RNA polymerase II carboxy-terminal domain with multiple connections

Abstract

The largest subunit of eukaryotic RNA polymerase II contains a unique domain at its carboxy-terminus, which is referred to as the carboxy-terminal domain (CTD). The CTD is made up of an evolutionarily conserved heptapeptide repeat (YSPTSPS). Over the past decade, there has been increasing attention on the role of the CTD in transcription regulation in the view of mRNA processing and chromatin remodeling. This paper provides a brief overview of the recent progress in the dynamic changes in CTD phosphorylation and its role in integrating multiple nuclear events.Keywords: carboxy-terminal domain kinase; chromatin; phosphorylation; histones; RNA polymerase II; RNA processing, post-transcriptional IntroductionThe largest subunit of eukaryotic RNA polymerase II (pol II) carboxy-terminal domain (CTD) consists of conserved heptapeptide repeats (Y 1 S 2 P 3 T 4 S 5 P 6 S 7 ) (Dahmus, 1996). Mammalian pol II CTD contains 52 repeats, whereas the yeast Saccharomyces cerevisiae CTD has 26-27. A deletion of the mouse, Drosophila, or yeast CTD is lethal. Therefore, the CTD is essential for the viability of an organism, even though the number of repeats can be reduced.Partial deletions of the CTD result in reduced transcription in vivo, and defective responses to various activators. The CTD acts as a platform to couple the mRNA metabolism and chromatin function to the transcription as it recruits various RNA processing/export and histone modifying factors to the transcription complex (Bentley, 2005;Buratowski, 2005;Phatnani and Greenleaf, 2006). This means that the CTD is very important for organizing various nuclear functions to acquire the proper regulation of gene expression. Those functions often depend on the CTD modification such as phosphorylation. Indeed, the CTD is rich in phosphoacceptor amino acid residues and undergoes reversible phosphorylation during the transcription cycle. Two forms of RNA pol II, which differ in the level of phosphorylation of the CTD, can be distinguished and are believed to have distinct functions in the transcription cycle; RNA pol IIa, with a hypophosphorylated CTD, is the form that assembles into the transcription initiation complexes, whereas pol IIo, with a hyperphosphorylated CTD is associated with the transcription elongation complexes. Phosphorylation occurs mainly at discrete serines (S) within the CTD repeats (S2, S5), which is then recognized by different proteins that interconnect the transcription to various nuclear metabolisms. Accordingly, serine phosphorylation is known as the 'CTD code', in a similar way that the 'histone code' refers to the histone modification (Buratowski, 2003). CTD with the phosphorylation codeEarlier models based on a two-step transcription cycle, in which pol IIa was assembled at the promoter and pol IIo carried out transcription elongation, have evolved to one with a more complex CTD phosphorylation cycle. Different modified forms of pol II dominate different stages of transcription (Komarnisky et al., 2000). Pol II assembled at the promoter is...

Sub1 Globally Regulates RNA Polymerase II C-Terminal Domain Phosphorylation

“…Although the RNAP II CTD is not required for transcription in promoterindependent assays in vitro, it is essential in vivo (50), and it is required for efficient capping, splicing, and cleavage/polyadenylation of pre-mRNAs (15,29,47). In fact, the CTD has been described as a platform that recruits RNA processing/ export and histone-modifying factors to the transcription complex, coupling mRNA metabolism to chromatin function (8, 54).…”

“…Although the RNAP II CTD is not required for transcription in promoterindependent assays in vitro, it is essential in vivo (50), and it is required for efficient capping, splicing, and cleavage/polyadenylation of pre-mRNAs (15,29,47). In fact, the CTD has been described as a platform that recruits RNA processing/ export and histone-modifying factors to the transcription complex, coupling mRNA metabolism to chromatin function (8, 54).The CTD is characterized by repetition of the consensus heptapeptide sequence Tyr-Ser-Pro-Thr-Ser-Pro-Ser, ranging from 26 repeats in yeast to 52 in mammals, which is subjected to highly regulated phosphorylation (14,15,47). Unphosphorylated RNAP II is mostly recruited to the preinitiation complex (PIC) (45), and hyperphosphorylated RNAP II is associated with initiation and elongation complexes (42).…”

“…The CTD is characterized by repetition of the consensus heptapeptide sequence Tyr-Ser-Pro-Thr-Ser-Pro-Ser, ranging from 26 repeats in yeast to 52 in mammals, which is subjected to highly regulated phosphorylation (14,15,47). Unphosphorylated RNAP II is mostly recruited to the preinitiation complex (PIC) (45), and hyperphosphorylated RNAP II is associated with initiation and elongation complexes (42).…”

RNA Polymerase II Phosphorylation and Gene Expression Regulation

“…In fact, a general view is that histone post-translational modifications draw parallel with either positive or negative transcriptional states. Numerous discoveries have led to the idea that such modifications regulate transcription either directly by causing structural changes to chromatin (e.g., histone acetylation) or indirectly by recruiting protein complexes (e.g., histone methylation) [255][256][257]. Therefore, chromatin not only plays an essential role in packaging the DNA, but also in regulating gene expression.…”

“…Serine/threonine phosphorylation of H3 in specific sites also marks activated transcription, and ubiquitination of H2B and H2A are associated with active and repressed transcription, respectively (reviewed by [255][256][257]. All histone modifications are removable by specific enzymes (e.g., histone deacetylases (HDACs), phosphatases, and ubiquitin proteases ( [255][256][257], and references therein). In fact HDACs play important regulatory roles during active transcription [262].…”