The export factor Yra1 modulates mRNA 3′ end processing

Abstract

The yeast mRNA export adaptor Yra1 binds the Pcf11 subunit of cleavage-polyadenylation factor CF1A linking export to 3’-end formation. We found a surprising consequence of this interaction is that Yra1 influences cleavage-polyadenylation. Yra1 competes with the CF1A subunit, Clp1, for binding to Pcf11, and excess Yra1 inhibits 3’ processing in vitro. Release of Yra1 at the 3’ ends of genes coincides with recruitment of Clp1, and depletion of Yra1 enhances Clp1 recruitment within some genes. These results suggest that CF1A is not necessarily recruited as a complete unit, but instead Clp1 can be incorporated co-transcriptionally in a process regulated by Yra1. Yra1 depletion causes widespread changes in poly(A) site choice particularly at sites where the efficiency element is divergently positioned. We propose that one way Yra1 modulates cleavage-polyadenylation is by influencing co-transcriptional assembly of the CF1A/B 3’ processing factor.

DNA damage induces targeted, genome-wide variation of poly(A) sites in budding yeast

“…Consistent with other large-scale measurements of yeast poly(A) sites (Ozsolak et al 2010;Yoon and Brem 2010;Johnson et al 2011), the distribution of poly(A) sites within distinct gene regions (Fig. 1A) demonstrates that the majority of sites in both 4NQO-treated and untreated samples are in the first 250 nucleotides (nt) of the 39 UTR.…”

“…For comparative purposes, we obtained and similarly analyzed the sequence data from a previous study focused on the effects of depletion of the mRNA export factor Yra1 (Johnson et al 2011). Our analysis of these data was largely consistent with the previous analysis, with ;1500 genes showing significant variation between control and Yra1-depleted samples (cf.…”

“…3). detected by Northern blot in other studies (Mandart 1998;Sparks and Dieckmann 1998;He et al 2003;Runner et al 2008;Johnson et al 2011). For NHX1 and RAD53, the upstream sites are far from any A-rich stretches, minimizing the likelihood that the 39 RACE products would be generated by internal priming.…”

The C terminus of Pcf11 forms a novel zinc-finger structure that plays an essential role in mRNA 3′-end processing

“…The middle region of Pcf11 helps in the assembly and localization of Rna14/Rna15 and Clp1 to the 3 ′ -UTR (Noble et al 2007;Qu et al 2007;Gordon et al 2011). Yra1 putatively interacts with Pcf11 through a region N-terminal to the very C-terminal zinc finger to facilitate assembly of the pre-mRNA for recognition by the RNA export machinery (Johnson et al 2009(Johnson et al , 2011. It is tempting to suggest, based on our data, that the C-terminal zinc finger of Pcf11 binds the remaining two proteins, Ydh1 and Ysh1, two main subunits of the CPF complex that form a heterodimer and are critical for both steps of 3 ′ -end processing (Dominski et al 2005;Xiang et al 2014).…”

“…Namely, mutations disrupting the Pcf11/Clp1 interaction cause defects in growth and 3 ′ -end processing (Noble et al 2007;Ghazy et al 2012). This region might also maintain interactions with Yra1, an mRNA export factor (Johnson et al 2009(Johnson et al , 2011. However, the function of the conserved zinc fingers in Pcf11 is not known.…”