Research Project 4

Long read RNA sequencing to annotate the genomes across the eukaryotic tree of life

About the Project

Centre for Genomic Regulation

Barcelona, Spain

Fabio Zanarello

Early Stage Researcher

Roderic Guigó

Main Supervisor

Universitat Pompeu Fabra

PhD enrolment

Research Objectives

lrRNA-seq will become essential for gene annotation in the Earth Biome Project. Challenges exist to capture the transcriptome comprehensively (for long or rare transcripts and from multiple tissues) and to map transcripts across species. Our objectives are:
  • Develop methods to efficiently map lrRNA-seq reads across species.
  • Develop methods to normalize lrRNA-seq libraries and/or to target low abundant transcripts.
  • Develop methods for targeting and sequencing very long RNA molecules.

Envisioned Secondments

  • Wobble Genomics (Richard Kuo): Learn company’s library normalization methods for lrRNA-se.
  • SU (Kristoffer Sahlin): Assess SU’s mapping algorithms for long transcripts and across-species mapping.

Early Stage Researcher

Fabio Zanarello

Centre for Genomic Regulation,
Spain

I completed a Bachelor’s degree in Plant Biotechnologies and a Master’s in Bioinformatics at the University of Milan. Where my thesis focused on transferring functional insights from model organisms to uncharacterized species using RNA sequencing. After graduating in 2019, I enhanced my bioinformatics skills through internships at the Sanger Institute and the European Commission’s Joint Research Center. From 2020 to 2023, I worked as a Bioinformatics Scientist at Illumina Inc., focusing on improving the readout of challenging genomic regions.

I am driven by the potential of sequencing technology to deepen our understanding of nature. Over the next four years, with the support of the LongTREC network, I plan to develop a framework for annotating genomes across the Tree of Life using long-read RNA sequencing. This PhD journey will not only enhance my expertise as a scientist through the network’s activities, but also facilitate collaborations with fellow students and scientific leaders across Europe.

About the Main Supervisor and Host Group

Roderic Guigó

Centre for Genomic Regulation,
Spain

The overarching theme of the research in Roderic Guigo’s lab at CRG is the understanding of the information encoding in genomic sequences, and how this information is processed in the pathway leading from DNA to protein sequences. More specifically, we are interested in the epigenetic regulation of gene expression and RNA processing, the relationship between molecular phenotypes and higher order endophenotypes and organismal phenotypes, and the identification of functional regions on the genome of all living beings. Our group is mostly computational, and we do both large-scale data analysis and development of methods, but it has also an important experimental component. We have participated and participate in many large scale international functional genomics projects, such as ENCODE, GTEx, BluePrint and others.