As part of the ENCODE (Encyclopedia of DNA Elements) Consortium (see Nature 447: 799, 2007), we use the technique of chromatin immunoprecipitation followed by high throughput sequencing (ChIP-seq) to investigate genome-wide binding of human transcription factors in a variety of cell lines and primary cell types. Several surprises have come from our studies, such as the fact that some in vivo binding sites of transcription factors lack sequences similar to consensus motifs derived from in vitro studies. Also, it is now clear that some transcription factors localize almost exclusively to proximal promoter regions whereas others bind to distal enhancer regions.

We are currently extending our studies on enhancer binding proteins and also performing genome-wide analyses of C2H2 zinc finger transcription factors (the largest family of site-specific factors encoded in the human genome). Gene regulation is also controlled at the level of chromatin, a dynamic structure that is modified on both its DNA and protein components. The distribution of DNA and histone modifications throughout the genome is referred to as the epigenome. Unlike our genomic sequences that are the same in all cells of a given individual, we have hundreds of different epigenomes, with different cell lineages and differentiation states giving rise to unique chromatin structures. Therefore, a comprehensive study of gene regulation requires developing complete epigenomic profiles of the cell type in which a given transcription factor is being analyzed. As part of an NIH Roadmap Epigenome Mapping Center (see Nat Biotech 28: 1045, 2010), we are currently mapping the epigenomes of a variety of different primary human cell types. In addition, we are extending our studies to include analysis of the epigenomes of several disease states, before and after treatment with inhibitors of transcription factors and chromatin modifiers.

Citation: Farnham, P. (2013), "Accessing and Using ENCODE Data", in Carey, M. and Smale, S. (eds), Eukaryotic Gene Regulation: From Chromatin to Transcription to mRNA Processing , The Biomedical & Life Sciences Collection, Henry Stewart Talks Ltd, London (online at HStalks)