Implementation of native RNA sequencing technology


Francesco Nicassio



Istituto Italiano di Tecnologia – IIT, Center for Genomic Science of IIT@SEMM, Milano



We aim at exploiting Oxford Nanopore direct RNA Sequencing (DRS) to dissect the complexity of human cancer transcriptome and epitranscriptome. We will adopts cutting edge experimental and computational approaches to provide key insights into the complexity, modification profile and regulation of cellular RNAs, with a particular focus on non-coding RNAs and their related functional mechanisms. Information on RNA isoforms and chemical modifications will be also exploited to elucidate RNA structure and interactomes. A proof-of-principle study focusing on breast cancer will be conducted, using cellular models and possibly clinical material, to provide an “ATLAS”, a resource of the community, with an updated repertoire of RNA molecules relevant for the biology of human breast cancer disease.


Relevant Publications

  1. Giuliani B, Tordonato C, Nicassio F. “Mechanisms of Long Non-Coding RNA in Breast Cancer”.  Int J Mol Sci. 2023 Feb 25;24(5):4538. doi: 10.3390/ijms24054538 – Review

  2. Mulroney L, Birney E, Leonardi T, Nicassio F. “Using Nanocompore to Identify RNA Modifications from Direct RNA Nanopore Sequencing Data.” Curr Protoc. 2023 Feb;3(2):e683. doi: 10.1002/cpz1.683.

  3. Ugolini C, Mulroney L, Leger A, Castelli M, Criscuolo E, Williamson MK, Davidson AD, Almuqrin A, Giambruno R, Jain M, Frigè G, Olsen H, Tzertzinis G, Schildkraut I, Wulf MG, Corrêa IR, Ettwiller L, Clementi N, Clementi M, Mancini N, Birney E, Akeson M, Nicassio F, Matthews DA, Leonardi T.  “Nanopore ReCappable sequencing maps SARS-CoV-2 5′ capping sites and provides new insights into the structure of sgRNAs” Nucleic Acids Res. 2022 Mar 4:gkac144. doi: 10.1093/nar/gkac144. Online ahead of print.

  4. Simeone I, Rubolino C, Noviello T, Farinello D, Cerulo L, Marzi MJ, Nicassio F. “Prediction and pan-cancer analysis of mammalian transcripts involved in target directed miRNA degradation Nucleic Acids Res. 2022. Feb 28;50(4):2019-2035. doi: 10.1093/nar/gkac057.

  5. Tordonato C, Marzi MJ, Giangreco G, Freddi S, Bonetti P, Tosoni D, Di Fiore PP, Nicassio F. miR-146 connects stem cell identity with metabolism and pharmacological resistance in breast cancer. J Cell Biol. 2021 May 3;220(5):e202009053. doi: 10.1083/jcb.202009053.

  6. Rossi M, Bucci G, Rizzotto D, Bordo D, Marzi MJ, Puppo M, Flinois A, Spadaro D, Citi S, Emionite L, Cilli M, Nicassio F, Inga A, Briata P, Gherzi R. LncRNA EPR controls epithelial proliferation by coordinating Cdkn1a transcription and mRNA decay response to TGF-β” Nat Commun. 2019 Apr 29;10(1):1969. doi: 10.1038/s41467-019-09754-1

  7. Santoro A, Vlachou T, Luzi L, Melloni G, Mazzarella L, D’Elia E, Aobuli X, Pasi CE, Reavie L, Bonetti P, Punzi S, Casoli L, Sabò A, Moroni MC, Dellino GI, Amati B, Nicassio F, Lanfrancone L, Pelicci PG. “p53 Loss in Breast Cancer Leads to Myc Activation, Increased Cell Plasticity, and Expression of a Mitotic Signature with Prognostic Value” Cell Rep. 2019 Jan 15; 26(3):624-638.e8. doi: 10.1016/j.celrep.2018.12.071

  8. Bonetti P, Climent M, Panebianco F, Tordonato C, Santoro A, Marzi MJ, Pelicci PG, Ventura A, Nicassio F. “Dual role for miR-34a in the control of early progenitor proliferation and commitment in the mammary gland and in breast cancer” Oncogene 2019 Jan; 38(3):360-374. doi: 10.1038/s41388-018-0445-3

  9. Tordonato C, Di Fiore PP, Nicassio F. “The role of non-coding RNAs in the regulation of stem cells and progenitors in the normal mammary gland and in breast tumors.” Front Genet. 2015 Feb 27;6:72. doi: 10.3389/fgene.2015.00072. eCollection 2015. Review.


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