Human prefoldin modulates co-transcriptional pre-mRNA splicing

Abstract

Prefoldin is a heterohexameric complex conserved from archaea to humans that plays a cochaperone role during the co-translational folding of actin and tubulin monomers. Additional functions of prefoldin have been described, including a positive contribution to transcription elongation and chromatin dynamics in yeast. Here we show that prefoldin perturbations provoked transcriptional alterations across the human genome. Severe pre-mRNA splicing defects were also detected, particularly after serum stimulation. We found impairment of co-transcriptional splicing during transcription elongation, which explains why the induction of long genes with a high number of introns was affected the most. We detected genome-wide prefoldin binding to transcribed genes and found that it correlated with the negative impact of prefoldin depletion on gene expression. Lack of prefoldin caused global decrease in Ser2 and Ser5 phosphorylation of the RNA polymerase II carboxy-terminal domain. It also reduced the recruitment of the CTD kinase CDK9 to transcribed genes, and the association of splicing factors PRP19 and U2AF65 to chromatin, which is known to depend on CTD phosphorylation. Altogether the reported results indicate that human prefoldin is able to act locally on the genome to modulate gene expression by influencing phosphorylation of elongating RNA polymerase II, and thereby regulating co-transcriptional splicing.

A genetic approach reveals different modes of action of prefoldins

“…Therefore, it is possible that plant PFDs also contribute directly to the gene expression process, performing functions similar to those described in animals. Indeed, a fraction of the Arabidopsis PFD5 is located in the chromatin ( Locascio et al, 2013 ), as occurs in yeast and animals where PFDs regulate various aspects of transcription ( Millan-Zambrano et al, 2013 ; Payán-Bravo et al, 2021 ). Although this location would be compatible with a role for the Arabidopsis PFD5 in proteostasis, exerted locally at this location, it is likely that it also reflects the direct involvement of PFDs in transcriptional regulation.…”

“…For example, genetic and molecular analyses in human and mice cell lines indicate that PFDN5 acts as bridge protein that recruits a corepressor complex to the c-Myc transcription factor (TF) ( Fujioka et al, 2001 ; Satou et al, 2001 ). Furthermore, PFDN5 is also required to recruit components of the RNAPII phosphorylation and splicing complexes to transcribed genes in humans ( Payán-Bravo et al, 2021 ). Nonetheless, it has not been demonstrated whether it is the only PFD involved or whether these roles are performed by the PFDc.…”

Prefoldin Function in Cellular Protein Homeostasis and Human Diseases

“…A strong genetic interaction between pfd4Δ (gim3 in yeast) and lsm8Δ in yeast (Costanzo et al, 2016) prompted Esteve-Bruna et al to the notion that the functional interaction between prefoldin and the spliceosome could be conserved. The implication of prefoldin in the regulation of co-translational splicing effects was also recently demonstrated for human prefoldin (Payán-Bravo et al, 2021). The binding of prefoldin to transcribed genes was detected genome-wide.…”

Identification of a non-canonical function of prefoldin subunit 5 in proteasome assembly

“…This interaction enhances the efficiency of folding reactions (Geissler et al, 1998; Gestaut et al, 2019) and is independent of ATP hydrolysis. Prefoldin not only binds and stabilizes nascent polypeptides but also interacts with various protein substrates involved in cellular pathways such as chromatin remodeling, transcription regulation, RNA splicing (Costanzo et al, 2016; Payan-Bravo et al, 2021), protein turnover, and cancer progression (Herranz-Montoya et al, 2021; Tahmaz et al, 2021). Structurally, eukaryotic prefoldin comprises six distinct subunits: two α-like (Pfd3/Gim2/Pac10 and Pfd5/Gim5) and four β-like (Pfd1/Gim6, Pfd2/Gim4, Pfd4/Gim3, and Pfd6/Gim1) subunits (Leroux et al, 1999; Martin-Benito et al, 2002; Vainberg et al, 1998).…”