Biology subjects

Mayr, C.

Publications and source records attributed to Mayr, C..

12 recordsLinked to original sources

bioRxiv2026

Intermolecular 3'UTR-3'UTR interactions drive Wnt gene activation through heteromeric protein assembly

Stem cell differentiation depends on transcription factors that are often encoded by mRNAs with highly conserved 3'UTRs. To determine their functional roles, we performed 3'UTR loss-of-function studies. Partial deletion of endogenous 3'UTRs altered stem cell differentiation efficiency in 7/10 cases. As 6/7 3'UTR deletions did not affect expression level of the encoded proteins, we reveal widespread abundance-independent regulatory roles of 3'UTRs. For example, 3'UTR deletion of CTNNB1, an mRNA that encodes the essential Wnt co-activator {beta}-catenin, keeps {beta}-catenin levels unaffected but impairs zebrafish embryogenesis and induction of the Wnt transcriptional program during human stem cell differentiation. We show that long intermolecular 3'UTR-3'UTR interactions between Wnt transcription factor mRNAs and CTNNB1 enable co-translational protein complex assembly of these transcription factors with {beta}-catenin. As antisense oligonucleotide-mediated blocking of 3'UTR interactions impairs Wnt program induction, our findings indicate that transcriptional regulators can form functional units during protein biogenesis to be fully active.

cell biology↗

bioRxiv2025

mRNA 3'UTRs chaperone intrinsically disordered regions to control protein activity

Nearly 3,000 human mRNA 3'UTRs have hundreds of highly conserved nucleotides, but their biological roles are unclear. These mRNAs mostly encode proteins with long intrinsically disordered regions (IDRs), including MYC, UTX, and JMJD3. We show that these proteins are only fully active when translated from mRNA templates that include their 3'UTRs, raising the possibility of functional interactions between 3'UTRs and IDRs. Rather than affecting protein abundance or localization, we find that the KDM6B 3'UTR in the mRNA template changes the folding of the encoded IDR-containing JMJD3 protein. It promotes IDR-IDR interactions and suppresses folding between domains, suggesting that RNA acts as IDR chaperone that prevents interference of hydrophobic clusters in the IDR with folding of the structured domain. mRNA-based IDR chaperones are enriched in meshlike cytoplasmic condensates, suggesting localized chaperone activity. As hydrophobic clusters in IDRs are widespread, our data suggest that 3'UTR-dependent protein folding could be a widely used mechanism for activity regulation of transcriptional regulators.

molecular biology↗

bioRxiv2024

Dynamics of compartment-specific proteomic landscapes of hepatotoxic and cholestatic models of liver fibrosis

Accumulation of extracellular matrix (ECM) in liver fibrosis is associated with changes in protein abundance and composition depending upon etiology of the underlying liver disease. Current efforts to unravel etiology-specific mechanisms and pharmacological targets rely on several models of experimental fibrosis. Here, we characterize and compare dynamics of hepatic proteome remodeling during fibrosis development and spontaneous healing in experimental models of hepatotoxic (carbon tetrachloride (CCl4) intoxication) and cholestatic (3,5-diethoxycarbonyl-1,4-dihydrocollidine (DDC) feeding) injury. Using detergent-based tissue extraction and mass spectrometry, we identified compartment-specific changes in the liver proteome with detailed attention to ECM composition and changes in protein solubility. Our analysis revealed distinct time-resolved CCl4 and DDC signatures, with identified signaling pathways suggesting limited healing and a potential for carcinogenesis associated with cholestasis. Correlation of protein abundance profiles with fibrous deposits revealed extracellular chaperone clusterin with implicated role in fibrosis resolution. Dynamics of clusterin expression was validated in the context of human liver fibrosis. Atomic force microscopy of fibrotic livers complemented proteomics with profiles of disease-associated changes in local liver tissue mechanics. This study determined compartment-specific proteomic landscapes of liver fibrosis and delineated etiology-specific ECM components, providing thus a foundation for future antifibrotic therapies.

pathology↗

bioRxiv2023

The FXR1 network acts as signaling scaffold for actomyosin remodeling

It is currently not known whether mRNAs fulfill structural roles in the cytoplasm. Here, we report the FXR1 network, an mRNA-protein (mRNP) network present throughout the cytoplasm, formed by FXR1-mediated packaging of exceptionally long mRNAs. These mRNAs serve as underlying condensate scaffold and concentrate FXR1 molecules. The FXR1 network contains multiple protein binding sites and functions as a signaling scaffold for interacting proteins. We show that it is necessary for RhoA signaling-induced actomyosin reorganization to provide spatial proximity between kinases and their substrates. Point mutations in FXR1, found in its homolog FMR1, where they cause Fragile X syndrome, disrupt the network. FXR1 network disruption prevents actomyosin remodeling--an essential and ubiquitous process for the regulation of cell shape, migration, and synaptic function. These findings uncover a structural role for cytoplasmic mRNA and show how the FXR1 RNA-binding protein as part of the FXR1 network acts as organizer of signaling reactions.

cell biology↗

bioRxiv2023

mRNA interactions with disordered regions control protein activity

The cytoplasm is compartmentalized into different translation environments. mRNAs use their 3'UTRs to localize to distinct cytoplasmic compartments, including TIS granules (TGs). Many transcription factors, including MYC, are translated in TGs. It was shown that translation of proteins in TGs enables the formation of protein complexes that cannot be established when these proteins are translated in the cytosol, but the mechanism is poorly understood. Here we show that MYC protein complexes that involve binding to the intrinsically disordered region (IDR) of MYC are only formed when MYC is translated in TGs. TG-dependent protein complexes require TG-enriched mRNAs for assembly. These mRNAs bind to a new and widespread RNA-binding domain in neutral or negatively charged IDRs in several transcription factors, including MYC. RNA-IDR interaction changes the conformational ensemble of the IDR, enabling the formation of MYC protein complexes that act in the nucleus and control functions that cannot be accomplished by cytosolically-translated MYC. We propose that certain mRNAs have IDR chaperone activity as they control IDR conformations. In addition to post-translational modifications, we found a novel mode of protein activity regulation. Since RNA-IDR interactions are prevalent, we suggest that mRNA-dependent control of protein functional states is widespread.

molecular biology↗

bioRxiv2022

Subcytoplasmic location of translation controls protein output

The cytoplasm is highly compartmentalized, but the extent and consequences of subcytopIasmic mRNA localization in non-polarized cells are largely unknown. We determined mRNA enrichment in TIS granules (TGs) and the rough endopIasmic reticuIum (ER) through particle sorting and isolated cytosolic mRNAs by digitonin extraction. When focusing on non-membrane protein-encoding mRNAs, we observed that 52% have a biased transcript distribution across these compartments. Compartment enrichment is determined by a combinatorial code based on mRNA length, exon length, and 3'UTR-bound RNA-binding proteins. Compartment-biased mRNAs differ in the functional classes of their encoded proteins: TG-enriched mRNAs encode low-abundance proteins with strong enrichment of transcription factors, whereas ER-enriched mRNAs encode large and highly expressed proteins. Compartment localization is an important determinant of mRNA and protein abundance, which is supported by reporter experiments showing that redirecting cytosolic mRNAs to the ER increases their protein expression. In summary, the cytoplasm is functionally compartmentaIized by local translation environments.

molecular biology↗

bioRxiv2021

Quantification of alternative 3'UTR isoforms from single cell RNA-seq data with scUTRquant

Approximately half of human genes generate mRNA isoforms that differ in their 3'UTRs while encoding the same protein. 3'UTR and mRNA length is determined by 3' end cleavage sites (CS). Here, we mapped and categorized mRNA 3' end CS in more than 200 primary human and mouse cell types, resulting in a 40% increase of CS annotations relative to the GENCODE database. We incorporated these annotations into a novel computational pipeline, called scUTRquant, for rapid, precise, and accurate quantification of gene and 3'UTR isoform expression from single-cell RNA sequencing (scRNA-seq) data. When applying scUTRquant to data from 474 cell types and 2,134 perturbations, we discovered extensive 3'UTR length changes across cell types that are as widespread and dynamically regulated as gene expression changes. Our data indicate that mRNA abundance and mRNA length are two independent axes of gene regulation that together determine the amount and spatial organization of protein synthesis.

bioinformatics↗

bioRxiv2021

Non-coding function for mRNAs in Focal Adhesion Architecture and Mechanotransduction

Messenger RNA (mRNA) compartmentalization within the cytosol is well-recognized as a key mechanism of local translation-mediated regulation of protein levels, but whether such localization could be a means of exercising non-coding mRNA function is unknown. Here, we explore non-coding functions for mRNAs associated with focal adhesions (FAs), cellular structures responsible for mediating cell adhesion and response to changes in the extracellular matrix (ECM). Using high-throughput single molecule imaging and genomic profiling approaches, we find that mRNAs with distinct sequence characteristics localize to FAs in different human cell types. Notably, [~]85% of FA-mRNAs are not translationally active at steady state or under conditions of FA dissolution or activation. Untranslated mRNA sequences are anchored to FA based on their functional states by the RNA binding protein, G3BP1, forming biomolecular granules. Removing RNA or G3BP1, but not blocking new polypeptide synthesis, dramatically changes FA protein composition and organization, resulting in loss of cell contractility and cellular ability to adapt to changing ECM. We have therefor uncovered a novel, non-coding role for mRNAs as scaffolds to maintain FA structure and function, broadening our understating of noncanonical mRNA functions.

cell biology↗

bioRxiv2020

Endogenous p53 expression in human and mouse is not regulated by its 3'UTR

The TP53 gene encodes the tumor suppressor p53, which is functionally inactivated in many human cancers. Numerous studies found that overexpression of specific microRNAs or RNA-binding proteins can alter p53 expression through binding to cis-regulatory elements in the TP53 3' untranslated region (3'UTR). Although these studies suggested that 3'UTR-mediated p53 expression regulation could play a role in tumorigenesis or could be exploited for therapeutic purposes, they did not investigate post-transcriptional regulation of the native TP53 gene. We used CRISPR/Cas9 to delete the human and mouse p53 3'UTRs while preserving endogenous mRNA processing. This revealed that the endogenous 3'UTR is not involved in regulating p53 mRNA or protein expression neither in steady state nor after genotoxic stress. As we were able to confirm the previously observed repressive effects of the isolated 3'UTR in reporter assays, our data highlight the importance of genetic models in the validation of post-transcriptional gene regulatory effects.

cancer biology↗

bioRxiv2020

Enhancers regulate polyadenylation site cleavage and control 3'UTR isoform expression

Multi-UTR genes are widely transcribed but show cell type-specific 3'UTR isoform expression. As transcriptional enhancers regulate mRNA expression, we investigated if they also regulate mRNA isoform expression. Deletion of an endogenous enhancer of a multi-UTR gene did not impair transcript production but prevented a switch in 3'UTR isoform expression. Also, the same enhancers are able to increase transcript production in the context of single-UTR gene promoters, but they increase 3' end processing activity when paired with multi-UTR gene promoters. We show that transcription factors regulate processing activity of weak polyadenylation sites to control cell type-specific alternative 3'UTR isoform expression of widely expressed genes.

biochemistry↗

bioRxiv2020

Unstructured mRNAs form multivalent RNA-RNA interactions to generate TIS granule networks

The TIS granule network is a constitutively expressed membraneless organelle that concentrates mRNAs with AU-rich elements and interacts with the major site of protein synthesis, the rough endoplasmic reticulum. Most known biomolecular condensates are sphere-like, but TIS granules have a mesh-like morphology. Through in vivo and in vitro reconstitution experiments we discovered that this shape is generated by extensive intermolecular RNA-RNA interactions. They are mostly accomplished by mRNAs with large unstructured regions in their 3'UTRs that we call intrinsically disordered regions (IDRs). As AU-rich RNA is a potent chaperone that suppresses protein aggregation and is overrepresented in mRNAs with IDRs, our data suggests that TIS granules concentrate mRNAs that assist protein folding. In addition, the proximity of translating mRNAs in TIS granule networks may enable co-translational protein complex formation.

molecular biology↗

bioRxiv2017

Widespread intronic polyadenylation diversifies immune cell transcriptomes

Alternative cleavage and polyadenylation (ApA) can generate mRNA isoforms with differences in 3UTR length without changing the coding region (CDR). However, ApA can also recognize intronic polyadenylation (IpA) signals to generate transcripts that lose part or all of the CDR. We analyzed 46 3-seq and RNA-seq profiles from normal human tissues, primary immune cells, and multiple myeloma (MM) samples and created an atlas of 4,927 high confidence IpA events. Up to 16% of expressed genes in immune cells generate IpA isoforms, a majority of which are differentially used during B cell development or in different cellular environments, while MM cells display a striking loss of IpA isoforms expressed in plasma cells, their cell type of origin. IpA events can lead to truncated proteins lacking C-terminal functional domains. This can mimic ectodomain shedding through loss of transmembrane domains or alter the binding specificity of proteins with DNA-binding or protein-protein interaction domains, thus contributing to diversification of the transcriptome.

genomics↗