## Description

This track displays Methylation Interference data for the NHGRI ENCODE target regions. Methylation interference identifies guanines and adenines in the DNA binding site that, when methylated, interfere with binding of the protein. a single end-labeled DNA probe that is methylated at an average of one site per molecule of probe. The labeled probe is a substrate for a protein-binding reaction. DNA-protein complexes are separated from the free probe by the mobility shift DNA-binding assay. A DNA probe that is methylated at a position which interferes with binding will not be retarded in this assay. Therefore, the specific DNA-protein complex is depleted for DNA that contains methyl groups on purines important for binding. After gel purification, DNA is cleaved with piperidine. Finally, these fragments are electrophoresed on polyacrylamide sequencing gels and autoradiographed. Guanines and adenines that interfere with binding are revealed by their absence in the retarded complex relative to a lane containing piperidine-cleaved free probe. This procedure offers a rapid and highly analytical means of characterizing DNA-protein interactions.

The long-term goal of the NHGRI ENCODE Project (ENCyclopedia of DNA Elements) is to identify all functional elements in the human genome sequence to facilitate a better understanding of human biology and disease.

During the pilot phase, 44 regions comprising 30 Mb -- approximately 1% of the human genome -- have been selected for intensive study to identify, locate and analyze functional elements within the regions. These targets are being studied by a diverse public research consortium to test and evaluate the efficacy of various methods, technologies, and strategies for locating genomic features. The outcome of this initial phase will form the basis for a larger-scale effort to analyze the entire human genome.

The ENCODE Project: Target Selection Process provides a description of how the initial target regions were selected.

To open a UCSC Genome Browser with a menu for selecting ENCODE regions, use ENCODE Regions in the UCSC Browser .

## Credits

Thanks to Laura Elnitski, Ross Hardison, and Webb Miller at Penn State and the NHGRI ENCODE project for providing this initial set of data.