ChIP-seq accurately predicts tissue-specific activity of enhancers

• Published in: Nature Vol. 457; no. 7231; pp. 854 - 858
• Main Authors: Visel, Axel, Blow, Matthew J., Li, Zirong, Zhang, Tao, Akiyama, Jennifer A., Holt, Amy, Plajzer-Frick, Ingrid, Shoukry, Malak, Wright, Crystal, Chen, Feng, Afzal, Veena, Ren, Bing, Rubin, Edward M., Pennacchio, Len A.
• Format: Journal Article
• Language: English
• Published: London Nature Publishing Group UK 12.02.2009; Nature Publishing Group
• Subjects: Animals; Binding sites; Chromatin Immunoprecipitation - methods; Chromosome Mapping - methods; Conserved Sequence; DNA sequencing; Embryo, Mammalian - embryology; Embryos; Extremities - embryology; Gene expression; Gene Expression Regulation, Developmental; Genetic regulation; Genetic research; Human genome; Humanities and Social Sciences; Mesencephalon - embryology; Methods; Mice; multidisciplinary; Nucleotide sequencing; p300-CBP Transcription Factors - metabolism; Prosencephalon - embryology; Proteins; Rodents; Science; Studies; Tissues; United States
• ISSN: 0028-0836; 1476-4687; 1476-4687; 1476-4679
• DOI: 10.1038/nature07730

A major yet unresolved quest in decoding the human genome is the identification of the regulatory sequences that control the spatial and temporal expression of genes. Distant-acting transcriptional enhancers are particularly challenging to uncover because they are scattered among the vast non-coding portion of the genome. Evolutionary sequence constraint can facilitate the discovery of enhancers, but fails to predict when and where they are active in vivo . Here we present the results of chromatin immunoprecipitation with the enhancer-associated protein p300 followed by massively parallel sequencing, and map several thousand in vivo binding sites of p300 in mouse embryonic forebrain, midbrain and limb tissue. We tested 86 of these sequences in a transgenic mouse assay, which in nearly all cases demonstrated reproducible enhancer activity in the tissues that were predicted by p300 binding. Our results indicate that in vivo mapping of p300 binding is a highly accurate means for identifying enhancers and their associated activities, and suggest that such data sets will be useful to study the role of tissue-specific enhancers in human biology and disease on a genome-wide scale. Mapping gene enhancers Determining the spatial and temporal activity patterns of enhancers, short DNA segments that can bind to regulatory proteins to enhance gene transcription levels, remains a challenge in the functional annotation of the human genome. The in vivo application of ChIP-seq (chromatin immunoprecipitation with massively parallel sequencing) has been used to map genome-wide occupancy of the enhancer-associated protein p300 in developing mouse tissues. There are several thousand p300 binding sites in the embryonic forebrain, midbrain and limb tissues, and testing a sample of these suggests that most are associated with reproducible enhancer activity. Data sets of this type will be useful in the study of the role of enhancers in human biology and in pathological processes. Determining the spatial and temporal activity patterns of enhancers remains a challenge in the functional annotation of the human genome. In this study, the genome-wide occupancy of the enhancer-associated protein p300 was determined in developing mouse tissues by using chromatin immunoprecipitation followed by massively parallel sequencing. Testing the p300-bound sequences in a transgenic mouse enhancer assay confirmed that p300 binding is a highly effective means to identify enhancers and to predict in which tissues they are active.