The nuclear cap-binding complex as choreographer of gene transcription and pre-mRNA processing

Abstract

The largely nuclear cap-binding complex (CBC) binds to the 5' caps of RNA polymerase II (RNAPII)-synthesized transcripts and serves as a dynamic interaction platform for a myriad of RNA processing factors that regulate gene expression. While influence of the CBC can extend into the cytoplasm, here we review the roles of the CBC in the nucleus, with a focus on protein-coding genes. We discuss differences between CBC function in yeast and mammals, covering the steps of transcription initiation, release of RNAPII from pausing, transcription elongation, cotranscriptional pre-mRNA splicing, transcription termination, and consequences of spurious transcription. We describe parameters known to control the binding of generic or gene-specific cofactors that regulate CBC activities depending on the process(es) targeted, illustrating how the CBC is an ever-changing choreographer of gene expression.

Keywords: CBC; CBP20; CBP80; RNA 3′ end formation; alternative splicing; pre-mRNA splicing; promoter-proximal pausing; transcription elongation; transcription initiation; transcription preinitiation complex; transcription termination.

Figure 1.

Model for the regulation of transcription initiation and elongation by the CBC. (Step i) In budding yeast and plants, upon stimulation (yellow lightning), the CBC bound to the 5′ cap (black ball) of an elongating transcript (blue line) promotes the recruitment of transcription initiation factors (TIFs) and TATA-box-binding protein (TBP)-like factors to the promoter, thereby facilitating preinitiation complex (PIC) assembly and transcription reinitiation. (Step ii) The CBC recruits the elongation factors CDK9 and CDK12 to release RNAPII from promoter-proximal and/or +1 nucleosome pausing (in mammals) and/or increase RNAPII processivity (in yeast and mammals). (Step iii) In budding yeast, the CBC promotes read-through transcription by inhibiting the selection of cryptic polyadenylation signals (PASs), thereby inhibiting the transcription of downstream genes. Wedges at the bottom of the figure represent the preferred mode of transcriptional regulation in lower versus higher eukaryotes.

Figure 2.

Model for the CBC-dependent removal of first introns. (Step i) The CBC facilitates the recruitment of U1 snRNP (U1) to the 5′ splice site (5′SS) of the first intron. (Step ii) The CBC promotes recruitment of the BBP–Mud2p (yeast)/SF1–U2AF (mammals) complex to the 3′ end of the first intron, which is comprised of the branchpoint sequence (BPS), the polypyrimidine tract (PT), and the 3′ splice site (3′SS). (Step iii) The CBC promotes recruitment of U2 snRNP (U2) to the 3′ end of the first intron. (Step iv) The CBC catalyzes the replacement of U1 snRNP by U6 snRNP (U6) at the 3′ splice site. Thick horizontal blue lines represent the first and second exons, and the intervening thin blue line represents the first intron.

Figure 3.

The CBC serves as a hub for many cofactors. Illustration of how the CBC teams up with a number of cofactors that often bind in mutually exclusive mechanisms to differentially regulate gene expression. Interactions and their effects on four types of transcripts are exemplified. The color of each “OR” specifies mutually exclusive interactions designated by lines with divergent arrowheads of the same color.

Figure 4.

Models for the inhibition of weak polyadenylation sites by the CBC. (A) In budding yeast, the yCBC recruits Npl3p to weak PASs, thereby inhibiting CFIA binding and premature 3′ end processing. (B) In humans, CBC–ARS2 inhibits the selection of intronic PASs by facilitating the recruitment of U1 snRNP to the 5′ splice site of the first intron. We predict that this mechanism depends on the CBC–ARS2 cofactor NCBP3.

Figure 5.

Models for the inhibition of spurious transcription by the CBC. (A) CBC–ARS2 recruits the CFI constituent CLP1 to promote the cleavage of spurious transcripts. CBC–ARS2 then recruits the exosome via ZC3H18 and NEXT or PAXT so as to degrade the cleaved transcript. CBC–ARS2 binding to ZC3H18, and thus recruitment of the exosome, is inhibited by PHAX, whose binding to CBC–ARS2 is itself inhibited by hnRNPC1/C2, a molecular ruler that wraps strings of 200–300 nt of unstructured RNA. The CBC often prevents spurious transcription by acting on cap-proximal PASs typically found in first introns of pre-mRNAs. (B) The CBC hands-off PARN to CstF-50 at sites of DNA damage, thereby releasing from inhibition its deadenylase activity to initiate RNA decay. (C, step i) In plants, CBC–ARS2 (that is, pCBC-SE) recruits the H3K27 monomethyl (me1) transferases ATXR5 and ATXR6 to promote heterochromatin formation and inhibit spurious transcription of transposable elements. (Step ii) In fission yeast, yCBC–ARS2 promotes H3K9 dimethylation (me2) through its binding to CCR4–NOT, thereby promoting heterochromatin formation and inhibiting spurious transcription of retrotransposons and coding genes containing cryptic introns.