NHGRI
The NHGRI stands for the National Human Genome Research Institute, formerly known as the National Center for Human Genome Research (NCHGR). Today, the NHGRI is one of the 27 Institutes that make up the National Institutes of Health (NIH). The ENCODE project was started as a follow-up to the Human Genome project. After the Human Genome was fully sequenced, the data was found to be useless as the functional elements and regulatory sequences were still unkown. In 1988, the plan for the Human Genome project was laid out. The NHGRI (back then knwon as NCHGR) was established in 1989 and the project began at the turn of the decade. Thirteen years later, the human genome is completely sequenced and the ENCODE project was launched October, 2003.
Mendelian Genetics
Mendelian Genetics was discovered by Gregor Mendel in 1865, but was intially controversial. Mendel is considered to be the father of modern genetics and founded the Laws of Inheritance, the first law that suggested that living organisms passed on traits from generation to generation. His laws of inheritance are as follows:
Law of Segregation:
During gamete formation, the alleles for each gene segregate from each other so that each gamete carries only one allele for each gene.
Law of Independent Assortment: Genes for different traits can segregate independently during the formation of gametes.
Law of Dominance:
Some alleles are dominant while others are recessive; an organism with at least one dominant allele will display the effect of the dominant allele.
ENCODE: Pilot Phase
The pilot phase of ENCODE was an open consortium for investigators and scientists from diverse backgrounds to confer on different methodology to identify and annotate the functional elements of the human genome. Existing methods and strategies were brought up and implemented on a target sequence that was 1% of the human genome. The NHGRI investigated the different techniques trying to derive a suite of methods that can be used to effectively annotate the human genome. The target sequence used for the pilot phase was 50% manually selected and 50% randomly selected. Manually selected sequences of DNA were selected based on the presence of well-known genes and functional elements such as promoters and transcription factors. The randomly selected sequences were selected using the a stratified random selection strategy that provided a good sampling of the DNA with adequate gene density and variety. Each time functional elements were succesfully mapped or developed, the scientist were publish the results in the public online database for referencing by other investigators. The final results were published in the Nature Magazine in 2007. Click here to view the paper.
ENCODE: Production Phase
The production phase of ENCODE was the expansion of the pilot phase and the continued study of the Human genomic sequence. The overall goal of the production phase was to study the entire human genome and annotate all the functional elements using existing technologies and derived methodology from the pilot study. Through the production phase, scientists were able to discover new elements about the human genome that were previously unclear. First, the NHGRI reported that 80% of the genome was biologically active. Before ENCODE, many scientists did not believe that such a high percentage of the DNA would have any function at all. Other notable developments included certain promoter sites, discovering transcription factor networks and discovering sequences used for recognition motifs for DNA-coding proteins. Assays such as next generation sequencing, (NGS), chIP-seq, DNA methylation, and RNA-seq proved to be faster in collecting Data than the old Sanger-method of sequencing DNA.
modENCODE project
The modENCODE project is an extension of the ENCODE project. Since many organisms other than homosapiens have been sequenced since the late 90s early 2000s, lots of the DNA sequencing data is already there for the genomes of various organisms such as Drosophilia, Canine, Bovine, and Chickens. Scientists from various areas of the world are working on this extension in order to learn more about the other organisms in our world. The modENCODE project follows the following goals:
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Gene structure
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mRNA and ncRNA expression profiling
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Transcription factor binding sites
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Histone modifications and replacement
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Chromatin structure
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DNA replication initiation and timing
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Copy number variation
This project also targets model organisms such as C. Elegans and Drosophilia.
Human Genome and DNA Structure
The human genome is the key to the understanding of the miracles of life. Everything from diseases to hereditary traits stem from the study of the Human Genome. The human genome was researched as early as the 1950s by Watson and Crick who discovered the double helical structure of DNA. Their discovery explained the DNA replication process. Additionally, The Human Genome, specifically the order of the 3 Billion base pairs, were studied from 1989-2003 in the Human Genome Project initiated by the NHGRI (national human genome research institute). The goal was to pave the way for furthur research into our genetic information. This project was an international effort that consisted of hundreds of researchers and investigators worldwide. Both the HGP, and the discovery of the double helical structure by Watson and Crick were the supporting structures of the ENCODE project. The HGP was especially important as the ENCODE project added on to the HGP and deepened our understanding of the meaning to the human sequence.
