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Nature Research, Nature, 7146(447), p. 799-816, 2007

DOI: 10.1038/nature05874

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Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project

Journal article published in 2007 by S. van Calcar, Zhengdong D. Zhang, Man Yu1, Sarah Wilcox, Man Yu, Deyou Y. Zheng, XiaoDong Zhao, Carine Wyss, As S. Zweig, Jiaqian Q. Wu, Xiaoling Xueqing Zhang, X. Q. Zhang, Mc C. Zody, Kris A. Wetterstrand, Simon Whelan and other authors.
This paper is made freely available by the publisher.
This paper is made freely available by the publisher.

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Abstract

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.