Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project The ENCODE Project Consortium Nature 2007 447 799 816

University of Lausanne, Lausanne, Vaud, Switzerland
Nature (Impact Factor: 41.46). 07/2007; 447(7146):799-816. DOI: 10.1038/nature05874
Source: PubMed


We report the generation and analysis of functional data from multiple, diverse experiments performed on a targeted 1% of the human genome as part of the pilot phase of the ENCODE Project. These data have been further integrated and augmented by a number of evolutionary and computational analyses. Together, our results advance the collective knowledge about human genome function in several major areas. First, our studies provide convincing evidence that the genome is pervasively transcribed, such that the majority of its bases can be found in primary transcripts, including non-protein-coding transcripts, and those that extensively overlap one another. Second, systematic examination of transcriptional regulation has yielded new understanding about transcription start sites, including their relationship to specific regulatory sequences and features of chromatin accessibility and histone modification. Third, a more sophisticated view of chromatin structure has emerged, including its inter-relationship with DNA replication and transcriptional regulation. Finally, integration of these new sources of information, in particular with respect to mammalian evolution based on inter- and intra-species sequence comparisons, has yielded new mechanistic and evolutionary insights concerning the functional landscape of the human genome. Together, these studies are defining a path for pursuit of a more comprehensive characterization of human genome function.

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Available from: Matthew J Oberley, Aug 25, 2014
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    • "To date, the majority of biomarker efforts have focused on proteincoding genes, which comprise only a subset of all transcribed genes [2] [3]. Among the more than 90% of transcription that generates noncoding genes, long noncoding RNAs (lncRNAs) most closely resemble protein-coding genes in that they are transcribed by RNA polymerase II, polyadenylated, and associated with specific epigenetic signatures (i.e., H3K4me3 at the promoter and H3K36me3 throughout the gene length) [4] [5]. "
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    • "Higher-density reference panels including more individuals from more diverse population groups will improve the utility of imputation in fine-mapping studies, providing more complete coverage of genetic variation across ethnicities without the need for re-sequencing. Advances in statistical method development, incorporating improved understanding of the genome from the ENCODE Project Consortium [42, 43], will augment causal variant localisation and provide further acumen as to the mechanisms through which GWAS loci influence T2D susceptibility, with the ultimate goal of translation of these findings into clinical practice and the resulting public health benefits. "
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    • "For this definition, it somewhat arbitrary could not distinguish lncRNAs from small regulatory RNAs. Now, there have been identified far greater amounts of lncRNAs than protein coding genes [7-9]. A majority of annotated eukaryotic protein-coding ORFs were characterized with high level of phylogenetic diversity and the conservation. "
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