The Farnham Laboratory

ENCODE

The National Human Genome Research Institute (NHGRI) recently initiated the Encyclopedia of DNA Elements (ENCODE) Project, the goal of which is to comprehensively identify sequence-based functional elements in the human genome. To begin, NHGRI has chosen 1% (30 Mb) of the human genome as a focus for analysis. The details of regions selected can be found at http://www.genome.gov/10005107.

In collaboration with Roland Green at NimbleGen Systems Inc, the Farnham lab has been awarded a grant from the NHGRI to study the ENCODE region. The goals of our project are to use the NimbleGen maskless array technology to create oligonucleotide-based microarrays to be used for the discovery of in vivo genomic transcription factor binding sites. In brief, our experiments are based on using chromatin immunoprecipitation (ChIP) to selectively enrich for all the binding sites in the human genome of a particular transcription factor. After immunoprecipitation, the fragments are labeled and used to probe a genomic microarray (i.e. a ChIP-chip assay).

Our initial results are quite promising (see below) and we are currently using the ChIP-chip assay: a) for gene and first exon discovery, b) to study chromatin modifications on a genome-wide scale, and c) to identify binding sites for transcription factors critical for proliferation of normal and cancer cells (e.g. E2F family members, components of Polycomb Repression Complexes, and Oct4). Our data will also be used to develop consensus sequences for transcription factor binding sites and to understand common promoter architectures.

There are postdoctoral position openings in both the experimental and bioinformatics aspects of this, and related, projects.

For further information, please contact
Dr. Peggy Farnham
pjfarnham@ucdavis.edu