Updating the CTD Story: From Tail to Epic

Abstract

Eukaryotic RNA polymerase II (RNAPII) not only synthesizes mRNA but also coordinates transcription-related processes via its unique C-terminal repeat domain (CTD). The CTD is an RNAPII-specific protein segment consisting of repeating heptads with the consensus sequence Y(1)S(2)P(3)T(4)S(5)P(6)S(7) that has been shown to be extensively post-transcriptionally modified in a coordinated, but complicated, manner. Recent discoveries of new modifications, kinases, and binding proteins have challenged previously established paradigms. In this paper, we examine results and implications of recent studies related to modifications of the CTD and the respective enzymes; we also survey characterizations of new CTD-binding proteins and their associated processes and new information regarding known CTD-binding proteins. Finally, we bring into focus new results that identify two additional CTD-associated processes: nucleocytoplasmic transport of mRNA and DNA damage and repair.

Figure 1

Revised “phospho-CTD cycle.” (a) (I) For protein-coding genes, RNAPII is recruited to the promoter with an unphosphorylated CTD (IIA form); moreover, it appears that CTD phosphorylation prior to preinitiation complex (PIC) formation has an inhibitory effect on transcription. (II) Upon preinitiation complex formation, the CTD is phosphorylated at the Ser5 (black) and Ser7 (red) positions. (III) During elongation, an increase in Ser2 phosphorylation (green) produces the hyperphosphorylated form of the CTD, which is probably an ensemble of singly, doubly, and triply phosphorylated heptads. (IV) As the polymerase elongates towards the 3′ end of the gene, the activity of Ser5-specific phosphatases decreases the Ser5 phosphorylation levels, while the Ser2 and Ser7 phosphate levels remain largely unchanged. (b) (I) For noncoding genes, RNAPII is also recruited to the promoter with an unphosphorylated CTD (IIA form), and CTD phosphorylation prior to preinitiation complex (PIC) formation seems to inhibit transcription. (II) Upon preinitiation complex formation, the CTD phosphorylation of Ser5 (black) and Ser7 (red) increases. (III) During elongation, Ser2 phosphorylation (green) increases, while Ser7 phosphorylation begins to decline, presumably due to the activity of a yet unidentified Ser7 phosphatase. (IV) At the 3′ end of the gene, the activity of Ser5-specific phosphatases decreases the Ser5 phosphorylation levels, Ser7 phosphorylation levels continue to decrease, and Ser2 phosphate levels remain largely unchanged.

Figure 2

CTD-mediated recruitment of Yra1. Yra1 (possibly in complex with THO and Sub2) does not bind to Ser5P containing CTD and is not observed at high level at the 5′ end of genes. Yra1 is recruited to active genes during elongation when the CTD is doubly phosphorylated on Ser2 and Ser5. As it is not known whether Yra1 can bind both the CTD and TREX, it is modeled in both contexts. Yra1 remains bound to the CTD until the nascent mRNA reaches a certain length or reaches the CTD-bound Yra1; this would avert premature export attempts. At the 3′ end of the gene, Yra1 dissociates from the CTD, either because the phosphorylation pattern changes to predominant Ser2 phosphorylation (in which Yra1 does not bind) or because Yra1 binds the nascent mRNA with higher affinity.