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H2020Doctoral network2015–2018

ZENCODE-ITN · Computational and functional annotation of genomic elements during development of the model vertebrate zebrafish

Horizon 2020 — Marie Skłodowska-Curie Actions

Duration
2015-01-01 → 2018-12-31
EU contribution
€3,724,036
Participants
15
Scheme
MSCA-ITN

Lines connect the coordinator with its partners.

Results in brief

Computational and functional annotation of genomic elements during development of the model vertebrate zebrafish

The recent explosion of next generation sequencing (NGS) data has led to a critical shortage of computational biology expertise. As NGS methods are expected to become pervasive from basic science to personalised medicine there is an urgent need for highly skilled young scientists trained in both computational biology and experimental wet lab biology. Our network addresses this important problem of the postgenomic era. We aim to provide multi-disciplinary skills for a solid foundation in computational biology and developmental genomics. Developmental genomics is central to understanding of ontogeny and many genetic and congenital anomalies, but was outside the scope of the landmark ENCODE project. ENCODE highlighted the need for an in vivo vertebrate model that enables high throughput in vivo functional testing of hypotheses generated from genome scale annotation. Zebrafish is an ideal model for extending the scope of genomics to vertebrate development with high throughout capabilities. We aim to comprehensively annotate functional elements, decipher genomic codes of transcription, as well as coding and non-coding gene function during development and enhance zebrafish as an attractive developmental, comparative and disease model. The participants include SMEs, major zebrafish genomics laboratories, eminent computational biologists and world-class genomics technology experts active in FANTOM and ENCODE. In our programme we have created an unique compendium of zebrafish genomics database and resource which consists of new genomics data generated by the network partner laboratories and collation of most of the available published data meticulously assembled and re-analysed by standardised pipelines by network partners. From the new data we were able to deduce novel biological observations for example on the genetic basis of endoderm and primordial germ cell specification, functional genetics of muscle development and nuclear and chromosomal topology organisation during development of a vertebrate animal model. The generation of the zebrafish genomics resource led by ZENCODE-ITN partners encompassed a larger global network of collaborators beyond ZENCODE-ITN, and called DANIO-CODE. ZENCODE-ITN partners played crucial roles in creating to a publicly accessible DANIO-CODE data coordination centre and a searchable genomics resource for both zebrafish model users and the wider genomics community.

Data: CORDIS, © European Union

Project objective

The recent explosion of next generation sequencing (NGS) data has caught Europe unprepared and led to a critical shortage of computational biology expertise. As NGS methods are expected to become pervasive from basic science to personalised medicine there is an urgent need for highly skilled young scientists trained in both computational biology and experimental wet lab biology. Our network addresses this important problem of the postgenomic era. We aim to provide multi-disciplinary skills for a solid foundation in computational biology and developmental genomics. Developmental genomics is central to understanding of ontogeny and many genetic and congenital anomalies, but was outside the scope of the landmark ENCODE and FANTOM projects. ENCODE highlighted the need for an in vivo vertebrate model that enables high throughput in vivo functional testing of hypotheses generated from genome scale annotation. Zebrafish is an ideal model for extending the scope of genomics to vertebrate development. We aim to comprehensively annotate functional elements, decipher genomic codes of transcription, as well as coding and non-coding gene function during development and enhance zebrafish as an attractive developmental, comparative and disease model. The participants include 7 non-academic members (2 of which are beneficiaries), major zebrafish genomics laboratories, eminent computational biologists and world class genomics technology experts active in FANTOM and ENCODE. The training program involves 15 ESRs, more than 40 intersectoral and interdisciplinary secondments totalling 19 months, 7 training courses and 2 workshops/conferences. The main outcome of this programme is a cohort of researchers with computational, experimental laboratory and transferable skills ready to further their career in academia, public health and the private sector.

Original text from CORDIS.

Participants

  • THE UNIVERSITY OF BIRMINGHAM · BirminghamCoordinatorUnited Kingdom
  • BGI EUROPE INSTITUTE FOND · KOBENHAVN NDenmark
  • D Young & Co LLP · LondonUnited Kingdom
  • FUNDACIO DE RECERCA CLINIC BARCELONA-INSTITUT D INVESTIGACIONS BIOMEDIQUES AUGUST PI I SUNYER · BarcelonaSpain
  • GENOME RESEARCH LIMITED LBG · SAFFRON WALDENUnited Kingdom
  • IMPERIAL COLLEGE OF SCIENCE TECHNOLOGY AND MEDICINE · LondonUnited Kingdom
  • KARLSRUHER INSTITUT FUER TECHNOLOGIE · KarlsruheGermany
  • KAROLINSKA INSTITUTET · STOCKHOLMSweden
  • KING'S COLLEGE LONDON · LondonUnited Kingdom
  • MAX-PLANCK-GESELLSCHAFT ZUR FORDERUNG DER WISSENSCHAFTEN EV · MUNCHENGermany
  • MICRODISCOVERY GMBH · BerlinGermany
  • RIKEN · WAKO SHI SAITAMAJapan
  • Skillstudio Limited · ChislehurstUnited Kingdom
  • UNIVERSITE DE LIEGE · LIEGEBelgium
  • Zebrafish Model Organism Database · EugeneUnited States

Links

Data: CORDIS, © European Union