Biology subjects

Dodel, M.

Publications and source records attributed to Dodel, M..

17 recordsLinked to original sources

bioRxiv2026

An RNA-centric atlas of human cell cycle regulation

Cell cycle progression is orchestrated by protein networks coordinating cell growth and division, yet the role of RNA-mediated mechanisms remains underexplored. Here, we define an RNA-centric landscape of human cell cycle control using palbociclib-synchronised normal diploid cells, profiling long non-coding RNAs (lncRNAs), transposable elements (TEs), alternative splicing (AS), and RNA-binding proteins (RBPs). We identify 104 cell cycle-regulated lncRNAs and validate lncRNA ENSG00000230615, whose perturbation alters cell cycle progression and downregulates neighbouring KLF17. Across the transcriptome, 297 TE loci exhibit differential expression dynamics during the cell cycle, with Alu elements upregulated during the G1-to-S transition. Cell-cycle-dependent AS changes affect 598 genes, with alternative 5' splice sites showing the largest shift in usage at the G1-to-S transition. Furthermore, we show that cytokinesis proteins act as non-canonical RBPs with RNA-dependent stability. This study provides a comprehensive resource on RNA-based cell cycle control and highlights an underappreciated layer of regulation mediated by RNA mechanisms.

cell biology↗

bioRxiv2026

LARP1-DM15/Sgt is a reader for cap-adjacent 2`-O-ribose methylation in TOP ribosomal protein mRNAs required for localization to synapses

The most prominent mRNA modification in animals and many of their parasites is 2`-O-ribose methylation of cap-adjacent nucleotides (cOMe) introduced by cap-methyl transferases (CMTrs). How these modifications impact on gene expression and are decoded by reader proteins, however, remains uncertain. Through analysis of transcriptional start-site usage, we discovered a bias in ribosomal protein mRNAs starting with the Terminal Oligo Pyrimidine (TOP) motif, but not other TOP mRNAs in the absence of cOMe. cOMe stabilizes TOP mRNAs, enhances binding of the LARP1-DM15 domain to the TOP mRNA 5` end and is assisted by the tetratricopeptide domain-containing protein Sgt/SGTA/B. This conserved complex is required for localization of TOP ribosomal protein mRNAs to Drosophila synapses. Our study reveals an mRNA methylation-mediated mechanism to maintain local protein synthesis remote from the nucleus for sustained synaptic functions.

molecular biology↗

bioRxiv2026

A pre-rRNA positive feedback loop drives malignant ribosome biogenesis

Altered nucleoli are a well-established hallmark of cancer1, but how oncogenic signalling remodels the nucleolus remains poorly understood. Here we used an inducible mouse model of pancreatic ductal adenocarcinoma (PDAC)2 to generate spatially resolved proteomic and phosphoproteomic maps of the nucleolus upon RAS oncogene activation. We identify a phosphorylation programme initiated by translocation of the Casein Kinase 2 (CK2) holoenzyme to the nucleolus. This programme amplifies rRNA synthesis and malignant ribosome biogenesis by phosphorylating factors that control RNA polymerase I transcription and early ribosomal RNA (rRNA) processing. Preventing the nucleolar activity of CK2 inhibits oncogene-induced rRNA production, while constitutive nucleolar trapping of CK2 is sufficient to activate rRNA synthesis in the absence of RAS oncogene. Mechanistically, CK2 accumulation in the nucleolus is mediated by direct binding to the 3 External Transcribed Sequence (3ETS) of nascent precursor rRNA, creating an RNA-dependent self-amplifying feedback loop. Nucleolar CK2 accumulation is conserved across diverse human cancers, and its disruption synergises with inhibition of oncogenic RAS signalling to suppress anchorage-independent growth and tumourigenesis. Our study reveals 3ETS as a CK2 signalling scaffold that amplifies oncogenic ribosome biogenesis, and defines a druggable nucleolar vulnerability that can be exploited by targeting this process.

cancer biology↗

bioRxiv2025

Coenzyme A homeostasis regulates hypoxic signalling via UBFD1in triple-negative breast cancer

Hypoxia-inducible factors (HIFs) orchestrate cellular responses to oxygen deprivation and are frequently activated in triple-negative breast cancer (TNBC), driving metastasis and poor prognosis1,2. However, the full mechanisms of how HIFs are activated are not completely understood. It has been long noted that certain tumours have decreased levels of coenzyme A compared to surrounding tissues3,4, but the functional consequences of this remain unknown. Here, we identify Coenzyme A Synthase (CoAsy) as a novel regulator of HIF signalling. We demonstrate that CoAsy loss stabilises HIF-1 and HIF-2 independently of the canonical oxygen sensing pathway. Proximity-labelling proteomics revealed that CoAsy deficiency disrupts the association between HIF-1 and the proteasome through UBFD1, a novel CoA-binding protein that scaffolds HIF for degradation. UBFD1s CoA-dependent interaction with HIF- is mediated by its PH domain, which undergoes CoAlation, an understudied post-translational modification. COASY loss of heterozygosity occurs in [~]1/3 of breast cancer patients and correlates with increased HIF activity, lack of hormone receptor expression and poor patient outcome. In vivo studies confirm that restoring CoAsy expression in tumours suppresses metastasis to the lung. These findings uncover a critical metabolic checkpoint regulating hypoxic signalling and identify CoAsy as a potential biomarker and therapeutic target in aggressive breast cancers.

molecular biology↗

bioRxiv2025

HCR-Proxy resolves site-specific proximal RNA proteomes at subcompartmental nanoscale resolution

The spatial organization of RNA condensates is fundamental for understanding of basic cellular functions, but may also provide pivotal insights into diseases. One of the major challenges to understanding the role of condensates is the lack of technologies to map condensate-scale protein architecture at subcompartmental or nanoscale resolution. To address this, we introduce HCR-Proxy, a proximity labelling technique that couples Hybridization Chain Reaction (HCR)-based signal amplification with in situ proximity biotinylation (Proxy), enabling proteomic profiling of RNA-proximal proteomes at subcompartmental resolution. We benchmarked HCR-Proxy using nascent pre-rRNA targets to investigate the distinct proteomic signatures of the nucleolar subcompartments and to uncover a spatial logic of protein partitioning shaped by RNA sequence. Our results demonstrate HCR-Proxys ability to provide spatially-resolved maps of RNA interactomes within the nucleolus, offering new insights into the molecular organisation and compartmentalisation of condensates. This subcompartment-specific nucleolar proteome profiling enabled integration with deep learning frameworks, which effectively confirmed a sequence-encoded basis for protein partitioning across nested condensate subcompartments, characterised by antagonistic gradients in charge, length, and RNA-binding domains. HCR-Proxy thus provides a scalable platform for spatially resolved RNA interactome discovery, bridging transcript localisation with proteomic context in native cellular environments. GRAPHICAL ABSTRACT O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=196 SRC="FIGDIR/small/656369v1_ufig1.gif" ALT="Figure 1"> View larger version (52K): org.highwire.dtl.DTLVardef@116015forg.highwire.dtl.DTLVardef@1b414f1org.highwire.dtl.DTLVardef@1caf0a1org.highwire.dtl.DTLVardef@7bf8b2_HPS_FORMAT_FIGEXP M_FIG C_FIG Bullet points- HCR-Proxy enables the first nanoscale-resolution mapping of RNA-proximal proteomes in situ. - HCR-Proxy establishes a broadly applicable modular platform for spatially resolved RNA- interactomics. - Subcompartmental proteomes are resolved across nucleolar subdomains by targeting specific pre-rRNA regions. - Deep learning confirms a sequence-encoded logic of protein partitioning within condensate subcompartments.

molecular biology↗

bioRxiv2025

The RNA-binding protein RSRC2 promotes mitotic fidelity by interacting with the lncRNA C1QTNF1-AS1

Mitotic fidelity depends on proper chromosome alignment at the spindle equator, a process known as chromosome congression, driven by well-established protein networks. Whereas RNA-binding proteins and noncoding RNAs have been implicated in cell division, their interplay during this process remains unknown. Here, we discover that RSRC2, an arginine/serine-rich RNA-binding protein, plays an essential role in cell division by interacting with the long non-coding RNA C1QTNF1-AS1. The loss of either RSRC2 or C1QTNF1-AS1 results in defects in chromosome congression and mitotic progression. We show that RSRC2 interacts with distinct sets of proteins involved in splicing and centrosome biogenesis, contributing to the fidelity of cell division through two different mechanisms: one linked to the splicing of mitotic regulators and the other by localising to mitotic centrosomes for which the interaction with the C1QTNF1-AS1 RNA is required. Our study uncovers RSRC2 as a new regulator of cell division and illustrates how RNA-protein complexes promote error-free mitosis.

cell biology↗

bioRxiv2024

STAG3 promotes exit from pluripotency through post-transcriptional mRNA regulation in the cytoplasm.

STAG proteins are key regulators of the cohesin complex and are often linked to alterations in cell identity and disease. Among the mammalian STAG paralogs, STAG3 has been less extensively studied beyond its known roles in meiosis. In this work, we demonstrate that STAG3 is expressed in mouse embryonic stem cells (mESCs) and primordial germ cell-like cells (PGCLCs), where it is required for cell fate decisions. Distinct from the other STAG proteins, STAG3 mediates its effects in the cytoplasm, facilitating the post-transcriptional regulation of gene expression. Furthermore, STAG3 localises to the centrosome independently of cohesin and interacts with proteins involved in mRNA localisation and stability. The knockdown of STAG3 in mESCs using siRNAs results in the destabilisation of the centrosome and the key P-body RNA-induced silencing complex (RISC) component TNRC6C, leading to the derepression of P-body localised mRNAs, such as DPPA3. Our results propose a model in which STAG3 collaborates with RNA-binding proteins (RBPs) and specific target mRNAs to control post-transcriptional gene expression and facilitate the transition from pluripotency in mESCs. Given that STAG3 is upregulated in various cancers, our results provide a novel perspective on how STAG proteins might contribute to cell identity and disease.

cell biology↗

bioRxiv2023

The stress-induced lincRNA JUNI is a critical factor for cancer cell survival whose interactome is a prognostic signature in clear cell renal cell carcinoma

Cancer cells rely on adaptive mechanisms to survive the multiple stressors they encounter, including replication stress, toxic metabolic products and exposure to genotoxic drugs. Understanding the factors involved in these stress responses is crucial for developing effective treatments. Here, we describe a previously unstudied long non-coding RNA (lncRNA), JUNI (JUN-DT, LINC01135), which is regulated by MAPK and responsive to stress. JUNI positively regulates the expression of its neighboring gene JUN, a key transducer of signals that regulate multiple transcriptional outputs. Our findings reveal that silencing JUNI sensitizes cancer cells to chemotherapeutic drugs or UV radiation, and that its prolonged silencing leads to cell death regardless of stress exposure, highlighting the pro-survival importance of JUNI. We identified 57 proteins that interact with JUNI and found that the activity of one of them, the MAPK phosphatase and inhibitor DUSP14, is inhibited by JUNI. This effect results in c-Jun induction following exposure of cancer cells to UV radiation and promotes cellular survival. Although JUNI regulates c-Jun and its downstream targets, the pro-survival effects in cells not exposed to stress are only partially dependent on c-Jun regulation. JUNI expression levels significantly correlate with patients survival across 11 different types of cancer. Interestingly, the correlation of DUSP14 expression levels with patients survival in nine of these tumors is coherently inverse, indicating contradicting effects that are relevant not only for c-Jun induction and cellular survival but also in human cancer. Notably, we observed particularly significant antagonistic correlations in clear cell renal cell carcinoma (ccRCC) (p=5.7E-05 for JUNI and p=2.9E- 05 for Dusp14). In fact, the expression levels of 76% of JUNI-interacting proteins predict the prognosis of ccRCC patients significantly. Furthermore, a combined hazard ratio calculation demonstrates that this gene combination serves as a highly specific prognostic signature for ccRCC. Overall, our findings reveal a new important factor in stress signaling and cellular survival that is involved in ccRCC.

cell biology↗

bioRxiv2023

TREX reveals proteins that bind to specific RNA regions in living cells

Different regions of RNA molecules can often engage in specific interactions with distinct RNA-binding proteins (RBPs), giving rise to diverse modalities of RNA regulation and function. However, there are currently no methods for unbiased identification of RBPs that interact with specific RNA regions in living cells under endogenous settings. Here, we introduce TREX (Targeted RNase H-mediated extraction of crosslinked RBPs), a highly sensitive approach for identifying proteins that directly bind to specific RNA regions in living cells. We demonstrate that TREX outperforms existing methods in identifying known interactors of U1 snRNA, and reveals endogenous region-specific interactors of NORAD lncRNA. Using TREX, we generated a comprehensive region-by-region interactome for 45S rRNA, uncovering both established and novel interactions that regulate ribosome biogenesis. With its applicability to any RNA in any cell-type, TREX is the first RNA-centric tool for unbiased positional mapping of endogenous RNA-protein interactions in living cells.

cell biology↗

bioRxiv2023

KIS counteracts PTBP2 and regulates alternative exon usage in neurons

Alternative RNA splicing is an essential and dynamic process to control neuronal differentiation and synapse maturation, and dysregulation of this process has been associated with neurodegenerative diseases. Recent studies have revealed the importance of RNA-binding proteins in the regulation of neuronal splicing programs. However, the molecular mechanisms involved in the control of these splicing regulators are still unclear. Here we show that KIS, a brain-enriched kinase with a domain shared by splicing factors, controls exon usage in differentiated neurons at a genome-wide level. KIS phosphorylates the splicing regulator PTBP2 complex and markedly counteracts its role in exon exclusion. At the molecular level, phosphorylation of unstructured domains within PTBP2 causes its dissociation from key co-regulators and hinders its RNA-binding capacity. Taken together, our data provide new insights into the post-translational control of splicing regulators and uncover an essential role of KIS in setting alternative exon usage in neurons.

molecular biology↗

bioRxiv2023

Systematic Identification of Post-Transcriptional Regulatory Modules

In our cells, a limited number of RNA binding proteins (RBPs) are responsible for all aspects of RNA metabolism across the entire transcriptome. To accomplish this, RBPs form regulatory units that act on specific target regulons. However, the landscape of RBP combinatorial interactions remains poorly explored. Here, we performed a systematic annotation of RBP combinatorial interactions via multimodal data integration. We built a large-scale map of RBP protein neighborhoods by generating in vivo proximity-dependent biotinylation datasets of 50 human RBPs. In parallel, we used CRISPR interference with single-cell readout to capture transcriptomic changes upon RBP knockdowns. By combining these physical and functional interaction readouts, along with the atlas of RBP mRNA targets from eCLIP assays, we generated an integrated map of functional RBP interactions. We then used this map to match RBPs to their context-specific functions and validated the predicted functions biochemically for four RBPs. This study highlights the previously underappreciated scale of the inter-RBP interactions, be it genetic or physical, and is a first step towards a more comprehensive understanding of post-transcriptional regulatory processes and their underlying molecular grammar.

systems biology↗

bioRxiv2022

Cancer cells survival is dependent on the lincRNA JUNI

Identification of key factors for cellular survival is a basis for therapy. We identified JUNI (linc01135) as a stress-regulated lncRNA, essential for cell survival and implicated in cancer. Besides regulating c-Jun expression we demonstrate c-Jun-independent, robust requirement for cell survival. Analysis of median survival of cancer patients suffering from various types of cancer reveals correlations of JUNI expression levels with alterations in patients survival. JUNIs antagonistic interaction with DUSP14, a negative regulator of the JNK pathway, underlies the regulation of c-Jun and partial effects on cellular survival. Consistently, DUSP14 expression is coherently inversely-correlated with the survival of patients suffering from the same types of cancer. Our data suggests that JUNI is a novel master regulator of cell fate. SummaryJUNI is a novel regulator of cell survival, JNK activation and c-Jun expression, implicated in survival of cancer patients

cell biology↗

bioRxiv2021

An RNA-binding switch drives ribosome biogenesis and tumorigenesis downstream of RAS oncogene

Oncogenic RAS signaling reprograms gene expression through both transcriptional and post-transcriptional mechanisms. While transcriptional regulation downstream of RAS is relatively well characterized, how RAS post-transcriptionally modulates gene expression to promote malignancy is largely unclear. Using quantitative RNA Interactome Capture analysis, we reveal that oncogenic RAS signaling reshapes the RNA-bound proteomic landscape of cancer cells, with a network of nuclear proteins centered around Nucleolin displaying enhanced RNA-binding activity. We show that Nucleolin is phosphorylated downstream of RAS, which increases its binding to pre-ribosomal-RNA (rRNA), boosts rRNA production, and promotes ribosome biogenesis. This Nucleolin-dependent enhancement of ribosome biogenesis is crucial for RAS-induced cancer cell proliferation, and can be targeted therapeutically to inhibit tumor growth. Our results reveal that oncogenic RAS signaling drives ribosome biogenesis by regulating the RNA-binding activity of Nucleolin, and highlight the crucial role of this process in RAS-mediated tumorigenesis.

cancer biology↗

bioRxiv2021

An mRNA processing pathway suppresses metastasis by governing translational control from the nucleus

Cancer cells often co-opt post-transcriptional regulatory mechanisms to achieve pathologic expression of gene networks that drive metastasis. Translational control is a major regulatory hub in oncogenesis, however its effects on cancer progression remain poorly understood. To address this, we used ribosome profiling to compare genome-wide translation efficiencies of poorly and highly metastatic breast cancer cells and patient-derived xenografts. We developed novel regression-based methods to analyze ribosome profiling and alternative polyadenylation data, and identified HNRNPC as a translational controller of a specific mRNA regulon. Mechanistically, HNRNPC, in concert with PABPC4, binds near to poly(A) signals, thereby governing the alternative polyadenylation of a set of mRNAs. We found that HNRNPC and PABPC4 are downregulated in highly metastatic cells, which causes HNRNPC-bound mRNAs to undergo 3 UTR lengthening and subsequently, translational repression. We showed that modulating HNRNPC expression impacts the metastatic capacity of breast cancer cells in xenograft mouse models. We also found that a small molecule, previously shown to induce a distal-to-proximal poly(A) site switching, counteracts the HNRNPC-PABPC4 driven deregulation of alternative polyadenylation and decreases the metastatic lung colonization by breast cancer cells in vivo.

cancer biology↗

bioRxiv2020

eEF1A2 controls local translation and actin dynamics in structural synaptic plasticity

Synaptic plasticity involves structural modifications in dendritic spines. Increasing evidence suggests that structural plasticity is modulated by local protein synthesis and actin remodeling in a synapsis-specific manner. However, the precise molecular mechanisms connecting synaptic stimulation to these processes in dendritic spines are still unclear. In the present study, we demonstrate that the configuration of phosphorylation sites in eEF1A2, an essential translation elongation factor in neurons, is a key modulator of structural plasticity in dendritic spines. A mutant that cannot be phosphorylated stimulates translation but reduces actin dynamics and spine density. By contrast, the phosphomimetic variant loosens its association with F-actin and becomes inactive as a translation elongation factor. Metabotropic glutamate receptor signaling triggers a transient dissociation of eEF1A2 from its GEF protein in dendritic spines, in a phospho-dependent manner. We propose that eEF1A2 establishes a crosstalk mechanism that coordinates local translation and actin dynamics during spine remodeling.

neuroscience↗

bioRxiv2020

Centrosome amplification mediates small extracellular vesicles secretion via lysosome disruption

Bidirectional communication between cells and their surrounding environment is critical in both normal and pathological settings. Extracellular vesicles (EVs), which facilitate the horizontal transfer of molecules between cells, are recognized as an important constituent of cell-cell communication. In cancer, alterations in EV secretion contribute to the growth and metastasis of tumor cells. However, the mechanisms underlying these changes remain largely unknown. Here, we show that centrosome amplification is associated with and sufficient to promote small extracellular vesicle (SEV) secretion in pancreatic cancer cells. This is a direct result due of lysosomal dysfunction, caused by increased reactive oxygen species (ROS) downstream of extra centrosomes. Defects in lysosome function promotes multivesicular body fusion with the plasma membrane, thereby enhancing SEV secretion. Furthermore, we find that SEVs secreted in response to amplified centrosomes are functionally distinct and activate pancreatic stellate cells (PSCs). These activated PSCs promote the invasion of pancreatic cancer cells in heterotypic 3-D cultures. We propose that SEVs secreted by cancer cells with amplified centrosomes influence the bidirectional communication between the tumor cells and the surrounding stroma to promote malignancy.

cell biology↗

bioRxiv2019

Subcellular mRNA localization regulates ribosome biogenesis in migrating cells

Translation of Ribosomal Protein-coding mRNAs (RP-mRNAs) constitutes a key step in ribosome biogenesis, but the mechanisms which modulate RP-mRNAs translation in coordination with other cellular processes are poorly defined. Here we show that the subcellular localization of RP-mRNAs acts as a key regulator of their translation during cell migration. As cells migrate into their surroundings, RP-mRNAs localize to actin-rich protrusions at the front the cells. This localization is mediated by La-related protein 6 (LARP6), an RNA binding protein that is enriched in protrusions. Protrusions act as hotspots of translation for RP-mRNAs, resulting in enhancement of ribosome biogenesis and overall protein synthesis, which is required for sustained migration. In human breast carcinomas, Epithelial to Mesenchymal Transition (EMT) upregulates LARP6 expression to enhance ribosome biogenesis and support invasive growth. Our findings reveal LARP6 mediated mRNA localization as a key regulator of ribosome biogenesis during cell migration, and demonstrate a role for this process in cancer progression downstream of EMT.

cell biology↗