Identification of dynamic RNA-binding proteins uncovers a Cpeb4-controlled regulatory cascade during pathological cell growth of cardiomyocytes

Riechert, Eva; Kmietczyk, Vivien; Stein, Frank; Schwarzl, Thomas; Sekaran, Thileepan; Jürgensen, Lonny; Kamuf-Schenk, Verena; Varma, Eshita; Hofmann, Christoph; Rettel, Mandy; Gür, Kira; Ölschläger, Julie; Kühl, Friederike; Martín, Judit; Ramirez-Pedraza, Marta; Fernández, Mercedes; Doroudgar, Shirin; Méndez, Raúl; Katus, Hugo A.; Hentze, Matthias W.; Völkers, Mirko

doi:10.1016/j.celrep.2021.109100

Cited by 20 publications

(23 citation statements)

References 56 publications

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“…These findings support a direct connection between CPEB phase separation behavior and their activity within CCR4-NOT repressor complexes. Our observations are also in line with another recent study showing that CPEB4 acts as a repressor of transcription factor expression in the heart, acting both at the level of translation and mRNA decay [90].…”

Section: Discussionsupporting

confidence: 93%

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

et al. 2022

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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.

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Section: Discussionsupporting

confidence: 93%

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

et al. 2022

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“…It was recently identified as a critical regulator of cardiomyocyte function (13). Depletion of CPEB4 led to pathological cellular growth both in vitro and in vivo in cardiomyocytes and decreased cardiac function (13). Taken together, we hypothesize a mechanism in which a genetic variant at the enhancer region of CPEB4 gene led to DNAm, which down-regulated the expression of the CPEB4 gene (for instance, by disrupting the binding of a transcription factor).…”

Section: Identifying Consistent Smr Associations Across Multi-omicsmentioning

confidence: 74%

“…Notably, in a recent work, Riechert et al reported CPEB4 as a key regulator of cardiac growth and function. CPEB4 knockdown increased the expression of NPPA-NPPB cluster (13), which are established risk markers for AF (22). Our results suggested CPEB4 as a potential drug target for AF prevention and treatment.…”

Section: Discussionmentioning

confidence: 99%

“…CPEB4, also called the cytoplasmic polyadenylation element-binding protein 4, is an RNA-binding protein. It was recently identified as a critical regulator of cardiomyocyte function (13). Depletion of CPEB4 led to pathological cellular growth both in vitro and in vivo in cardiomyocytes and decreased cardiac function (13).…”

Section: Identifying Consistent Smr Associations Across Multi-omicsmentioning

confidence: 99%

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Mendelian Randomization Integrating GWAS, eQTL, and mQTL Data Identified Genes Pleiotropically Associated With Atrial Fibrillation

Liu

et al. 2021

Front. Cardiovasc. Med.

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Background: Atrial fibrillation (AF) is the most common arrhythmia. Genome-wide association studies (GWAS) have identified more than 100 loci associated with AF, but the underlying biological interpretation remains largely unknown. The goal of this study is to identify gene expression and DNA methylation (DNAm) that are pleiotropically or potentially causally associated with AF, and to integrate results from transcriptome and methylome.Methods: We used the summary data-based Mendelian randomization (SMR) to integrate GWAS with expression quantitative trait loci (eQTL) studies and methylation quantitative trait loci (mQTL) studies. The HEIDI (heterogeneity in dependent instruments) test was introduced to test against the null hypothesis that there is a single causal variant underlying the association.Results: We prioritized 22 genes by eQTL analysis and 50 genes by mQTL analysis that passed the SMR & HEIDI test. Among them, 6 genes were overlapped. By incorporating consistent SMR associations between DNAm and AF, between gene expression and AF, and between DNAm and gene expression, we identified several mediation models at which a genetic variant exerted an effect on AF by altering the DNAm level, which regulated the expression level of a functional gene. One example was the genetic variant-cg18693985-CPEB4-AF axis.Conclusion: In conclusion, our integrative analysis identified multiple genes and DNAm sites that had potentially causal effects on AF. We also pinpointed plausible mechanisms in which the effect of a genetic variant on AF was mediated by genetic regulation of transcription through DNAm. Further experimental validation is necessary to translate the identified genes and possible mechanisms into clinical practice.

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“…Accordingly, numerous monogenic diseases in the human population, including some heart diseases (see below), are caused by damaging mutations in RBP genes. 10 Using RNA interactome capture, 2 laboratories recently purified hundreds of RBPs from cultured or primary rodent cardiomyocytes, 11,12 many of which were cardiomyocytespecific, suggesting that they perform specialized functions in heart muscle. Among those identified were several RBPs with previously documented roles in cardiomyocytes, primarily as mediators of alternative splicing, which dictate the properties of target RNAs and the activities of encoded proteins based on exon composition.…”

mentioning

confidence: 99%

RBPMS2 Is a Myocardial-Enriched Splicing Regulator Required for Cardiac Function

Akerberg

Trembley

Butty

et al. 2022

Circulation Research

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Background: RBPs (RNA-binding proteins) perform indispensable functions in the post-transcriptional regulation of gene expression. Numerous RBPs have been implicated in cardiac development or physiology based on gene knockout studies and the identification of pathogenic RBP gene mutations in monogenic heart disorders. The discovery and characterization of additional RBPs performing indispensable functions in the heart will advance basic and translational cardiovascular research. Methods: We performed a differential expression screen in zebrafish embryos to identify genes enriched in nkx2.5 -positive cardiomyocytes or cardiopharyngeal progenitors compared to nkx2.5 -negative cells from the same embryos. We investigated the myocardial-enriched gene RNA-binding protein with multiple splicing (variants) 2 [ RBPMS2 )] by generating and characterizing rbpms2 knockout zebrafish and human cardiomyocytes derived from RBPMS2 -deficient induced pluripotent stem cells. Results: We identified 1848 genes enriched in nkx2.5 -positive population. Among the most highly enriched genes, most with well-established functions in the heart, we discovered the ohnologs rbpms2a and rbpms2b , which encode an evolutionarily conserved RBP. Rbpms2 localizes selectively to cardiomyocytes during zebrafish heart development and strong cardiomyocyte expression persists into adulthood. Rbpms2-deficient embryos suffer from early cardiac dysfunction characterized by reduced ejection fraction. The functional deficit is accompanied by myofibril disarray, altered calcium handling, and differential alternative splicing events in mutant cardiomyocytes. These phenotypes are also observed in RBPMS2 -deficient human cardiomyocytes, indicative of conserved molecular and cellular function. RNA-sequencing and comparative analysis of genes mis-spliced in RBPMS2 -deficient zebrafish and human cardiomyocytes uncovered a conserved network of 29 ortholog pairs that require RBPMS2 for alternative splicing regulation, including RBFOX2 , SLC8A1 , and MYBPC3 . Conclusions: Our study identifies RBPMS2 as a conserved regulator of alternative splicing, myofibrillar organization, and calcium handling in zebrafish and human cardiomyocytes.

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Identification of dynamic RNA-binding proteins uncovers a Cpeb4-controlled regulatory cascade during pathological cell growth of cardiomyocytes

Cited by 20 publications

References 56 publications

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

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

Mendelian Randomization Integrating GWAS, eQTL, and mQTL Data Identified Genes Pleiotropically Associated With Atrial Fibrillation

RBPMS2 Is a Myocardial-Enriched Splicing Regulator Required for Cardiac Function

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