Disengaging polymerase: terminating RNA polymerase II transcription in budding yeast

Abstract

Termination of transcription by RNA polymerase II requires two distinct processes: The formation of a defined 3' end of the transcribed RNA, as well as the disengagement of RNA polymerase from its DNA template. Both processes are intimately connected and equally pivotal in the process of functional messenger RNA production. However, research in recent years has elaborated how both processes can additionally be employed to control gene expression in qualitative and quantitative ways. This review embraces these new findings and attempts to paint a broader picture of how this final step in the transcription cycle is of critical importance to many aspects of gene regulation. This article is part of a Special Issue entitled: RNA polymerase II Transcript Elongation.

Fig. 1

Schematic drawing of chromatin environment associated with Pol II transcription. A) Nucleosome free regions (left panel) determine, where Pol II finds access to DNA, establishing transcription units (coloured in green, right panel). B) Co-transcriptional phosphorylation of the Rpb1 CTD influences which proteins can bind to the polymerase. Left panel: CTD phosphorylation.The average is taken over 339 yeast genes of medium length (1,238 ± 300 nt). Only those genes belonging to the 50% most highly expressed genes and that were at least 200 nucleotides away from neighboring genes are considered. Based on results from Michael Lidschreiber and Patrick Cramer . The right panel shows the prevalent phosphorylation form likely to be sensed by Pol II based on the left panel colour coding. C) Some of the proteins bound to the CTD will affect histone modifications. Colour-coded histone modifications characterize distinct regions of transcription units (adapted from [228]).

Fig. 2

3′ end formation signals in yeast. A) Left: CPF/CF specific binding sites are characterised by the AU-rich efficiency element (EE), the A-rich positioning element (PE) and U-rich regions surrounding the cleavage site (upper). Polyadenylation signals of two mRNAs are shown to exemplify the low conservation of the different sequence elements (lower). Right: NRD-dependent terminators, characteristically have 1 to several Nrd1 or Nab3 binding sites, where Nrd1 binding sites have the tendency to cluster, and Nab3 binding sites can occur in isolation (upper). Two RNAs with NRD dependent terminators are shown to exemplify the variation in spacing and composition of Nrd1 and Nab3 binding sites in the RNA sequence (lower). B) Left: Genome wide analysis shows the percent-distribution of the EE (TARYTA) and PE (AAWAAA) elements with respect to the cleavage site (left and middle), as well as a preference for AT richness 40–50 nt upstream of cleavage positions (right) . Due to little conservation and lack of motifs in the sequences surrounding mapped cleavage sites of polyadenylated messages, the nucleotide distribution is depicted as percentages and TGCA are depicted in dark blue, blue, green or red respectively. Right: Nrd1 (left hand side) and Nab3 (right hand side) consensus sequences as identified by genetic screening (Porrua-Fuerte et al. 2012). C) Suggested stoichiometry and organisation of the CPF/CF complex on mRNAs (left) and the NRD-CFI-APT complex on non-coding RNAs (right). Sub-complexes are colour-coded: blue, pink, grey, CPF with the subcomplexes APT (grey) and CFII (blue). Green and red (Hrp1) are CFI. The NRD-CFI-APT complex has not been biochemically purified, but been inferred from genetic studies.

Fig. 3

Posttranslational modifications of 3′ end processing factors. A) Component factors of CPF/CF or NRD that are subject to posttranscriptional modifications and that can influence termination efficiency and choice (red phosphorylation, green ubiquitination, blue methylation). Phosphorylation: Pti1 is possibly phosphorylated and activated as a polyadenylation suppressor in situations that activate nuclear surveillance . Pta1 is, when phosphorylated unable to support polyadenylation . Ubiquitination: Swd2 ubiquitination feeds back on H3K4 di- and tri-methylation establishing a kinetic feedback loop . Methylation: Hrp1 methylation is required for its nuclear export in an intricate network connecting elongation rate, termination and mRNA export involving Npl3 and the THO complex .