Talks

Long non-coding RNAs (lncRNA) is emerging as a key regulatory RNA in the brain. The activity of lncRNAs in neurons have been majorly limited to the nucleus and our understanding of their functions in subcellular space remains elusive. We have used the genome-wide transcriptomic profiling of total RNA isolated from the synaptic compartment and identified synapse-enriched lncRNAs from the mouse hippocampus. Among these transcripts, we find a synapse-centric role for a novel lncRNA, SynLAMP (Synapse-enriched LncRNA Associated with Memory and Plasticity). SynLAMP is specifically transported to the synaptic compartment upon contextual fear conditioning (CFC). We observed that CFC triggers interaction between SynLAMP and translation repressor FUS. The knockdown of SynLAMP prevents activity-induced dendritic translation. Our data suggests that SynLAMP functions as an activity-regulated molecular decoy to sequester translation repressor FUS. We find that the knockdown of SynLAMP partially occludes the fear memory. The decoy function of synaptic lncRNAs was further favoured by our findings on Cerox1 (Cytoplasmic endogenous regulator of oxidative phosphorylation 1), a synapse-enriched lncRNA that acts as a competitive decoy for miRNAs. We observed that Cerox1 levels decrease following sleep loss, a condition known to impair memory. Sleep deprivation or Cerox1 knockdown led to reduced mitochondrial Electron Transport Chain (ETC) activity and diminished ATP production, whereas overexpression of Cerox1 was sufficient to restore ETC function and ATP levels, even under conditions of sleep deprivation. This regulation is mediated by Cerox1’s ability to sequester miRNAs that target both Cerox1 and essential subunits of ETC complex I, thereby sustaining their expression in a sleep-dependent manner. Importantly, overexpression of Cerox1 alleviated memory deficits caused by sleep loss, while a Cerox1 variant lacking miRNA-binding sites failed to produce such effects. Collectively, these findings uncover a previously unrecognized mechanism of memory regulation mediated by the decoy activity of synapse-enriched lncRNAs.

Long non-coding RNAs (lncRNA) is emerging as a key regulatory RNA in the brain. The activity of lncRNAs in neurons have been majorly limited to the nucleus and our understanding of their functions in subcellular space remains elusive. We have used the genome-wide transcriptomic profiling of total RNA isolated from the synaptic compartment and identified synapse-enriched lncRNAs from the mouse hippocampus. Among these transcripts, we find a synapse-centric role for a novel lncRNA, SynLAMP (Synapse-enriched LncRNA Associated with Memory and Plasticity). SynLAMP is specifically transported to the synaptic compartment upon contextual fear conditioning (CFC). We observed that CFC triggers interaction between SynLAMP and translation repressor FUS. The knockdown of SynLAMP prevents activity-induced dendritic translation. Our data suggests that SynLAMP functions as an activity-regulated molecular decoy to sequester translation repressor FUS. We find that the knockdown of SynLAMP partially occludes the fear memory. The decoy function of synaptic lncRNAs was further favoured by our findings on Cerox1 (Cytoplasmic endogenous regulator of oxidative phosphorylation 1), a synapse-enriched lncRNA that acts as a competitive decoy for miRNAs. We observed that Cerox1 levels decrease following sleep loss, a condition known to impair memory. Sleep deprivation or Cerox1 knockdown led to reduced mitochondrial Electron Transport Chain (ETC) activity and diminished ATP production, whereas overexpression of Cerox1 was sufficient to restore ETC function and ATP levels, even under conditions of sleep deprivation. This regulation is mediated by Cerox1’s ability to sequester miRNAs that target both Cerox1 and essential subunits of ETC complex I, thereby sustaining their expression in a sleep-dependent manner. Importantly, overexpression of Cerox1 alleviated memory deficits caused by sleep loss, while a Cerox1 variant lacking miRNA-binding sites failed to produce such effects. Collectively, these findings uncover a previously unrecognized mechanism of memory regulation mediated by the decoy activity of synapse-enriched lncRNAs.

Following the discovery that the RNA-binding proteome is far larger than previously anticipated (Castello et al., 2012), riboregulation, the direct control of protein function by RNA, has begun to emerge as a new paradigm of biological control (Horos et al., 2019; Huppertz et al., 2022; Chatterjee et al., 2024; Hentze et al., 2025). We are beginning to understand molecular mechanisms of riboregulation, and I will discuss their implications for cell biology, metabolism and disease mechanisms as well as the new therapeutic opportunities. I will also share very recent unpublished data that add a new dimension to the concept of riboregulation…

Castello, A., B. Fischer, K. Schuschke, R. Horos, B.M. Beckmann, C. Strein, N.E. Davey, D.T. Humphreys, T. Preiss, L.M. Steinmetz, J. Krijgsveld and M.W. Hentze. Insights into RNA biology from an atlas of mammalian mRNA-
binding proteins. Cell 149, 1393-1406, 2012.

Hentze, M.W., P. Sommerkamp, V. Ravi and F. Gebauer, Rethinking RNA-binding proteins: riboregulation challenges prevailing views. Cell, in press, 2025.

Horos, R., M. Büscher, R. Kleinendorst, A.-M. Alleaume, A.K. Tarafder, T. Schwarzl, D. Dziuba, C. Tischer, E.M. Zielonka, A. Adak, A. Castello, W. Huber, C. Sachse and M.W. Hentze, The small non-coding vault RNA1-1 acts
as a riboregulator of autophagy. Cell 176, 1054-1067, 2019.

Huppertz, I., J.I. Perez-Perri, P. Mantas, T. Sekaran, T. Schwarzl, F. Russo, D. Ferring-Appel, L. Dimitrova-Paternoga, E. Kafkia, J. Hennig, P.A. Neveu, K. Patil and M.W. Hentze. Riboregulation of Enolase 1 Activity Controls
Glycolysis and Embryonic Stem Cell Differentiation. Mol. Cell 82, 2666-2680, 2022.

Chatterjee, A., M. Noble, T. Sekaran, V. Ravi, D. Ferring-Appel, T. Schwarzl, R. Rampelt and M.W. Hentze. RNA promotes mitochondrial import of F1-ATP synthase subunit alpha (ATP5A1). doi: https://doi.org/10.1101/2024.08.19.608659.

The ongoing evolutionary arms race between bacteria and their predatory phages gives rise to the evolution of different anti-phage defense systems. Among these, CRISPR-Cas represents an RNA-mediated adaptive and heritable immune system that protects the bacteria and archaea against the invasion of mobile genetic elements such as phages and plasmids. Exploitation of this immune system gave rise to a widely acclaimed and versatile genome editing technology referred as CRISPR/Cas9 and several variants thereof. In this talk, I will emphasize the centrality of RNA in orchestrating the defense response. The defense mechanism proceeds via three distinct stages: (i) acquisition of immunological memory from the foreign genetic elements and storing it in the genome, (ii) retrieving this immunological memory in the form of RNA and (iii) using this RNA as a guide for target recognition and cleavage. This talk will introduce CRISPR-Cas as a prokaryote-specific defense response and highlight the molecular mechanism that underlie the fascinating functional diversity. Finally, I will provide a compelling narrative how mechanistic understanding of this defense system was instrumental for repurposing them as precision genetic scissors.

The ongoing evolutionary arms race between bacteria and their predatory phages gives rise to the evolution of different anti-phage defense systems. Among these, CRISPR-Cas represents an RNA-mediated adaptive and heritable immune system that protects the bacteria and archaea against the invasion of mobile genetic elements such as phages and plasmids. Exploitation of this immune system gave rise to a widely acclaimed and versatile genome editing technology referred as CRISPR/Cas9 and several variants thereof. In this talk, I will emphasize the centrality of RNA in orchestrating the defense response. The defense mechanism proceeds via three distinct stages: (i) acquisition of immunological memory from the foreign genetic elements and storing it in the genome, (ii) retrieving this immunological memory in the form of RNA and (iii) using this RNA as a guide for target recognition and cleavage. This talk will introduce CRISPR-Cas as a prokaryote-specific defense response and highlight the molecular mechanism that underlie the fascinating functional diversity. Finally, I will provide a compelling narrative how mechanistic understanding of this defense system was instrumental for repurposing them as precision genetic scissors.

The interplay between viruses and host cells is extremely complex, as is the resulting disease dynamics. In the cytoplasm of host cells, (+) ss viral RNAs interact with numerous RNA-binding proteins (RBPs).
Work from our laboratory has shown that HuR, an RBP with multiple functions in RNA processing and translation, relocalizes from the nucleus to the cytoplasm upon Hepatitis C virus (HCV) infection. We have shown that two viral proteins, NS3 and NS5A, act co-ordinately to alter the equilibrium of the nucleo-cytoplasmic movement of HuR. NS3 activates protein kinase C (PKC)-δ, which in turn phosphorylates HuR on S318 residue, triggering its export to the cytoplasm. NS5A inactivates AMP-activated kinase (AMPK) resulting in diminished nuclear import of HuR through blockade of AMPK-mediated phosphorylation and acetylation of importin-α1.
In parallel, we have shown that HuR binds to SARS-CoV-2 5’UTR. The knock-down and knock-out of HuR reduced viral RNA levels and viral titres. Using an antisense strategy, we were able to reduce the viral RNA level in wildtype cells but not in HuR-knockout cells. Interestingly, results suggest HuR supports SARS-CoV-2 life by promoting differential translational reprogramming of both genomic and subgenomic RNAs.
Taken together, we demonstrate important roles of an RNA binding protein HuR, in two RNA viruses, HCV and SARS-CoV-2, and explored different ways to target it for tackling virus infections.

Ribosome biogenesis is a complex process requiring rRNA and several proteins. Ribosomal RNA processing factor 2 (RPF2) is known to be involved in the processing of 25S rRNA and 5S rRNA. We report the role of RPF2 in plants in growth, development and drought stress response. RPF2 interact with plant-specific SOC1, NAC1 transcription factors and with RPL10, and plays a role in the regulation of flowering and root development. The RPF2 binds to promoters of flowering and root-associated genes. Overexpression of RPF2 in Arabidopsis and N.benthamiana showed a robust phenotype, higher trichomes and early flowering, and the mutants or RNAi lines showed the opposite phenotype. RPF2-OE plants are insensitive to ABA, and mutants showed higher water loss. The RPF2-OE plants are resistant to drought stress compared to wild type and RNAi lines.

Untranslated RNA (UTR) at the 3’-end of a messenger RNA (mRNA) plays an essential role in gene expression. It is marked by addition of a long poly(A)-tail that occurs in two concerted steps - endonucleolytic cleavage followed by polyadenylation. Poly(A) polymerase (PAP) carries out polyadenylation in a cleavage and polyadenylation (CPA) complex associated with >85 protein components. Canonical PAPα/γ is the primary PAP for mRNA polyadenylation in the nucleus. We have identified a variant non-canonical PAP, Star-PAP that selects mRNAs for polyadenylation. Unlike PAPα, Star-PAP targets do not require certain canonical cis-elements such as the U-rich downstream sequence and instead harbor an -AUA- motif sandwiched in a GC rich region for Star-PAP binding. In addition, they are dispensable of canonical CPA factors CstF-64 or WDR33 that recognize the polyadenylation site, and instead require additional coregulator protein RBM10 to assemble the CPA complex. This specificity of target mRNA selection is in turn modulated by kinases including casein kinase, protein kinase C, or phosphatidyl inositol kinase, PIPKI affecting Star-PAP-RBM10 nexus to regulates key cellular processes and disease pathology.

Interestingly, over 70% of human genes have multiple PA-sites at the 3′-UTR that are alternately used (alternative polyadenylation, APA) generating more than one mRNA isoform with different UTR lengths. Changes in the UTR length alter protein expression, and/or affect protein function. We have shown that Star-PAP regulates APA genome wide of genes particularly involved in cardiovascular diseases such as hypertrophy and heart failure. Inherent downregulation of Star-PAP or RBM10 during cardiac hypertrophy results in the PA-site shift altering overall hypertrophy gene program. In addition to the polyadenylation step, cleavage step is also critical in gene control during cardiac remodeling in hypertrophy. We have shown a regulated cleavage imprecision resulting cleavage site (CS) heterogeneity (CSH) centring around a primary CS versus several subsidiary CS affecting gene expression. We discovered an inverse relationship between CSH and antioxidant gene expression on hypertrophic induction. A decrease in the CSH and an increase in the primary CS usage induces antioxidant gene expression. Hypertrophic stimulus stimulates oxidative stress, yet the antioxidant response progressively goes down with hypertrophic progression. This is mediated by compromised CSH from Star-PAP down regulation underscoring the critical role of the two steps of 3’-end processing in the gene regulation.