Ivano Legnini

Ivano Legnini is a molecular and systems biologist interested in gene regulation.

He graduated in Genetics and Molecular Biology at Sapienza University of Rome in 2012. He worked on non-coding RNA and post-transcriptional gene regulation in the lab of Irene Bozzoni, where he completed his PhD in 2016. He then won an EMBO fellowship and joined the lab of Nikolaus Rajewsky at the Max Delbrück Center – Berlin Institute for Medical Systems Biology, where he established different lines of research, for example developing FLAM-seq for studying poly(A) tail regulation, and combining optogenetics with spatial transcriptomics to study spatial regulation of gene expression in organoid models of neurodevelopment. He moved to Milan and started his lab at HT in March 2023, working in the fields of gene regulation and RNA metabolism, as well as on developing new genomic technologies for perturbing and profiling gene expression.

Email: ivano.legnini [at] fht.org

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  • 09/2023 - Nature Methods

    Spatiotemporal, optogenetic control of gene expression in organoids

    Organoids derived from stem cells have become an increasingly important tool for studying human development and modeling disease. However, methods are still needed to control and study spatiotemporal patterns of gene expression in organoids. Here we combined optogenetics and gene perturbation technologies to activate or knock-down RNA of target genes in programmable spatiotemporal patterns. To […]

  • 06/2023 - Nature Microbiology

    Modelling viral encephalitis caused by herpes simplex virus 1 infection in cerebral organoids

    Herpes simplex encephalitis is a life-threatening disease of the central nervous system caused by herpes simplex viruses (HSVs). Following standard of care with antiviral acyclovir treatment, most patients still experience various neurological sequelae. Here we characterize HSV-1 infection of human brain organoids by combining single-cell RNA sequencing, electrophysiology and immunostaining. We observed strong perturbations of […]

  • 05/2023 - Cell

    Sites of transcription initiation drive mRNA isoform selection

    The generation of distinct messenger RNA isoforms through alternative RNA processing modulates the expression and function of genes, often in a cell-type-specific manner. Here, we assess the regulatory relationships between transcription initiation, alternative splicing, and 3′ end site selection. Applying long-read sequencing to accurately represent even the longest transcripts from end to end, we quantify […]

  • 05/2023 - BioRxiv

    High-resolution molecular atlas of a lung tumor in 3D

    Cells live and interact in three-dimensional (3D) cellular neighborhoods. However, histology and spatial omics methods mostly focus on 2D tissue sections. Here we present a 3D spatial atlas of a routine clinical sample, an aggressive human lung carcinoma, by combining in situ quantification of 960 cancer-related genes across ∼340,000 cells with measurements of tissue-mechanical components. 3D cellular […]

  • 12/2022 - iScience

    Rapid nuclear deadenylation of mammalian messenger RNA

    Poly(A) tails protect RNAs from degradation and their deadenylation rates determine RNA stability. Although poly(A) tails are generated in the nucleus, deadenylation of tails has mostly been investigated within the cytoplasm. Here, we combined long-read sequencing with metabolic labeling, splicing inhibition and cell fractionation experiments to quantify, separately, the genesis and trimming of nuclear and […]