-Cutter et al. 2009; Hsin et al. 2011). "
    [Show abstract] [Hide abstract]
    ABSTRACT: The transcription cycle of RNA polymerase II (Pol II) is regulated at discrete transition points by cyclin-dependent kinases (CDKs). Positive transcription elongation factor b (P-TEFb), a complex of Cdk9 and cyclin T1, promotes release of paused Pol II into elongation, but the precise mechanisms and targets of Cdk9 action remain largely unknown. Here, by a chemical genetic strategy, we identified ∼ 100 putative substrates of human P-TEFb, which were enriched for proteins implicated in transcription and RNA catabolism. Among the RNA processing factors phosphorylated by Cdk9 was the 5 ′ -to-3 ′ “ torpedo ” exoribonuclease Xrn2, required in transcription termination by Pol II, which we validated as a bona fide P-TEFb substrate in vivo and in vitro. Phosphorylation by Cdk9 or phos- phomimetic substitution of its target residue, Thr439, enhanced enzymatic activity of Xrn2 on synthetic substrates in vitro. Conversely, inhibition or depletion of Cdk9 or mutation of Xrn2-Thr439 to a nonphosphorylatable Ala residue caused phenotypes consistent with inefficient termination in human cells: impaired Xrn2 chromatin localization and increased readthrough transcription of endogenous genes. Therefore, in addition to its role in elongation, P-TEFb regulates termination by promoting chromatin recruitment and activation of a cotranscriptional RNA processing enzyme, Xrn2.
    Preview · Article · Jan 2016 · Genes & development
    • "There is some sequence similarity between the polymerases and some of the accessory factors between all domains (Bartlett et al. 2000; Bell and Jackson 2001), but others have evolved independently. The transition for initiation to elongation can also be a point of control (Nechaev and Adelman 2011) as can termination . RNA polymerase can bind to a promoter and then 'stall' (Core et al. 2008; Muse et al. 2007; Nechaev et al. 2010) through several, different mechanisms (FitzGerald et al. 2006; Hendrix et al. 2008; Li and Gilmour 2013). "
    [Show abstract] [Hide abstract]
    ABSTRACT: The evolution of life from the simplest, original form to complex, intelligent animal life occurred through a number of key innovations. Here we present a new tool to analyze these key innovations by proposing that the process of evolutionary innovation may follow one of three underlying processes, namely a Random Walk, a Critical Path, or a Many Paths process, and in some instances may also constitute a "Pull-up the Ladder" event. Our analysis is based on the occurrence of function in modern biology, rather than specific structure or mechanism. A function in modern biology may be classified in this way either on the basis of its evolution or the basis of its modern mechanism. Characterizing key innovations in this way helps identify the likelihood that an innovation could arise. In this paper, we describe the classification, and methods to classify functional features of modern organisms into these three classes based on the analysis of how a function is implemented in modern biology. We present the application of our categorization to the evolution of eukaryotic gene control. We use this approach to support the argument that there are few, and possibly no basic chemical differences between the functional constituents of the machinery of gene control between eukaryotes, bacteria and archaea. This suggests that the difference between eukaryotes and prokaryotes that allows the former to develop the complex genetic architecture seen in animals and plants is something other than their chemistry. We tentatively identify the difference as a difference in control logic, that prokaryotic genes are by default 'on' and eukaryotic genes are by default 'off.' The Many Paths evolutionary process suggests that, from a 'default off' starting point, the evolution of the genetic complexity of higher eukaryotes is a high probability event.
    No preview · Article · Jul 2015 · Journal of Molecular Evolution
  • Source
    • "Subsequently, this transcription bubble is unwound to approximately 18–25 bases, and a short DNA-RNA hybrid is synthesized. Transcripts of ten or more nucleotides result in promoter escape and stabilization of a mature bubble (Liu et al., 2011; Luse, 2013; Nechaev and Adelman, 2011). The number of nucleotides unwound in a mature bubble is still a matter of debate, since sizes ranging from 8 to 22 nucleotides have been reported for bacterial, archaeal, and eukaryotic polymerases (Fiedler and Timmers, 2001; Naryshkin et al., 2000; Pal et al., 2005). "
    [Show abstract] [Hide abstract]
    ABSTRACT: Notwithstanding numerous published structures of RNA Polymerase II (Pol II), structural details of Pol II engaging a complete nucleic acid scaffold have been lacking. Here, we report the structures of TFIIF-stabilized transcribing Pol II complexes, revealing the upstream duplex and full transcription bubble. The upstream duplex lies over a wedge-shaped loop from Rpb2 that engages its minor groove, providing part of the structural framework for DNA tracking during elongation. At the upstream transcription bubble fork, rudder and fork loop 1 residues spatially coordinate strand annealing and the nascent RNA transcript. At the downstream fork, a network of Pol II interactions with the non-template strand forms a rigid domain with the trigger loop (TL), allowing visualization of its open state. Overall, our observations suggest that "open/closed" conformational transitions of the TL may be linked to interactions with the non-template strand, possibly in a synchronized ratcheting manner conducive to polymerase translocation. Copyright © 2015 Elsevier Inc. All rights reserved.
    Full-text · Article · Jul 2015 · Molecular cell
Show more