What does our genome encode?
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In its first production phase, The ENCODE Project Consortium (ENCODE) has generated thousands of genome-scale data sets, resulting in a genomic “parts list” that encompasses transcripts, sites of transcription factor binding, and other functional features that now number in the millions of distinct elements. These data are reshaping many long-held beliefs concerning the information content of the human and other complex genomes, including the very definition of the gene. Here I discuss and place in context many of the leading findings of ENCODE, as well as trends that are shaping the generation and interpretation of ENCODE data. Finally, I consider prospects for the future, including maximizing the accuracy, completeness, and utility of ENCODE data for the community.Keywords:
ENCODE
The ENCyclopedia Of DNA Elements (ENCODE) project is an international research consortium that aims to identify all functional elements in the human genome sequence. The second phase of the project comprised 1640 datasets from 147 different cell types, yielding a set of 30 publications across several journals. These data revealed that 80.4% of the human genome displays some functionality in at least one cell type. Many of these regulatory elements are physically associated with one another and further form a network or three-dimensional conformation to affect gene expression. These elements are also related to sequence variants associated with diseases or traits. All these findings provide us new insights into the organization and regulation of genes and genome, and serve as an expansive resource for understanding human health and disease.
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Abstract The ENCyclopedia Of DNA Elements (ENCODE) project is an international research consortium that aims to identify all functional elements in the human genome sequence. The second phase of the project comprised 1640 datasets from 147 different cell types, yielding a set of 30 publications across several journals. These data revealed that 80.4% of the human genome displays some functionality in at least one cell type. Many of these regulatory elements are physically associated with one another and further form a network or three-dimensional conformation to affect gene expression. These elements are also related to sequence variants associated with diseases or traits. All these findings provide us new insights into the organization and regulation of genes and genome, and serve as an expansive resource for understanding human health and disease.
ENCODE
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Sequence (biology)
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The ENCyclopedia Of DNA Elements (ENCODE) Project aims to identify all functional elements in the human genome sequence. The pilot phase of the Project is focused on a specified 30 megabases (E1%) of the human genome sequence and is organized as an international consortium of computational and laboratory-based scientists working to develop and apply high-throughput approaches for detecting all sequence elements that confer biological function. The results of this pilot phase will guide future efforts to analyze the entire human genome. With the complete human genome sequence now in hand (1–3), we face the enormous challenge of interpreting it and learning how to use that information to understand the biology of human health and disease. The ENCyclopedia Of DNA Elements (ENCODE) Project is predicated on the belief that a comprehensive catalog of the structural and functional components encoded in the human genome sequence will be critical for understanding human biology well enough to address those fundamental aims of biomedical research. Such a complete catalog, or Bparts list,[ would include protein-coding genes, non–protein-coding genes, transcriptional regulatory elements, and sequences that mediate chromosome structure and dynamics; undoubtedly, additional, yet-to-bedefined types of functional sequences will also need to be included. To illustrate the magnitude of the challenge involved, it only needs to be pointed out that an inventory of the best-defined functional components in the human genome— the protein-coding sequences—is still incomplete for a number of reasons, including the fragmented nature of human genes. Even with essentially all of the human genome sequence in hand, the number of protein-coding genes can still only be estimated (currently 20,000 to 25,000) (3). Non–protein-coding genes are much less well defined. Some, such as the ribosomal RNA and tRNA genes, were identified several decades ago, but more recent
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In September,2012,more than 30 papers published on Nature,Genome Research,and Genome Biology,the ENCODE(Encyclopedia of DNA Elements) project achieved its first success.After the HGP(Human Genome Project) came to an end with a map of human genome sequence in 2001,we didn't know clearly how/where genes regulated by other factors.So,in September 2003,National Human Genome Research Institute launched a public research consortium named ENCODE,the Encyclopedia of DNA Elements,to identify all functional elements in the human genome sequence.Researchers pinpointed hundreds of thousands of landing spots for proteins that influence gene activity,many thousands of stretches of DNA that code for different types of RNA,and lots of places where chemical modifications serve to silence stretches of our chromosomes,concluding that 80% of the genome was biochemically active.Here,we review correlative information of about ENCODE and give readers instructions to recognize and apply achievements of ENCODE for human health service.
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The ENCyclopedia Of DNA Elements (ENCODE) Project aims to identify all functional elements in the human genome sequence. The pilot phase of the Project is focused on a specified 30 megabases (approximately 1%) of the human genome sequence and is organized as an international consortium of computational and laboratory-based scientists working to develop and apply high-throughput approaches for detecting all sequence elements that confer biological function. The results of this pilot phase will guide future efforts to analyze the entire human genome.
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The mission of the Encyclopedia of DNA Elements (ENCODE) Project is to enable the scientific and medical communities to interpret the human genome sequence and apply it to understand human biology and improve health. The ENCODE Consortium is integrating multiple technologies and approaches in a collective effort to discover and define the functional elements encoded in the human genome, including genes, transcripts, and transcriptional regulatory regions, together with their attendant chromatin states and DNA methylation patterns. In the process, standards to ensure high-quality data have been implemented, and novel algorithms have been developed to facilitate analysis. Data and derived results are made available through a freely accessible database. Here we provide an overview of the project and the resources it is generating and illustrate the application of ENCODE data to interpret the human genome.
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The completion of the Human Genome Project in 2003 led to the launch of several major projects, including the international HapMap Project to identify genetic variants and haplotypes in the human genome (1), the 1000 Genomes Project to characterize the frequency of genetic variants in human populations (2), the ENCODE project to identify functional elements in the human genome (3,4), and the ROADMAP project to assess epigenetic alternation of DNA sequences (5). All these projects have yielded unprecedented information on the human genome: for instance, exon regions of genes are seen to make up less than 2% of the human genome. Most of the human genome (98%) is thus non-coding but contains many regulatory elements, including enhancers, silencers, insulators, or locus control regions (LCR).
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Abstract The Human Genome Project (HGP) was initiated in 1990 and completed in 2003. It aimed to sequence the whole human genome. Although it represented an advance in understanding the human genome and its complexity, many questions remained unanswered. Other projects were launched in order to unravel the mysteries of our genome, including the ENCyclopedia of DNA Elements (ENCODE). This review aims to analyze the evolution of scientific knowledge related to both the HGP and ENCODE projects. Data were retrieved from scientific articles published in 1990–2014, a period comprising the development and the 10 years following the HGP completion. The fact that only 20,000 genes are protein and RNA‐coding is one of the most striking HGP results. A new concept about the organization of genome arose. The ENCODE project was initiated in 2003 and targeted to map the functional elements of the human genome. This project revealed that the human genome is pervasively transcribed. Therefore, it was determined that a large part of the non‐protein coding regions are functional. Finally, a more sophisticated view of chromatin structure emerged. The mechanistic functioning of the genome has been redrafted, revealing a much more complex picture. Besides, a gene‐centric conception of the organism has to be reviewed. A number of criticisms have emerged against the ENCODE project approaches, raising the question of whether non‐conserved but biochemically active regions are truly functional. Thus, HGP and ENCODE projects accomplished a great map of the human genome, but the data generated still requires further in depth analysis. © 2016 by The International Union of Biochemistry and Molecular Biology, 44:215–223, 2016.
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