Modifications of RNA polymerase II are pivotal in regulating gene expression states

Abstract

The regulation of gene expression programmes is essential for the generation of diverse cell types during development and for adaptation to environmental signals. RNA polymerase II (RNAPII) transcribes genetic information and coordinates the recruitment of accessory proteins that are responsible for the establishment of active chromatin states and transcript maturation. RNAPII is post-translationally modified at active genes during transcription initiation, elongation and termination, and thereby recruits specific histone and RNA modifiers. RNAPII complexes are also located at silent genes in promoter-proximal paused configurations that provide dynamic transcriptional regulation downstream from initiation. In embryonic stem cells, silent developmental regulator genes that are repressed by Polycomb are associated with a form of RNAPII that can elongate through coding regions but that lacks the post-translational modifications that are important for coupling RNA synthesis to co-transcriptional maturation. Here, we discuss the mechanisms through which the transcription of silent genes might be dissociated from productive expression, and the sophisticated interplay between the transcriptional machinery, Polycomb repression and RNA processing.

Figure 1

RNA polymerase II phosphorylation during paused, active and poised transcription cycles. RNAPII is depicted at genes with distinct transcriptional states. (A) Hypo-phosphorylated RNAPII is recruited to the promoter, where TFIIH phosphorylates Ser 5 residues. The initiating RNAPII is unstable and could abort transcription after 2–10 nucleotides (top cycle). RNAPII then progresses to the pause site (10–50 nucleotides) where it is halted by negative elongation factors. Recent evidence suggests that all paused genes produce full-length transcripts at low levels (dashed arrows and cross-hatching of RNAPII indicate rare events). (B) At active genes, a fraction of RNAPII probably undergoes pausing. Phosphorylation of Ser 2 residues by P-TEFb allows elongation. At the 3' end of coding regions, RNAPII terminates and dissociates from its full-length transcript and the DNA template. Phosphatases are involved in RNAPII dissociation and recycling. (C) Poised RNAPII becomes phosphorylated at Ser 5 residues. It is not known whether poised RNAPII undergoes abortive cycles of initiation (top cycle) or pausing. The onset of elongation occurs in the absence of Ser 2P and RNA transcripts are produced at low levels. The CTD of poised RNAPII has a configuration (marked by a cross) that is not compatible with antibody 8WG16 binding and might involve as yet undefined CTD modifications or structural changes. CTD, carboxy-terminal domain; PPase, phosphatase; P-TEFb, positive transcription elongation factor b; RNAPII, RNA polymerase II; TFIIH, transcription factor IIH; TSS, transcription start site.

Figure 2

Integration of carboxy-terminal domain modifications with chromatin structure, RNA processing and Polycomb repression. Distinct modifications of the CTD assist in recruiting different chromatin modifying enzymes and RNA processing factors. (A) At active gene promoters, the phosphorylation of RNAPII at Ser 5 (Ser 5P) recruits HMTs to methylate H3K4 and the RNA capping machinery to add an m7G cap to nascent RNAs. Ser 2P creates an elongating polymerase that recruits the HMTs responsible for trimethylation of H3K36 and RNA processing factors. The mRNA, which is released after termination, is stabilized by its cap and poly(A) tail, thereby promoting mRNA transport and protein expression. (B) At poised bivalent promoters, Ser 5P residues recruit H3K4 HMTs and potentially the capping machinery. PRC2-mediated H3K27 trimethylation is also present at the promoters of poised genes, and PRC1-mediated H2AK119 monoubiquitination tracks RNAPII across the gene, preventing gene expression. RNAPII escape from promoter regions occurs in the absence of Ser 2P, which probably explains the lack of H3K36 trimethylation in coding regions. A deficiency of Ser 2P could hinder the recruitment of RNA processing machinery, leading to the degradation of immature transcripts. CTD, carboxy-terminal domain; HMT, histone methyltransferase; m7G, 7-methyl-guanosine; PRC, Polycomb repressive complex; RNAPII, RNA polymerase II.

Figure 3

RNA polymerase II carboxy-terminal domain modifications influence 8WG16 antibody recognition. The CTD of RPB1 comprises 52 repeats of the heptad consensus sequence that is indicated in the figure. Antibody 8WG16 recognizes unphosphorylated Ser 2 residues and has been used as a marker for total RNAPII (that is, all isoforms), on the assumption that not all CTD repeats are simultaneously phosphorylated. However, the detection of RNAPII by 8WG16 is affected by CTD phosphorylation (Doyle et al, 2002; Patturajan et al, 1998; Stock et al, 2007; Xie et al, 2006) and, therefore, the use of this antibody underestimates RNAPII presence. Modifications to the CTD (depicted by different coloured circles) influence its detection, configuration and the factors it recruits. (A) RNAPII is recruited to gene promoters with a hypo-phosphorylated CTD, which is accessible to 8WG16 antibody binding. Promoter escape coincides with phosphorylation of Ser 5 residues and the CTD retains its recognition by 8GW16. (B) RNAPII at active promoters is associated with Ser 5P and Ser 7P. Phosphorylation of Ser 2 residues converts RNAPII into a productively elongating complex. Ser 2P and Ser 7P are refractory to 8WG16 binding within the same heptad (D. Eick, personal communication). As the transcription unit is traversed, Ser 5 phosphorylation diminishes by the action of phosphatases, whereas Ser 2P and Ser 7P increase, thereby obscuring 8WG16 binding sites. (C) Poised RNAPII is highly phosphorylated on Ser 5 residues and shows little (or no) recognition by 8WG16. Additional modifications of CTD residues could obscure 8WG16 binding to poised RNAPII. Alternatively, poised RNAPII could adopt an unusual structure that obscures 8WG16 epitopes, possibly through proline isomerization, which is known to influence CTD conformation. CTD, carboxy-terminal domain; RNAPII, RNA polymerase II; RPB1, RNA polymerase II subunit B1.