Research Project 10

Characterization of microRNA primary transcripts by Nanopore direct RNA sequencing

About the Project

Instituto Italiano di Tecnologia

Genova, Italy

Pablo Angulo

Early Stage Researcher

Tommaso Leonardi

Main Supervisor

Francesco Nicassio

Co-Supervisor

Universitat de València

PhD enrolment

Research Objectives

The primary sequence and secondary structure of pri-miRNAs as well as their post-transcriptional editing and modifications affect miRNA biogenesis and processing by Drosha. Little is known about these mechanisms. Our objectives are:
  • Develop analysis pipeline to annotate the primary sequence, exon connectivity and 5′ capping sites of miRNA primary transcripts.
  • Profile RNA modifications and A to I editing sites in pri-miRNAs.
  • Probe the secondary structure of pri-miRNAs and generate a comprehensive model of processing regulation by the Microprocessor.

Envisioned Secondments

  • Nanopore (Aino Järvelin): Collaboration direct RNA Sequencing of pre-miRNAs.
  • CRG (Eva Maria Novoa): Collaboration for modification detection in Nanopore data.

Early Stage Researcher

Pablo Angulo

Instituto Italiano di Tecnologia,
Italy

I am originally from Spain. I earned a Bachelor’s degree in Biotechnology at the Polytechnic University of Madrid (2016-2020) and subsequently pursued a Master’s degree in Computational Biology at the same university (2020-2021). During my Master’s program, I completed my external internship and the final Master’s thesis at the Complutense University of Madrid, in collaboration with the Hospital 12 de Octubre. The project I worked on was titled “Predictive modelling of complications arising from preeclampsia in pregnant mothers from clinical data”.

Upon completing my studies, I was hired as a research assistant and bioinformatician at the Complutense University of Madrid. In this role, I focused on studying apicomplexan protists, virulence factors and their impact in the field of health.

What particularly attracted me of the LongTREC program was the opportunity to pursue a PhD in the field of computational biology, guided by leading experts in the promising area of RNA long reads sequencing, all within an international and interdisciplinary environment. As a LongTREC Doctoral Candidate, my goal is to become a specialist researcher in computational biology. I am eager to be enriched by the LongTREC international and collaborative environment and to participate in innovative and cutting-edge projects that will revolutionize our understanding of biology.

About the Main Supervisor and Host Group

Tommaso Leonardi

Istituto Italiano di Tecnologia,
Italy

The “Non-Coding Genome” consists of 14 people (1 technologist, 2 affiliated researchers, 3 senior post-docs, 2 junior post docs, 3 PhD students, 2 research fellows and 1 undergraduate student). Scientific interests are centered on the exploitation of genomic approaches to the study of mechanisms in control of gene expression provided by non-coding RNAs (microRNAs and long noncoding RNAs) and their impact on cell behaviour and human disease, with emphasis on Cancer. Research activity is based on the integration of Experimental models with Computational methodologies. The lab is in the Center for Genomic Science of IIT@SEMM in Milan, an outstation of the Istituto Italiano di Tecnologia (IIT). The center benefits from large technological infrastructure, a wide scientific network on RNA biology and Genomics and close ties with European Institute of Oncology (IEO-hospital, Milan), one of the largest cancer hospitals in Italy, which hosts our lab spaces and provides us with complementary infrastructure as well access to clinical data and biological samples for cancer studies. The Non-coding Genome Lab is part of a vibrant international scientific network, centered on RNA biology, which includes the RNA initiative (iRNA@IIT) promoted by the IIT and aimed at generating ground-breaking interdisciplinary knowledge in the fields of RNA biology, RNA technologies and RNA-based therapeutics and many collaborators form outstanding international research institutes, including the EMBL-EBI; the RIKEN Institute; Karolinska Institutet and Human Technopole (HT).