ENCODE
Encyclopedia
ENCODE is a public research consortium launched by the US National Human Genome Research Institute (NHGRI) in September 2003. The goal is to find all functional elements in the human genome
, one of the most critical projects by NHGRI after it completed the successful Human Genome Project
. All data generated in the course of the project will be released rapidly into public databases.
and the availability of comparative data. Methods currently being evaluated include chromatin immunoprecipitation
(ChIP) and quantitative PCR.
The ENCODE pilot project rapidly released all of its data into public databases. The pilot phase was successfully finished and the results were published in June 2007 in Nature and a special issue of Genome Research.
Like the pilot project, the production effort is organized as an open consortium. In October 2007, NHGRI awarded grants totaling more than $80 million over four years. The production phase also includes a Data Coordination Center, a Data Analysis Center, and a Technology Development Effort.
As of 2010 over 1000 genome-wide data sets have been produced by the ENCODE project. These data sets between them show what regions are transcribed into RNA, what regions are likely to control what genes are used in a particular type of cell, and what regions are associated with a wide variety of proteins. The primary assays used in ENCODE are ChIP-seq
, DNAse Hypersensitivity, and RNA-seq
, and assays of DNA methylation.
genomes, specifically, Drosophila melanogaster
and Caenorhabditis elegans
. The extension to model organisms permits biological validation of the computational and experimental findings of the ENCODE project, something that is difficult or impossible to do in humans.
Funding for the modENCODE project was announced by the NIH in 2007 and included several different research institutions in the US.
In late 2010, the modENCODE consortium unveiled its first set of results with publications on annotation and integrative analysis of the worm and fly genomes in Science. Data from these publications is available from modencode.org.
Genome
In modern molecular biology and genetics, the genome is the entirety of an organism's hereditary information. It is encoded either in DNA or, for many types of virus, in RNA. The genome includes both the genes and the non-coding sequences of the DNA/RNA....
, one of the most critical projects by NHGRI after it completed the successful Human Genome Project
Human Genome Project
The Human Genome Project is an international scientific research project with a primary goal of determining the sequence of chemical base pairs which make up DNA, and of identifying and mapping the approximately 20,000–25,000 genes of the human genome from both a physical and functional...
. All data generated in the course of the project will be released rapidly into public databases.
Pilot phase
The project was initiated with a $12 million pilot phase. The aim of this was to evaluate a variety of different methods for use in later stages. Essentially this involved using a number of existing techniques to analyse a portion of the genome equal to about 1% (30mb). The results of these analyses will then be evaluated based on their ability to identify regions of DNA which are known or suspected to contain functional elements. 50% of the sample area selected for study under this phase was manually selected whilst the other 50% was selected at random. The manually selected regions have been selected based on the presence of well studied genesGênes
Gênes is the name of a département of the First French Empire in present Italy, named after the city of Genoa. It was formed in 1805, when Napoleon Bonaparte occupied the Republic of Genoa. Its capital was Genoa, and it was divided in the arrondissements of Genoa, Bobbio, Novi Ligure, Tortona and...
and the availability of comparative data. Methods currently being evaluated include chromatin immunoprecipitation
Chromatin immunoprecipitation
Chromatin Immunoprecipitation is a type of immunoprecipitation experimental technique used to investigate the interaction between proteins and DNA in the cell. It aims to determine whether specific proteins are associated with specific genomic regions, such as transcription factors on promoters or...
(ChIP) and quantitative PCR.
The ENCODE pilot project rapidly released all of its data into public databases. The pilot phase was successfully finished and the results were published in June 2007 in Nature and a special issue of Genome Research.
Production Phase
In September 2007 NHGRI began funding the production phase of the ENCODE project. In this phase, the goal is to analyze the entire genome and to conduct "additional pilot-scale studies."Like the pilot project, the production effort is organized as an open consortium. In October 2007, NHGRI awarded grants totaling more than $80 million over four years. The production phase also includes a Data Coordination Center, a Data Analysis Center, and a Technology Development Effort.
As of 2010 over 1000 genome-wide data sets have been produced by the ENCODE project. These data sets between them show what regions are transcribed into RNA, what regions are likely to control what genes are used in a particular type of cell, and what regions are associated with a wide variety of proteins. The primary assays used in ENCODE are ChIP-seq
Chromatin immunoprecipitation
Chromatin Immunoprecipitation is a type of immunoprecipitation experimental technique used to investigate the interaction between proteins and DNA in the cell. It aims to determine whether specific proteins are associated with specific genomic regions, such as transcription factors on promoters or...
, DNAse Hypersensitivity, and RNA-seq
RNA-Seq
RNA-seq, also called "Whole Transcriptome Shotgun Sequencing" and dubbed "a revolutionary tool for transcriptomics", refers to the use of high-throughput sequencing technologies to sequence cDNA in order to get information about a sample's RNA content, a technique that is quickly becoming...
, and assays of DNA methylation.
modENCODE project
The Model Organism ENCyclopedia Of DNA Elements (modENCODE) project is a continuation of the original ENCODE project targeting the identification of functional elements in selected model organismModel organism
A model organism is a non-human species that is extensively studied to understand particular biological phenomena, with the expectation that discoveries made in the organism model will provide insight into the workings of other organisms. Model organisms are in vivo models and are widely used to...
genomes, specifically, Drosophila melanogaster
Drosophila melanogaster
Drosophila melanogaster is a species of Diptera, or the order of flies, in the family Drosophilidae. The species is known generally as the common fruit fly or vinegar fly. Starting from Charles W...
and Caenorhabditis elegans
Caenorhabditis elegans
Caenorhabditis elegans is a free-living, transparent nematode , about 1 mm in length, which lives in temperate soil environments. Research into the molecular and developmental biology of C. elegans was begun in 1974 by Sydney Brenner and it has since been used extensively as a model...
. The extension to model organisms permits biological validation of the computational and experimental findings of the ENCODE project, something that is difficult or impossible to do in humans.
Funding for the modENCODE project was announced by the NIH in 2007 and included several different research institutions in the US.
In late 2010, the modENCODE consortium unveiled its first set of results with publications on annotation and integrative analysis of the worm and fly genomes in Science. Data from these publications is available from modencode.org.