The Farnham laboratory has been a leader in developing the technique of chromatin immunoprecipitation (ChIP) to study mammalian transcription factors. Recently, they have extended these studies to allow a high throughput, global analysis of transcription factor target genes by combining chromatin immunoprecipitation with genomic microarray hybridization (ChIP-chip assays) and with high throughput sequencing (ChIP-seq). Current projects include the analysis of chromatin structure in embryonic stem cells and other normal and tumor cell types and the genome-wide identification of target genes of a variety of human transcription factors. In addition to bench work, the Farnham lab is also developing programs to assist in the analysis of genome-scale ChIP-chip and ChIP-seq data and to derive consensus motifs from experimentally identified binding sites. Dr. Farnham is a member of the ENCODE Consortium, whose goal is to map all the functional elements in the human genome. She is also a member of the recently funded NIH Roadmap UC Reference Epigenome Mapping Center; her lab will be determining the histone modifications for a variety of different human cell types.

Research Support

NIH/NCI R21 CA128471. Through 2009: Scaling the ChIP-chip assay to improve analysis of clinical biospecimens

NIH/NCI R01 CA045240. Through 2011: Transcriptional Regulation of Growth Related Genes

NIH/NHGRI 1U54HG004558 (PI: Snyder/Yale; Farnham, co-investigator). Through 2011:Production Center for Global Mapping of Regulatory Elements

NIH U01 NIH/NCI 1U01ES017154 (PI: Costello/UCSF; Farnham, co-investigator). Through 2013: Integrated epigenetic maps of human embryonic and adult cells

International Consortia

NHGRI: Encyclopedia of DNA Elements (ENCODE)
NIH Roadmap: Reference Epigenome Mapping Centers (REMC)

Editorial Boards

Current: Editorial Board Member for Genome Research.
Past: Associate Editor of the Journal of Biological Chemistry, Editorial Board Member for Molecular and Cellular Biology.

Representative Publications

Weinmann AS, Yan PS, Oberley MJ, Huang HMT, and Farnham PJ. Isolating human transcription factor targets by combining chromatin immunoprecipitation and CpG microarray analysis. Genes & Dev. 16:235-244,2002.

Kirmizis A., Bartley SM, Kuzmichev A, Margueron R, Reinberg R, Green R, and Farnham PJ. Silencing of human polycomb target genes is associated with methylation of histone H3 lysine 27. Genes & Devel. 18:1592-1605, 2004.

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

Squazzo SL, Komashko VM, O’Geen H, Krig S, Jin VX, Jang S-W, Green R, Margueron R, Reinberg D, Farnham PJ. Suz12 silences large regions of the genome in a cell type-specific manner. Genome Research 16:890-900, 2006.

Jin VX, Rabinovich A, Squazzo SL, Green R, Farnham PJ. 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

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 SL, Iyengar S, Blahnik K, Rinn JL, Chang HY, Green R, Farnham PJ. Genome-wide Analysis of KAP1 Binding Suggests an Auto-regulation of KRAB-ZNFs. PLOS Genetics 3, e89, 2007.

Xu X, Bieda M, Jin VX, Rabinovich A, Oberley MJ, Green R, Farnham PJ. A comprehensive ChIP-chip analysis of E2F1, E2F4, and E2F6 in normal and tumor cells reveals interchangeable roles of E2F family members. Genome Research 17:1550-61, 2007.

Acevedo LG, Bieda M, Green R, Farnham PJ. Analysis of the mechanisms mediating tumor specific changes in gene expression in human liver tumors. Cancer Research 68:2641-2651, 2008.

Komashko VM, Acevedo LG, Squazzo SL, Iyengar SS, Rabinovich A, O’Geen H, Green R, Farnham PJ. Using ChIP-chip technology to reveal common principles of transcriptional repression in normal and cancer cells. Genome Research 18:521-532, 2008

Rabinovich A, Jin VX, Rabinovich R, Xu X, Farnham PJ E2F in vivo binding specificity: comparison of consensus vs. non-consensus binding sites. Genome Research 18:1763-1777, 2008

Frietze S, Lan X, Jin VX, Farnham PJ. Genome-wide targets of the KRAB and SCAN domain-containing xzinc finger protein ZNF263. J. Biol. Chem. In Press, 2009.

Blahnik KR, Dou L, O’Geen H, McPhillips T, Xu X, Cao AR, Iyengar S, Nicolet CM, Ludäscher B, Korf I, Farnham PJ. Sole-Search: An integrated analysis program for peak detection and functional annotation using ChIP-seq data. Nuc. Acids Res. In Press, 2009.

See: Complete List of Publications

Recent/Current Teaching

IOR for Pharm 250: Functional Genomics
Regular Lecturer in:
MCB 200B: Current Techniques in Biochemistry
MMI 280: Molecular Pathobiology