Integrative -omics in mRNA biology: computational and functional genomics between RNA and protein

Dr Lorenzo Calviello; Genomics Research Centre, Human Technopole

Lorenzo Calviello is a Group Leader in the Genomics Research Centre – Functional Genomics Programme, adjunct with the Computational Biology Research Centre. His lab is interested in post-transcriptional gene regulation in humans, employing computational (genomic data analysis, advanced machine learning, signal processing) and experimental methods (protein and RNA biochemistry, transcriptomics and proteomics techniques, cell biology, genome and transcriptome engineering) revolving around the -omics of translation, a fundamental process which dictates the functions of the transcribed genome, and impacts the cytoplasmic fate of mRNAs and proteins. In 2012 he obtained his Master’s degree in Molecular Biology at the University of Pisa with Roberto Marangoni, working on stochastic simulation of biochemical networks in the study of quasi-cellular systems. In 2017 he obtained his PhD at the Berlin Institute for Medical Systems Biology at the MDC in Berlin, Germany, under the supervision of Prof. Uwe Ohler. During his PhD, he developed computational methods for the analysis of RNA-seq and Ribo-seq datasets, focusing on the discovery of translated Open Reading Frames, quantification of translation on alternative transcripts isoforms, and integration with tandem mass spectrometry data. From 2018 to 2021 he was a postdoc at the University of California, San Francisco, in the laboratory of Stephen Floor, to study translational control by RNA helicases, and the consequences of their mis-regulation in disease, with a focus on neurodevelopmental disorders.

With a multitude of molecular processes regulating the information flow from DNA to RNA and protein, the integration between transcriptomics and proteomics remains a major challenge in the post-genomics era. At the center of the gene expression cascade, translation allows us to bridge between mRNA and protein functions, allowing for new integrative and unbiased views of gene expression control. From proteogenomics approaches in disease transcriptomes, multimodal RNA regulation by RNA binding proteins, and subcellular -omics profiling in human cells, I will present an overview of recent efforts of the lab, paving the way for new approaches in integrative mRNA biology.