LongTREC: The Long-Reads Transcriptomics European Consortium. The next generation transcriptome biology revealed by single molecule seq. technologies
Lead Research Organisation:
Earlham Institute
Department Name: Research Faculty
Abstract
Third-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 Early Stage Researchers 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, ERS 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.
Publications
Etherington G
(2023)
Schizosaccharomyces versatilis represents a distinct evolutionary lineage
Mincarelli L
(2023)
Single-cell gene and isoform expression analysis reveals signatures of ageing in haematopoietic stem and progenitor cells.
in Communications biology
Shen A
(2023)
U6 snRNA m6A modification is required for accurate and efficient cis- and trans-splicing of C. elegans mRNAs.
in bioRxiv : the preprint server for biology
Description | Astrazeneca |
Organisation | AstraZeneca |
Department | Research and Development AstraZeneca |
Country | United Kingdom |
Sector | Private |
PI Contribution | Analysis of long read bulk RNA-Seq for the detection of splicing variation in human cell lines upon chemical compounds exposure |
Collaborator Contribution | Experimental data (cell exposed to different compounds), sequencing data |
Impact | Multidisciplinary collaboration combining molecular biologists and computational biologists |
Start Year | 2023 |
Description | Collaboration King College London |
Organisation | King's College London |
Department | Maurice Wohl Clinical Neuroscience Institute |
Country | United Kingdom |
Sector | Academic/University |
PI Contribution | Computational analyses of long read bulk and single cell data from human IPSCs with engineered mutation for Amyotrophic lateral sclerosis and derived neurons, bulk long reads RNA-Seq from mouse brains with human mutations for Amyotrophic lateral sclerosis |
Collaborator Contribution | Generation of IPSC lines with causative mutations, generation of the mice lines with human mutation |
Impact | The work is highly collaborative including clinicians, clinical geneticists, molecular biologists, cellular biologists, computational biologists |
Start Year | 2023 |
Description | Collaboration UEA Medical School |
Organisation | University of East Anglia |
Department | School of Medicine UEA |
Country | United Kingdom |
Sector | Academic/University |
PI Contribution | Computational analyses of long read data to assess polyAdenylation sites usage during cardiomyocytes maturation, both in wild type background and in cell lines with mutations for cardiac disorders |
Collaborator Contribution | IPSC generation, cardiomyocytes maturation |
Impact | Computational analyses of differential polyadenylation usage during cardiomyocytes maturation |
Start Year | 2024 |
Description | Wellcome Trust Sanger Institute |
Organisation | The Wellcome Trust Sanger Institute |
Country | United Kingdom |
Sector | Charity/Non Profit |
PI Contribution | Computational analyses of single cell long read data (PacBio, ONT) for human IPSC and differentiated neuronal lineages (astrocytes, motor neurons) |
Collaborator Contribution | Cells (IPSCs, derived neuronal lineages), sequencing data |
Impact | The work is multidisciplinary bringing together cellular biologists, molecular biologists, and computational biologists |
Start Year | 2023 |
Description | Invited seminar - Stockholm - What Your Are Missing Matters - Characterisation of novel splicing events across brain tissues and during development |
Form Of Engagement Activity | A talk or presentation |
Part Of Official Scheme? | No |
Geographic Reach | International |
Primary Audience | Professional Practitioners |
Results and Impact | Invited talk at a Oxford Nanopore Technology Event |
Year(s) Of Engagement Activity | 2024 |
URL | https://nanoporetech.com/about/events/nanopore-days/nanopore-day-stockholm-2024#event-overview |
Description | Presentation - Invited Seminar - University College Dublin - Characterization of novel splicing events across tissues and during cellular differentiation |
Form Of Engagement Activity | A talk or presentation |
Part Of Official Scheme? | No |
Geographic Reach | International |
Primary Audience | Professional Practitioners |
Results and Impact | Invited seminar at the School of Biology and Environmental Science University College Dublin |
Year(s) Of Engagement Activity | 2023 |
Description | Presentation - Invited talk -BioIndustry Association - Genomics Advisory Committee - Characterisation of novel potential targets through the characterisation of novel splicing events |
Form Of Engagement Activity | A formal working group, expert panel or dialogue |
Part Of Official Scheme? | No |
Geographic Reach | National |
Primary Audience | Industry/Business |
Results and Impact | Presentation as part of the Q1 genomics advisory committee meeting (BioIndusrty Association) |
Year(s) Of Engagement Activity | 2024 |
Description | Presentation - LongTrec meeting - Single cell sequencing with PACBIO |
Form Of Engagement Activity | A talk or presentation |
Part Of Official Scheme? | No |
Geographic Reach | International |
Primary Audience | Postgraduate students |
Results and Impact | Presentation of library preparation and data analysis of single cell long read sequencing to graduate students as part of the Maric Curie LongTrec network |
Year(s) Of Engagement Activity | 2023 |
Description | Presentation - Oral Presentation - Characterization of novel splicing events across tissues and during cellular differentiation - WCBR |
Form Of Engagement Activity | A talk or presentation |
Part Of Official Scheme? | No |
Geographic Reach | International |
Primary Audience | Professional Practitioners |
Results and Impact | Presentation at the Winter Conference on Brain Research as part of the session Fostering Successful Partnerships Between Academia and Industry |
Year(s) Of Engagement Activity | 2024 |
Description | Presentation - Quantitative gene profiling of long noncoding RNAs with targeted RNA sequencing |
Form Of Engagement Activity | Participation in an activity, workshop or similar |
Part Of Official Scheme? | No |
Geographic Reach | International |
Primary Audience | Postgraduate students |
Results and Impact | Presentation to the LongTrec Consortium |
Year(s) Of Engagement Activity | 2023 |
Description | Presentation to the Kick-off meeting of LongTrec - Single cell sequencing on PACBIO |
Form Of Engagement Activity | Participation in an activity, workshop or similar |
Part Of Official Scheme? | No |
Geographic Reach | International |
Primary Audience | Postgraduate students |
Results and Impact | Attendance and presentation to the LongTrec kickoff meeting in Valencia |
Year(s) Of Engagement Activity | 2023 |