Ten years after the completion of the human genome project, the ENCODE project marks the next revolutionary milestone for genome and systems bioinformatics. In the Sep 6 issue of Nature, the ENCODE project celebrates its completion with six articles plus commentaries and more than 20 additional scientific articles in other journals such as Genome Research and Genome Biology.
The lecture series given by Prof. Zimmer and his group will present the ENCODE project and the accompanying publications. It will provide a thorough introduction into the foundations, the current results and the future prospects of ENCODE for Bioinformatics. Students will also get an in-depth practical hands-on experience with ENCODE data, its analysis and use.
The techniques and data types employed in ENCODE will spur the further development of molecular and genome biology, bioinformatics and systems biology.
ENCODE is expected to be the basis and one of the most important key resources for a large part of bioinformatics research for the years to come.
As the editorial of the Nature issue states (Nature, Sep 6, p.45): „2001 will always be remembered as the year of the human genome. The availability of its sequence transformed biology, and the exemplary way in which hundreds of researchers came together to form a public consortium paved the way for 'big science' in biology. It was an incredible achievement but it was always clear that knowing the 'code' was only the beginning. To understand how cells interpret the information locked within the genome much more needed to be learnt. This became the task of ENCODE, the Encyclopedia Of DNA Elements, the aim of which was to describe all functional elements encoded in the human genome. Nine years after launch, its main efforts culminate in the publication of 30 coordinated papers, 6 of which are in this issue of Nature.
Collectively, the papers describe 1,640 data sets generated across 147 different cell types. Among the many important results there is one that stands out above them all: more than 80% of the human genome's components have now been assigned at least one biochemical function.”
What is ENCODE? (Ref. http://www.nature.com/encode):
„ENCODE, the Encyclopedia of DNA Elements, is a project funded by the National Human Genome Research Institute to identify all regions of transcription, transcription factor association, chromatin structure and histone modification in the human genome sequence. Thanks to the identification of these functional elements, 80% of the components of the human genome now have at least one biochemical function associated with them. This expansive resource of functional annotations is already providing new insights into the organization and regulation of our genes and genome.“
The following topics will be addressed (roughly following the 'ENCODE threads'):
- Transcription factor motifs
- Chromatin patterns at transcription factor binding sites
- Characterization of intergenic regions and gene definition
- RNA and chromatin modification patterns around promoters
- Epigenetic regulation of RNA processing
- Non-coding RNA characterization
- DNA methylation
- Enhancer discovery and characterization
- Three-dimensional connections across the genome
- Characterization of network topology
- Machine learning approaches to genomics
- Impact of functional information on understanding variation
- Impact of evolutionary selection on functional regions
