RNA polymerase II speed: a key player in controlling and adapting transcriptome composition

Abstract

RNA polymerase II (RNA Pol II) speed or elongation rate, i.e., the number of nucleotides synthesized per unit of time, is a major determinant of transcriptome composition. It controls co-transcriptional processes such as splicing, polyadenylation, and transcription termination, thus regulating the production of alternative splice variants, circular RNAs, alternatively polyadenylated transcripts, or read-through transcripts. RNA Pol II speed itself is regulated in response to intra- and extra-cellular stimuli and can in turn affect the transcriptome composition in response to these stimuli. Evidence points to a potentially important role of transcriptome composition modification through RNA Pol II speed regulation for adaptation of cells to a changing environment, thus pointing to a function of RNA Pol II speed regulation in cellular physiology. Analyzing RNA Pol II speed dynamics may therefore be central to fully understand the regulation of physiological processes, such as the development of multicellular organisms. Recent findings also raise the possibility that RNA Pol II speed deregulation can be detrimental and participate in disease progression. Here, we review initial and current approaches to measure RNA Pol II speed, as well as providing an overview of the factors controlling speed and the co-transcriptional processes which are affected. Finally, we discuss the role of RNA Pol II speed regulation in cell physiology.

Keywords: RNA polymerase II; co-transcriptional processes; transcription speed.

Figure 1. Main regulated steps of the RNA Pol II transcription cycle

The RNA Pol II transcription cycle can be divided into four main regulated steps. First, transcription initiation starts with recruitment of RNA Pol II to the promoter and assembly of the pre‐initiation complex (PIC) which is composed of many factors including, but not restricted to, the general transcription factors TFIIA (IIA), TFIIB (IIB), TFIID (IID), TFIIE (IIE), TFIIF (IIF), TFIIH (IIH), RNA Pol II, and Mediator. The PIC opens the DNA and RNA Pol II starts transcription. Shortly after transcription initiation, RNA Pol II enters a paused state known as promoter‐proximal pausing. Promoter‐proximal pausing involves a conformational change in the RNA:DNA hybrid in the polymerase active site that prevents the addition of incoming NTPs by canonical base pairing. In many metazoans, the negative elongation factors NELF (Negative elongation factor) and DSIF (DRB‐sensitivity inducing factor) stabilize and extend the lifetime of the paused complex. After its release from promoter‐proximal pausing, RNA Pol II enters into productive elongation. During productive transcription elongation, many factors travel with RNA Pol II and help coordinate pre‐mRNA processing with transcription. These factors include elongation factors (EF, represented by an orange oval) and splicing factors (SF, represented by a green oval). The term transcription elongation includes at least two regulated processes: RNA Pol II processivity, i.e., the ability of RNA Pol II to travel the entire length of the gene and transcription speed, defined as the number of nucleotides synthesized per unit of time. Finally, transcription termination involves poly(A) site recognition by the cleavage and polyadenylation complex which cleaves the nascent pre‐mRNA that is then polyadenylated (A_n). Transcription of the poly(A) site induces an elongation slow‐down which promotes transcription termination upon catch‐up of RNA Pol II by the exonuclease Xrn2, which degrades the RNA synthesized beyond the poly(A) site from its 3′ end.

Figure 2. Co‐transcriptional processes regulated by RNA Pol II speed

RNA Pol II speed can influence the following:

1. Splicing‐related processes such as constitutive splicing, alternative splicing, and back‐splicing;

2. The RNA methylome by controlling the deposition of N⁶‐methyladenosine in RNAs;

3. Normal 3′ end processing of replication‐dependent core histone mRNAs by controlling the folding of nascent RNA at histone genes;

4. Termination‐related processes such as alternative polyadenylation (represented by two poly(A) sites) and the distance traveled by RNA Pol II beyond the poly(A) site, i.e., read‐through transcription;

5. Protein modifications on gene bodies: post‐translational modifications of RNA Pol II CTD such as serine 2 phosphorylation and chromatin modifications such as tri‐methylation of lysine 36 of histone H3.

Figure 3. RNA Pol II speed is regulated in order to adapt the transcriptome composition in response to intra‐ or extra‐cellular stimuli

In response to intra‐ or extra‐cellular stimuli such as oncogenic stress, cell depolarization, or cell differentiation, RNA Pol II can either accelerate or slow down locally, inducing a change in alternative splicing or the extent of read‐through which could play a role in the response to stimuli.