Biology subjects

Matus, D.

Publications and source records attributed to Matus, D..

3 recordsLinked to original sources

bioRxiv2024

RNA-Protein Interaction Classification via Sequence Embeddings

RNA-protein interactions (RPI) are ubiquitous in cellular organisms and essential for gene regulation. In particular, protein interactions with non-coding RNAs (ncRNAs) play a critical role in these processes. Experimental analysis of RPIs is time-consuming and expensive, and existing computational methods rely on small and limited datasets. This work introduces RNAInterAct, a comprehensive RPI dataset, alongside RPIembeddor, a novel transformer-based model designed for classifying ncRNA-protein interactions. By leveraging two foundation models for sequence embedding, we incorporate essential structural and functional insights into our task. We demonstrate RPIembeddors strong performance and generalization capability compared to state-of-the-art methods across different datasets and analyze the impact of the proposed embedding strategy on the performance in an ablation study.

bioinformatics↗

bioRxiv2023

The Essential Role of Latrophilin-1 Adhesion GPCR Nanoclusters in Inhibitory Synapses

Latrophilin-1 (Lphn1, a.k.a. CIRL1 and CL1; gene symbol Adgrl1) is an Adhesion GPCR that has been implicated in excitatory synaptic transmission as a candidate receptor for -latrotoxin. Here we analyzed conditional knockin/knockout mice for Lphn1 that contain an extracellular myc-epitope tag. Surprisingly, we found that Lphn1 is localized in cultured neurons to synaptic nanoclusters that are present in both excitatory and inhibitory synapses. Conditional deletion of Lphn1 in cultured neurons failed to elicit a detectable impairment in excitatory synapses but produced a decrease in inhibitory synapse numbers and synaptic transmission that was most pronounced for synapses close to the neuronal soma. No changes in axonal or dendritic outgrowth or branching were observed. Our data indicate that Lphn1 is among the few postsynaptic adhesion molecules that are present in both excitatory and inhibitory synapses and that Lphn1 by itself is not essential for excitatory synaptic transmission but contributes to inhibitory synaptic connections.

neuroscience↗

bioRxiv2023

The N terminus-only (trans) function of the Adhesion GPCR Latrophilin-1 controls multiple processes in reproduction of C. elegans

Adhesion G protein-coupled receptors (aGPCR) are unique molecules. They are able to transmit classical signals via G-protein activation (7TM-dependent/cis signaling) as well as to mediate functions solely through their extracellular N termini, completely independent of the seven transmembrane helices domain (7TM) and the C terminus (7TM-independent/N terminus-only/trans function). This dual mode of action is highly unusual for GPCRs and allows for a plethora of possible cellular consequences. However, the physiological implications and molecular details of this N terminus-mediated signaling are not well understood. Here, we identify three distinct 7TM-independent/trans functions of the aGPCR Latrophilin homolog LAT-1 in the nematode Caenorhabditis elegans together regulating reproduction: sperm guidance, germline apoptosis and proliferative activity of germ cells in the gonadal stem cell niche. In these contexts, the receptor elicits its functions in a non-cell autonomous manner from adjacent somatic cells. These functions might be realized through alternative splicing of the receptor specifically generating N terminus-only variants. Thus, our findings shed light on the versatility of 7TM-independent/N terminus-only/trans functions of aGPCR and discusses possible molecular details.

physiology↗