Simplicity is the Ultimate Sophistication-Crosstalk of Post-translational Modifications on the RNA Polymerase II

Abstract

The highly conserved C-terminal domain (CTD) of the largest subunit of RNA polymerase II comprises a consensus heptad (Y₁S₂P₃T₄S₅P₆S₇) repeated multiple times. Despite the simplicity of its sequence, the essential CTD domain orchestrates eukaryotic transcription and co-transcriptional processes, including transcription initiation, elongation, and termination, and mRNA processing. These distinct facets of the transcription cycle rely on specific post-translational modifications (PTM) of the CTD, in which five out of the seven residues in the heptad repeat are subject to phosphorylation. A hypothesis termed the "CTD code" has been proposed in which these PTMs and their combinations generate a sophisticated landscape for spatiotemporal recruitment of transcription regulators to Pol II. In this review, we summarize the recent experimental evidence understanding the biological role of the CTD, implicating a context-dependent theme that significantly enhances the ability of accurate transcription by RNA polymerase II. Furthermore, feedback communication between the CTD and histone modifications coordinates chromatin states with RNA polymerase II-mediated transcription, ensuring the effective and accurate conversion of information into cellular responses.

Keywords: RNA polymerase II; crosstalk; histone; phosphorylation; transcription.

Figure 1:

RNA Pol II exhibits different post-translational modifications at various stages of transcription. (a) The CTD is highly phosphorylated at Ser5 at the beginning of transcription. Ser2 gets phosphorylated during the pausing release. At the end of transcription, it is believed that both phosphorylation marks are removed. (b) Sequences of the yeast, Drosophila and human CTD are shown in a heptad-wise manner. Heptads with light blue background are consensus heptads (Sequence - YSPTSPS). Conservation maps for yeast and human CTD are shown using LogOdds Sequence Logo. https://www.ncbi.nlm.nih.gov/CBBresearch/Yu/logoddslogo/ (c) Frames of references for heptads are shown with potential starting residue for each heptad. (d) All mono-phosphorylated heptad possibilities are shown. (e) All bis-phosphorylated heptad possibilities with the total number of combinations are shown.

Figure 2:

Ssu72 dephosphorylates Ser5 of the CTD with the requirement of Pro6 is in the cis configuration. (a) The complex structures of Ssu72 bound to its substrates reveal that the proline residue is always in the cis configuration next to the dephosphorylation sites. (b) Chemical structures of the Isostere homologs mimic proline residues locked in cis or trans configurations. (c) Ssu72 has little activity towards Ser2 of the CTD because the flanking residues would cause steric clashes. (d) Crosstalk of Tyr1 and Ser2 phosphorylation leads to differentiated outcomes in transcription. Tyr1 phosphorylation primes the P-TEFb mediated Ser2 phosphorylation to promote elongation.

Figure 3:

Cross-talks of the identities and PTMs of the 7^th residues with Tyr1. (a) The conserved active sites of c-Abl and ABL2 show a highly positively charged pocket close to the reaction center. Modeling reveals close proximity of the pocket with the binding site of the 7^th residue from the previous repeat. (b) A schematic model of how citrullination of Arg1810 promotes transcription elongation. (c) Favorable electrostatic interactions between the CTD and c-Abl when the 7^th residue has a negatively-charged side chain such as glutamate.

Figure 4:

Crosstalks between the histone code and the CTD code. (a) The phosphorylation states of the CTD regulates histone methylation. (b) crosstalks of the CTD and histone acetylation controls elongation speed and prevents cryptic transcription.