Peggy Farnham

Professor
Ph.D., Yale University, 1982
Office Phone: (530) 754-4988
E-mail: pjfarnham@ucdavis.edu

Research Interest:
Genome-wide approaches toward understanding transcriptional regulation

Research Synopsis:
My laboratory has been a leader in developing the technique of chromatin immunoprecipitation (ChIP) to study the function of mammalian transcription factors, such as c-Myc, E2Fs, and Polycomb Group complexes. Recently, we have extended these studies to allow a high throughput, global analysis of transcription factor target genes by combining chromatin immunoprecipitation with CpG microarray hybridization (ChIP-chip assays). We are currently developing high density oligonucleotide microarrays which will allow a comprehensive analysis of transcription factor binding sites and chromatin modifications on a genome-wide scale.

Current projects include the analysis of changes in chromatin structure as embryonic stem cells differentiate, changes in chromatin structure in normal vs tumor cells, the identification of target genes of transcription factors such as Oct4 (a key regulator of stem cell self renewal), SUZ12 (a Polycomb Group protein involved in development and tumor progression), the retinoblastoma tumor suppressor protein (a key cell cycle regulator) and E2F6 (a transcriptional repressor).

Selected Publications

Graveel, C.R., Jatkoe, T., Madore, S., Holt, A.L., and Farnham, P.J. Expression profiling and identification of novel genes in hepatocellular carcinomas. Oncogene 20: 2704-2712-2001. Abstract.

Weinmann, A.S., Bartley, S.M., Zhang, M.Q., Zhang, T., and Farnham, P.J. The use of chromatin immunoprecipitation to clone novel E2F target promoters. Mol. Cell. Biol. 21: 6820-6832, 2001. Abstract.

Weinmann, A.S., Yan, P.S., Oberley, M.J., Huang, H.-M.T., and Farnham, P.J. Isolating human transcription factor targets by combining chromatin immunoprecipitation and CpG microarray analysis. Genes & Devel. 16:235-244, 2002. Abstract. This article was given a "must read" ranking at Faculty of 1000: http://www.f1000biology.com/article/11799066

Wells, J., Yan, P.S., Cechvala, M., Huang, H.-M.T, and Farnham, P.J. Identification of novel pRb binding sites using CpG microarrays suggests that E2F recruits pRb to specific genomic sites during S phase. Oncogene 22:1445-1460, 2003. Abstract.

Graveel, C.R., Harkins-Perry, S.R., Acevedo, L.G., and Farnham, P. J. Identification and characterization of CRG-L2, a new marker for liver tumor development. Oncogene 22:1730-1736, 2003. Abstract.

Kirmizis, A., Bartley, S. M., Kuzmichev, A., Margueron R., Reinberg. R., Green, R., and Farnham, P. J. Silencing of human polycomb target genes is associated with methylation of histone H3 lysine 27. Genes & Devel. Genes & Devel. 18:(13)1592-1605, 2004. Abstract

Bieda, M., Xu, S., Singer, M., Green, R., and Farnham, P.J. Unbiased location of analysis of E2F1 binding sites suggests a widespread role for E2F1 in the Human Genome. Genome Research, 16:595-605, 2006. Abstract

Squazzo, S. L., Komashko, V. M., O'Geen, H., Krig, S., Jin, V.X., Jang, S-W., Green, R., Margueron, R., Reinberg, D. and Farnham, P. J. Suz12 silences large regions of the genome in a cell type-specific manner. Genome Research, 16:1890-900, 2006.

Jin, V. X., Rabinovich, A., Squazzo, S. L., Green, R. and Farnham, P.J. A computational genomics approach to identify cis-regulatory modules from chromatin immunoprecipitation microarray data - a case study using E2F1. Genome Research, 16:1585-1595, 2006.

Jin, V. X., O'Geen, H., Iyengar, S., Green, R. and Farnham, P. J. Identification of an OCT4 and SRY regulatory module using integrated computational and experimental genomics approaches. Genome Research, 17:807-817, 2007.

Krig, S. R., Jin, V. X., Bieda, M. C., O'Geen, H., Yaswen, P., Green R. and Farnham, P. J. Identification of genes directly regulated by the oncogene ZNF217 using ChIP-chip assays. J. Biol. Chem. 282:9703-9712, 2007.

The ENCODE Project Consortium. The ENCODE pilot project; identification and analysis of functional elements in 1% of the human genome. Nature, 447:799-816, 2007.

O' Geen, H., Squazzo, S. L., Iyengar, S., Blahnik, K., Rinn, J. L., Chang, H. Y., Green, R. and Farnham, P. J. Genome-wide analysis of KAP1 binding reveals auto-regulation of KRAB-ZNFs. PLOS Genetics 3, e89 doi:10.1371/journal.pgen.0030089, 2007.