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HEDoctoral network2022–2026

LongTREC · Long-TREC: The Long-Reads Transcriptomics European Consortium. The next generation transcriptome biology revealed by single molecule sequencing technologies

Horizon Europe — Marie Skłodowska-Curie Actions

Duration
2022-10-01 → 2026-09-30
EU contribution
€2,621,931
Participants
30
Scheme
HORIZON-TMA-MSCA-DN

Lines connect the coordinator with its partners. CORDIS does not always give exact coordinates for projects before 2014. These points are placed at city or country level.

Results in brief

Long-TREC: The Long-Reads Transcriptomics European Consortium. The next generation transcriptome biology revealed by single molecule sequencing technologies

Long-reads RNA sequencing (lrRNA-seq) is the near future of the transcriptomics field. It will improve the knowledge in very different areas such as biomedicine, agriculture or biodiversity among others, which will impact the society by improving, for example, disease diagnosis for patients, develop targeted treatments or vaccines, and identify genes for drought resistance, higher yield or plan disease resistance or ecosystem monitoring. Although some of these applications can be undertaken by short-reads, information is missed by the main limitation of short-read sequencing, the lack of reads spanning full isoforms. This limitation can be addressed by long-reads. LongTREC researchers are working together to improve the methodology associated with lrRNA-seq. New bioinformatics tools are being developed to help analyze RNA sequences more efficiently, detect modifications in RNA, understand gene regulation, and even classify cancer patients more accurately; these tools are useful in studying various organisms and diseases. Advanced methods, including artificial intelligence, are helping LongTREC researchers detect changes in genes linked to diseases like cancer. Another exciting development is the use of RNA sequencing to study marine ecosystems, revealing new insights into ocean life. LongTREC members are expanding their work into multiomics looking at how different molecular processes work together. Some of these techniques are being fine-tuned to ensure they work across different species. Lastly, the team is dedicated to making these tools more user-friendly and widely available to scientists with non-bioinformatics knowledge. We are integrating our work into existing software platforms and creating easy-to-use workflows that help non-computational scientists analyze their data more effectively. Finally, LongTREC team is also developing a central resource for documentation, making it easier for others to learn and use these methods.

Data: CORDIS, © European Union

Project objective

Thrid-generation, single-molecule long-read sequencing technologies such as Nanopore and Pacbio are revolutionizing transcriptome research and are expected to outcompete short-reads sequencing for gene expression studies. However, technical and bioinformatics challenges exist to the realization of this full potential. In this project, we will train a team of excellent Doctoral Candidates to become the European and world leaders in the field of long reads transcriptome sequencing (lrRNA-seq). The team will address three fundamental aspects of current barriers to the progress that these technologies face. a) Obtaining high-quality sequencing and preprocessed data from improved library preparation protocols and bioinformatics preprocessing methods, b) Establishment of benchmarked analysis pipelines for the application of these approaches to genome annotation and isoform usage analysis both in bulk and single-cell samples, and c) Extension of long reads to multi-omics applications for the study of regulatory biology. Additionally, DC will follow an intensive and comprehensive training program composed of scientific and soft skills training, including activities related to pressing societal challenges such as climate change, diversity and inclusion, and the ethics of science. Students will complement their education through secondments in top European laboratories and Companies as well as through exposure to a network of worldwide experts in the field of RNA research.

Original text from CORDIS.

Participants

  • AGENCIA ESTATAL CONSEJO SUPERIOR DE INVESTIGACIONES CIENTIFICAS · MadridCoordinatorSpain
  • BARCELONA SUPERCOMPUTING CENTER CENTRO NACIONAL DE SUPERCOMPUTACION · BARCELONASpain
  • BIOBAM BIOINFORMATICS SL · ValenciaSpain
  • CENTRE NATIONAL DE LA RECHERCHE SCIENTIFIQUE CNRS · ParisFrance
  • COMMISSARIAT A L ENERGIE ATOMIQUE ET AUX ENERGIES ALTERNATIVES · ParisFrance
  • EARLHAM INSTITUTE · NORWICHUnited Kingdom
  • FONDAZIONE ISTITUTO ITALIANO DI TECNOLOGIA · GenovaItaly
  • FREIE UNIVERSITAET BERLIN · BerlinGermany
  • FUNDACIO CENTRE DE REGULACIO GENOMICA · BarcelonaSpain
  • INSTITUTO GULBENKIAN DE CIENCIA · OeirasCity levelPortugal
  • ISTITUTO UNIVERSITARIO DI STUDI SUPERIORI ( I.U.S.S.) DI PAVIA · PaviaItaly
  • Joan & Sanford I. Weill Medical College of Cornell University · New YorkUnited States
  • MAX-PLANCK-GESELLSCHAFT ZUR FORDERUNG DER WISSENSCHAFTEN EV · MUNCHENGermany
  • MEDNARODNA PODIPLOMSKA SOLA JOZEFA STEFANA · LjubljanaSlovenia
  • NACIONALNI INSTITUT ZA BIOLOGIJO · LJUBLJANASlovenia
  • OXFORD NANOPORE TECHNOLOGIES LTD · OxfordUnited Kingdom
  • SB SCIENCE MANAGEMENT UG · BerlinGermany
  • STOCKHOLMS UNIVERSITET · StockholmSweden
  • Stichting Global Organisation for Bioinformatics Learning, Education and TrainingNetherlands
  • Storm Therapeutics · CambridgeCity levelUnited Kingdom
  • THE UNIVERSITY OF NOTTINGHAM · NottinghamUnited Kingdom
  • UNIVERSIDAD POMPEU FABRA · BarcelonaSpain
  • UNIVERSITAT DE VALENCIA · ValenciaSpain
  • UNIVERSITE COTE D'AZUR · NiceFrance
  • UNIVERSITE PARIS-SACLAY · Gif-Sur-YvetteFrance
  • UNIVERSITY OF EAST ANGLIA · NorwichUnited Kingdom
  • UNIVERSITY OF FLORIDA · GainesvilleUnited States
  • UPPSALA UNIVERSITET · UppsalaSweden
  • Wobble Genomics Limited · EdinburghUnited Kingdom
  • university of california santa cruz genomics institute · Santa Cruz, CaCountry levelUnited States

Links

Data: CORDIS, © European Union