Control of immediate early gene expression by CPEB4-repressor complex-mediated mRNA degradation

Abstract

Background Cytoplasmic polyadenylation element-binding protein 4 (CPEB4) is known to associate with cytoplasmic polyadenylation elements (CPEs) located in the 3′ untranslated region (UTR) of specific mRNAs and assemble an activator complex promoting the translation of target mRNAs through cytoplasmic polyadenylation. Results Here, we find that CPEB4 is part of an alternative repressor complex that mediates mRNA degradation by associating with the evolutionarily conserved CCR4-NOT deadenylase complex. We identify human CPEB4 as an RNA-binding protein (RBP) with enhanced association to poly(A) RNA upon inhibition of class I histone deacetylases (HDACs), a condition known to cause widespread degradation of poly(A)-containing mRNA. Photoactivatable ribonucleoside-enhanced crosslinking and immunoprecipitation (PAR-CLIP) analysis using endogenously tagged CPEB4 in HeLa cells reveals that CPEB4 preferentially binds to the 3′UTR of immediate early gene mRNAs, at G-containing variants of the canonical U- and A-rich CPE located in close proximity to poly(A) sites. By transcriptome-wide mRNA decay measurements, we find that the strength of CPEB4 binding correlates with short mRNA half-lives and that loss of CPEB4 expression leads to the stabilization of immediate early gene mRNAs. Akin to CPEB4, we demonstrate that CPEB1 and CPEB2 also confer mRNA instability by recruitment of the CCR4-NOT complex. Conclusions While CPEB4 was previously known for its ability to stimulate cytoplasmic polyadenylation, our findings establish an additional function for CPEB4 as the RNA adaptor of a repressor complex that enhances the degradation of short-lived immediate early gene mRNAs.

Comparative analyses of vertebrate CPEB proteins define two subfamilies with coordinated yet distinct functions in post-transcriptional gene regulation

“…These two groups have specific properties in target/ motif recognition, large-order complex co-factors, and dynamic properties and regulation during cell cycle. Thus, while CPEB1 only recognizes canonical CPEs, CPEB2-4 also bind to "G-variants" (UUU UGU ), reminiscent of the Orb/Orb2 targets [16] and consistent with the findings by Poetz et al for CPEB4 [43]. This differential binding implies that, while CPEB1 targets are shared with CPEB2-4, this second CPEB subfamily has also other specific targets.…”

Control of poly(A)-tail length and translation in vertebrate oocytes and early embryos

“…This increased degeneracy might have resulted from the binding of two alternative CPEB paralogs: CPEB1 (cpeb1a/b in fish) and CPEB4 (cpeb4a/b in fish). As indicated from in vitro binding assays 42,61 and in vivo crosslinking sites, 43,62 CPEB1 prefers to bind sites ending in A, whereas CPEB4 favors sites ending in U. Moreover, in fish embryos, translation of the CPEB1 mRNA, as measured by ribosome-footprint profiling, is only ~3-fold 9,41 more than that of the CPEB4 mRNA, whereas in frog oocytes and embryos the difference is 80-fold, implying that in fish embryos but not frog oocytes and embryos expression of CPEB4 protein might reach a level that can substantially impact cytoplasmic polyadenylation.…”

Regulation of eukaryotic mRNA deadenylation and degradation by the Ccr4-Not complex

“…By contrast, phosphorylation of a specific residue within the PAM2 motif (Ser-254 of TOB2) occurs via a JNK-independent pathway and enhances the interaction between PABPC1 and TOB2 (Chen et al, 2020). In addition to recruitment via PABPC1, TOB1 -but not BTG1/ BTG2-can be targeted to mRNAs by the cytoplasmic polyadenylation element-binding proteins (CPEBs) (Hosoda et al, 2011;Ogami et al, 2014;Poetz et al, 2022). In this case, a short peptide motif located Frontiers in Cell and Developmental Biology frontiersin.org between the BTG domain and the first PAM2 motif is required (Hosoda et al, 2011).…”