2. 1. Launched by the US National Human Genome Research Institute (NHGRI) in September
2003.
2. A follow-up to the Human Genome Project (1990-2003).
3. A world-wide effort involving more than 30 research groups and 400 scientists.
4. Aims to identify and map the location of all the functional elements in the Human Genome
and their relationship with regulome (regulatory components of the cell)
5. The 20,000 protein-coding genes accounts for about 1.5% of DNA in human genome and
the rest of the genome component was regarded as “Junk”.
3. 1. Pilot Phase: Selection of a set of experimental and computational methods.
2. Technology Development Phase: The refinement of technologies, capable of
generating high through-put data.
3. Production phase (2007-2012 and 2013-Present) : Analyze the entire genome
and to conduct additional pilot-scale studies. This phase was supported by
Data Coordination Center (DCC) – Data repository.
5. 1. DNA- binding proteins are crosslinked to
DNA with formaldehyde in vivo.
2. Chromatin is isolated and DNA is sheared
along with bound proteins into small
fragments.
3. Antibodies bound specifically to the DNA
binding protein and the DNA is isolated by
precipitation.
4. Cross-linking is reversed to release DNA and
digest the proteins.
5. PCR is used to amplify specific DNA
sequences followed by DNA sequencing.
Credit: bio.brandeis.edu
6. 1. Sites of hypersensitivity (HS) are
susceptible to cleaving by DNase I.
2. Cleavage results in release of many
fragments of variable length from
each HS region.
3. The fragments are purified,
sequenced on one end and tagged
(sequence tags) on the other end.
4. The resultant sequence tags are
mapped back to the genome.
5. A peak detection algorithm is used to
identify DHS peaks.
Credit: semanticscholar.org
7. 1. Assay used to determine DNA-Protein interaction.
2. If a protein binds to DNA, that bound region is protected from DNase digestion.
3. The protected region is known as “Footprint Region”.
4. The DNA from the DNA-Protein complex is extracted and used to prepare a sequencing
library.
8. 1. Genomic DNA is treated with MNase.
2. Sequences bound by chromatin proteins are protected from MNase
digestion.
3. The DNA from the DNA-Protein complex is extracted and used to prepare a
sequencing library.
4. Deep sequencing provides accurate representation of the location of
regulatory DNA-binding proteins in the genome.
9. 1. It is a high-throughput technique used to analyse the organization of chromosomes in a cell’s
natural state.
2. It is used to study the structural properties and spatial organization of chromosome in order
to understand gene expression, DNA replication, repair and recombination.
3. This study aids the genetic and epigenetic study of chromosomes.
10. 1. It is an approach used in genetic research to associate specific genetic variations with
particular diseases.
2. The method involves scanning the genomes from many different people and looking for
genetic markers that can be used to predict the presence of a disease.
13. 1. Came up with a catalogue of functional elements in the human genome, that is
being utilized by the scientific communities.
2. Favours the medical communities to interpret the genome sequence.
3. Helps in determining the regulatory element that control cells and cellular
situations in which the gene is active.
4. The data is being used in the fields like Basic Biology, Human Disease, Human
Evolution and Genetics, Model Organism Biology, Data standard and database
building, Bioinformatics etc.
14. 1. To enlarge the data set to additional factors, modifications and cell types,
complementing the other related projects.
2. To constitute foundational resource for Human Genomics.
3. To link variations in the expression of certain genes, to the development of
disease, with assurance.
4. New assays are underway namely, CRISPR screens, STARR seq and
massively parallel reporter assays to more directly assess the function of
ENCODE elements.
5. DCC will host and provide access to updated genome annotations using
algorithm like chromHMM.
6. To make Genomic research increasingly collaborative.
15. 1. ENCODE Project Consortium. (2011). A user's guide to the encyclopedia of DNA elements
(ENCODE). PLoS biology, 9(4), e1001046.
2. Ling, G., & Waxman, D. J. (2013). Isolation of nuclei for use in genome-wide DNase
hypersensitivity assays to probe chromatin structure. In Gene Regulation (pp. 13-19).
Humana Press, Totowa, NJ.
3. Liu, Y., Fu, L., Kaufmann, K., Chen, D., & Chen, M. (2018). A practical guide for DNase-
seq data analysis: from data management to common applications. Briefings in
bioinformatics.
4. Luo, Y., Hitz, B. C., Gabdank, I., Hilton, J. A., Kagda, M. S., Lam, B., ... & Baymuradov, U.
K. (2019). New developments on the Encyclopedia of DNA Elements (ENCODE) data
portal. Nucleic acids research.
5. Qu, H., & Fang, X. (2013). A brief review on the Human Encyclopedia of DNA Elements
(ENCODE) project. Genomics, proteomics & bioinformatics, 11(3), 135-141.
