The RNA polymerase II CTD "orphan" residues: Emerging insights into the functions of Tyr-1, Thr-4, and Ser-7

Abstract

The C-terminal domain (CTD) of the RNA polymerase II largest subunit consists of a unique repeated heptad sequence of the consensus Tyr1-Ser2-Pro3-Thr4-Ser5-Pro6-Ser7. An important function of the CTD is to couple transcription with RNA processing reactions that occur during the initiation, elongation, and termination phases of transcription. During this transcription cycle, the CTD is subject to extensive modification, primarily phosphorylation, on its non-proline residues. Reversible phosphorylation of Ser2 and Ser5 is well known to play important and general functions during transcription in all eukaryotes. More recent studies have enhanced our understanding of Tyr1, Thr4, and Ser7, and what have been previously characterized as unknown or specialized functions for these residues has changed to a more fine-detailed map of transcriptional regulation that highlights similarities as well as significant differences between organisms. Here, we review recent findings on the function and modification of these three residues, which further illustrate the importance of the CTD in precisely modulating gene expression.

Keywords: RNA processing; kinases; phosphatases; phosphorylation; transcription.

Figure 1.

Ser7 facilitates mRNA capping in S. pombe and snRNA processing in H. sapiens. (A) In S. pombe, Cdk9 (with cyclin partner Pcm1) binds to CTD Ser7P, and enables the recruitment of 5′ cap methyltransferase Pcm1 to a Ser5P CTD. Ser7 is phosphorylated by TFIIH subunit Cdk7/Mcs6, as well as by Bur1. (B) In H. sapiens, the 12-subunit Integrator complex preferentially recognizes a Ser7P-Ser2P CTD at the 3′ end of snRNA genes. Ser7P recruits RPAP2 to the CTD, which dephosphorylates Ser5P, and Integrator is able to recognize both the Ser7P-Ser2P CTD as well as the 3′ box of the snRNA, enabling cleavage and processing of the snRNA. TFIIH subunit Cdk7 phosphorylates Ser7, while phosphatase Ssu72 has been shown to dephosphorylate Ser7P.

Figure 2.

Divergent functions of Thr4 between S. cerevisiae and H. sapiens. (A) In S. cerevisiae, Thr4P has been shown to recruit the multi-subunit Ino80 chromatin remodeling complex to certain classes of promoters (see text), which evicts the promoter-proximal H2A.Z (red)/H2B (blue) histone dimers. Upon eviction of these dimers and replacement with H2A/H2B dimers, transcription of these genes is enabled. (B) In H. sapiens, histone mRNA synthesis requires Thr4 for efficient 3′ processing. Thr4 is required for recruitment of stem-loop binding protein (SLBP) and CPSF100, required along with other canonical 3′ processing factors such as Symplekin and CPSF73, to replication-dependent histone genes. In S. cerevisiae, histone mRNA 3′ ends are formed identically to all other mRNAs, and evidence shows that instead Thr4P plays a role in post-transcriptional splicing and Rtt103 (and Rat1/Rai1) recruitment during termination. In H. sapiens, Cdk9 and Plk1/Plk3 have been shown to phosphorylate Thr4, the later perhaps specifically in M phase, and Thr4P is dephosphorylated by Fcp1. Neither the kinase(s) nor phosphatase that acts on Thr4 is known in S. cerevisiae.

Figure 3.

Tyr1 has multiple functions across species. (A) At the 5′ ends of genes, Tyr1 in vertebrates is phosphorylated, likely by c-Abl, and Tyr1P is important for efficient turnover of 5′ upstream antisense RNAs (uaRNAs). Tyr1 phosphorylation also enhances stability and prevents degradation of the unstructured CTD by the 23S proteasome in vertebrate cells. In S. cerevisiae, this function has not been described, and Tyr1 phosphorylation (by Slt2 or other unidentified kinases) is associated with antitermination, as it prevents efficient binding of Nrd1 (in yeast) or Rtt103 (yeast and humans) to a Ser5P or Ser2P CTD, respectively. (B) At 3′ ends of genes, CTD Tyr1P is dephosphorylated by Glc7, a subunit of cleavage and polyadenylation factor (CPF). This leads to Ser2P-CTD recognition by Pcf11 and Rtt103/Rat1/Rai1, which facilitates efficient termination. This function appears conserved from yeast to human.