Faculty Profile
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Peggy J Farnham
PROFESSOR Medical Pharmacology and Toxicology (School of Medicine) Associate Director of Genomics, Genome Center 4512 GBSF Office 530-754-4988 Lab 530-754-9653 pjfarnham@ucdavis.edu http://genomics.ucdavis.edu/farnham/ |
Degrees:
1982 - PhD - Yale University - Molecular Biophysics and Biochemistry
1978 - BA - Rice University - Biochemistry
Awards:
NIH Predoctoral Trainee, 1978-1982.
Damon Runyon-Walter Winchell Postdoctoral Fellow, 1982-1983.
NIH Postdoctoral Fellow, 1983-1986.
Outstanding Mentor in the U.W. Medical School, 1997, 1998
Vilas Associates Award, 1999-2000.
Department and Center Affiliations:
Pharmacology
Genome Center
Cancer Center
Professional Societies:
Associate Editor for the Journal of Biological Chemistry (2001-2006)
Editorial Board Member for Molecular and Cellular Biology (1998-2006)
Secretary for the American Society of Biochemistry and Molecular Biology (ASBMB)
Member, American Association for Cancer Research
Grad Group Affiliations and Specialties:
Biochemistry and Molecular Biology
Cell and Developmental Biology
Genetics
Publications:
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, In Press, 2008
Acevedo LG, Bieda M, Green R, and Farnham PJ. Analysis of the mechanisms mediating tumor specific changes in gene expression in human liver tumors. Cancer Research, In Press, 2008.
Johnson DS, et al. Systematic evaluation of variability in simulated ChIP-chip experiments. Genome Research, In press, 2008
Rinn JL, Kertesz M, Wang J. Squazzo SL, Xu X, Brugmann S, Goodnough H, Helms JA, Farnham PJ, Segal E, Chang HY. Functional Demarcation of Active and Silent Chromatin Domains in Human HOX Loci by Non-Coding RNAs. Cell 129, 1311-1323, 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 doi:10.1371/journal.pgen.0030089, 2007.
Yasui DH, Peddada S, Bieda MC, Vallero RO, Hogart A, Nagarajan RP, Thatcher KN, Farnham PJ, LaSalle JM. Integrated epigenomic analyses of neuronal MeCP2 reveal a role for long-range regulation of active genes. PNAS, 104:19416-21, 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.
Jin VX, O'Geen H., Iyengar S, Green R, Farnham PJ. Identification of an OCT4 and SRY regulatory module using integrated computational and experimental genomics approaches. Genome Res. 17:807-817, 2007.
Krig SR, Jin VX, Bieda MC, O’Geen H, Yaswen P, Green R, Farnham PJ Identification of genes directly regulated by the oncogene ZNF217 using ChIP-chip assays. J. Biol. Chem. 282:9703-9712, 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 Res. 17:1550-1561, 2007.
Acevedo LG, Iniguez AL, Holster HL, Zhang X, Green R, Farnham PJ. In Press. Genome-scale ChIP-chip analysis using 10,000 human cells. Biotechniques. 43: 791-797, 2007
Squazzo SL, Komashko VM, OGeen H, Krig S, Jin VX, Jang S-W, Green R, Margueron R, Reinberg D, and Farnham PJ. Suz12 silences large regions of the genome in a cell type-specific manner. Genome Research, 16:890-900, 2006
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
Lieb JD, Beck S., Bulyk ML, Farnham P, Hattori N, Henikoff S, Liu XS, Okumura K, Shiota K, Ushijima T, Greally JM. Applying whole-genome studies of epigenetic regulation to study human disease. Cytogenet. Genome Res. 114:1-15, 2006
O'Geen H, Nicolet CM, Blahnik K, Green R, Farnham PJ. Comparison of sample preparation methods for ChIP-chip assays. Biotechniques, 41:577-580, 2006.
Kuzmichev A, Margueron R, Vaquero A, Preissner TS, Scher M, Kirmizis A, Ouyang X, Brockdorff N, Abate-Shen C, Farnham P, Reinberg D. Composition and Histone Substrates of Polycomb Repressive Group Complexes Change during Cellular Differentiation. Proc. Natl. Acad. Sci. USA 102:1859-64, 2005.
Elnitski L, Jin VX, Farnham PJ, and Jones SJM. Locating mammalian transcription factor binding sites: a survey of computational and experimental techniques. Genome Research, 16: 1455-1464, 2006
Jin VX, Rabinovich A, Squazzo SL, Green R, and 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
Heisler LE, Torti D, Boutros PC, Watson J, Chan C, Winegarden N, Takahashi M, Yau P, Huang TH, Farnham PJ, Jurisica I, Woodgett JR, Bremner R, Penn LZ, Der SD. CpG Island microarray probe sequences derived from a physical library are representative of CpG Islands annotated on the human genome. Nucleic Acids Res. 33:2952-2961, 2005.
Oberley MO, Kirmizis A, Schelman WR, Farnham PJ. Using RNA interference to validate target genes identified by coupling chromatin immunoprecipitation with CpG-island microarrays. DNA Press, 2005.
Oberley MJ, Farnham PJ. Identification of mammalian E2F regulatory networks using DNA microarray hybridization analyses. In: Shannon MF, Rao S, eds. Microarrays and Transcription Networks. Georgetown: Landes Bioscience/Eurekah.com. 2005
Farnham, PJ. New insights into transcriptional regulation by RB: One size no longer fits all. In: Fanciulli, M. ed. Rb Regulation of Oncogenesis, Georgetown: Landes Bioscience/Eurekah.com, 2005.
Farnham, PJ. New insights into transcriptional regulation by RB: One size no longer fits all. In: Fanciulli, M. ed. Rb Regulation of Oncogenesis, Georgetown: Landes Bioscience/Eurekah.com, 2005.
Oberley MJ, Farnham PJ. Identification of mammalian E2F regulatory networks using DNA microarray hybridization analyses. In: Shannon MF, Rao S, eds. Microarrays and Transcription Networks. Georgetown: Landes Bioscience/Eurekah.com, 2005
Townsend, M. J., Weinmann, A. S., Matsuda, J., Saloman, R., Farnham, P., Biron, C. A., Gapin, L.,and Glimcher, L. H. T-bet regulates the terminal maturation and homeostasis of NK and Va14i NKT cells. Immunity, 20: 477-494.2004.
Reinberg D, Chuikov S, Farnham P, Karachentsev D, Kirmizis A, Kuzmichev A, Margueron R, Nishioka K, Preissner TS, Sarma K, Abate-Shen C, Steward R, Vaquero A. Steps toward understanding the inheritance of repressive methyl-lysine marks in histones. Cold Spring Harb Symp Quant Biol. 69:171-182, 2004.
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. 18:1592-1605, 2004.
Kirmizis, A. and Farnham, PJ. Genomic approaches that aid in the identification of transcription factor target genes. Exp Biol Med 229:705-721, 2004
Lavrrar, J.L. and Farnham, P. J. The use of transient chromatin immunoprecipitation assays to test models for E2F1-specific transcriptional activation. J Biol Chem. 279:46343-46349, 2004
Oberley, M.J., Tsao, J., Yau, P., and Farnham, P. J. High-throughput screening of chromatin immunoprecipitates using CpG-island microarrays. Methods in Enzymology 376: 315-333 2004.
Feingold et al. (see http://www.sciencemag.org/cgi/content/full/306/5696/636/DC1 for a complete list of authors). The ENCODE (ENCyclopedia Of DNA Elements) Project. Science, 306:636-640, 2004.
Mao, D.Y. L., Watson, J.D., Yan, P.S., Barsyte-Lovejoy, D., Khosravi, F., Wong, W.W.-L., Farnham, P. J., Huang, T.H.-M., Penn, L.Z. Analysis of Myc bound loci identified by CpG island arrays shows that Max is essential for Myc-dependent repression. Current Biology 13;1-20, 2003.
Oberley, M.J., Inman, D.R., and Farnham, P.J. E2F6 negatively regulates BRCA1 in human cancer cells without methylation of histone H3 on lysine 9. Journal of Biological Chem. 278:42466-42476-2003.
Oberley, M.J. and Farnham, P. J. Probing chromatin immunoprecipitates with CpG island microarrays to identify genomic sites occupied by DNA-binding proteins. Methods in Enzymology 371:577-596, 2003.
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.
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
Kirmizis, A, Bartley, S.M., and Farnham, P.J. Identification of the Polycomb Group protein SU(Z)12 as a new b-catenin target gene which is upregulated in colon tumors. Mol. Cancer Therapeutics, 2:113-121, 2003.
Eberhardy, S.R. and Farnham, P.J. Myc recruits P-TEFb to mediate the final step in the transcriptional activation of the cad promoter. J. Biol. Chem, 277: 40156-40162, 2002.
Wells, J. and Farnham, P.J. Characterizing transcription factor binding sites using formaldehyde crosslinking and immunoprecipitation. Methods 26:48-56, 2002.
Weinmann, A.S. and Farnham, P.J. Identification of unknown target genes of human transcription factors using chromatin immunoprecipitation. Methods 26:37-47, 2002.
Wells, J., Graveel, C.R., Bartley, S.M., and Farnham, P.J. The identification of E2F1-specific target genes. Proc. Natl. Acad. Sci. USA, 99:3890-3895,2002.
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
Eberhardy, S.R. and Farnham, P.J. c-Myc mediates activation of the cad promoter via a post-RNA polymerase II recruitment mechanism. J. Biol. Chem. 276:48562-48571, 2001.
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.
Maser, R.S., Mirzoeva, O., Wells, J., Olivares, H., Williams, B., Zinkel, R., Farnham, P.J., and Petrini, J.H.J. The MRE11 complex: diverse roles in S phase progression. Mol. Cell. Biol. 21: 6006-6016, 2001.
Albert, T., Wells, J., Funk, J.-O., Pullner, A., Raschke, E.-E., Stelzer, G., Meisterernst, M., Farnham, P.J., and Eick, D. Chromatin remodeling and acetylation of the dual c-myc promoters P1/P2 is regulated by separate elements. J. Biol. Chem. 276: 20482-20490, 2001.
Kel, A.E., Kel-Margoulis, O.V., Bartley, S.M., Farnham, P.J., Wingender, E.,and Zhang, M.Q.. Computer-assisted identification of cell cycle-related genes - new targets for E2F transcription factors. J. Mol. Biol. 309: 99-120, 2001.
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.
Eberhardy, S.R. and Farnham, P.J. Direct examination of histone acetylation of c-Myc target genes using chromatin immunoprecipitation. J. Biol. Chem. 275: 33798-33805, 2000.
Mac, S.M., DCunha, C., and Farnham, P.J. Direct recruitment of N-Myc to target gene promoters. Molecular Carcinogenesis 29:76-86, 2000.
Wells, J., Boyd, K.E., Fry, C.J., Bartley, S.M., and Farnham, P.J. Target gene specificity of E2F and pocket protein family members in living cells. Mol. Cell Biol. 20: 5987-5807, 2000.
Lee, T.A. and Farnham, P.J. Exogenous E2F1 is growth inhibitory before, during, and after neoplastic transformation, Oncogene. 19:2257-2268, 2000.
Mac, S.M. and Farnham, P.J. Cad, a c-Myc target gene, is not deregulated in Burkitts lymphomas, Molecular Carcinogenesis 27: 84-96, 2000.
Boyd, K.E. and Farnham, P.J. Co-examination of site-specific transcription factor binding and promoter activity in living cells. Mol. Cel. Biol. 19: 8393-8399, 1999.
Lukas, E.R., Bartley, S.M., Graveel, C.R., Diaz, Z.M., Dyson, N., Harlow, E., Yamasaki, L., and Farnham, P.J. Loss of E2F1 does not affect liver regeneration or hepatocarcinogenesis in C57BL/6J or C3H/HeJ mice. Molecular Carcinogenesis: 25:295-303, 1999.
Fry, C.J., Bartley, S.M., Malinowski, E., Pearson, A., Greenblatt, J., and Farnham, P.J. E2F1-dependent transactivation of the dhfr promoter: A requirement for recruitment of CBP. J. Biol. Chem 274:15883-15891, 1999.
Fry, C.J. and Farnham, P.J. Context-dependent activation of transcription, J. Biol. Chem. 274: 29583-29586, 1999.
Boyd, K.E. and Farnham, P.J. Identification of Target Genes of Oncogenic Transcription Factors, Proc. Soc. Exp. Biol. Med. 222:9-28, 1999.
Farnham, P.J. Review of the 1998 Keystone Symposium on Transcriptional Mechanisms, Taos, NM, February 21-26, 1998. BBA 1378: R33-R42, 1998.
Boyd, K.E., Wells, J., Gutman, J., Bartley, S.M., and Farnham, P.J. c-Myc target gene specificity is determined by post-DNA binding specificity. Proc. Natl. Acad. Sci. USA 95:13887-13892, 1998.
Bartley, S.M., Szakaly, R.J., and Farnham, P.J. Characterization of the 3' untranslated region of mouse E2F1 mRNA. Gene,223: 355-360, 1998.
van Ginkle, P.R., Hsiao, K.- M., Schjerven, H., and Farnham, P.J. E2F-mediated growth regulation requires transcription factor cooperation. J. Biol. Chem., 272: 18367-18374, 1997.
Dagnino, L., Fry, C.J., Bartley, S.M., Farnham, P., Gallie, B.L., and Phillips, R.A. Expression patterns of the E2F family of transcription factors during murine nervous system development. Mech. of Devel. 66: 13-25, 1997.
Dagnino, L., Fry, C.J., Bartley, S.M., Farnham, P., Gallie, B.L., and Phillips, R.A. Expression patterns of the E2F family of transcription factors during murine epithelial development. Cell Growth and Diff. 8: 553-563, 1997.
Boyd, K.E. and Farnham, P.J. Myc versus USF: Discrimination at the cad gene is determined by core promoter elements. Mol. Cell. Biol., 17:2529-2537, 1997.
Fry, C.J., Slansky, J.E., and Farnham, P.J. Position-dependent transcriptional regulation of the murine dihydrofolate reductase promoter by the E2F transactivation domain. Mol. Cell. Biol., 17: 1966-1976, 1997.
Boyd, K.E. and Farnham, P.J. Understanding the link between cad gene expression and cell growth. in Paths to Pyrimidines,Vol. 5, 1997.
Slansky, J.E. and Farnham, P.J. Introduction to the E2F family: Protein structure and gene regulation. in "Transcriptional Control of Cell Growth: The E2F Gene Family" Springer-Verlag, Current Topics in Microbiology and Immunology, Vol. 208: pp 1-30, 1996.
Slansky, J.E. and Farnham, P.J. Transcriptional Regulation of the Dihydrofolate Reductase Gene. in BioEssays, Vol. 18: 55-62, 1996.
Bennett, L.M. , Farnham, P.J., and Drinkwater, N.R. Strain-specific differences in DNA synthesis and gene expression in the regenerating livers of C57BL/6J and C3H/HeJ mice. Molecular Carcinogenesis 14: 46-52, 1995.
Miltenberger, R.J., Sukow, K.A., and Farnham, P.J. An E box-mediated increase in cad transcription at the G1/S-phase boundary is suppressed by inhibitory c-Myc mutants. Mol. Cell . Biol. 15: 2527-2535, 1995.
Miltenberger, R.J., Farnham, P.J., Smith, D.E., Stommel, J.M., and Cornwell, M.M. v-Raf activates transcription of growth-responsive promoters via GC-rich sequences that bind the transcription factor Sp1. Cell Growth and Diff. 6: 549-556, 1995.
Schilling, L.J. and Farnham, P.J. Bidirectional transcription from the DHFR/REP-3 locus is growth-regulated via two distinct mechanisms. Cell Growth and Diff. 6: 541-548, 1995.
Buermeyer, A.B., McMahon, S.L., Strasheim, L., and Farnham, P.J. Identification of cis-acting elements that can obviate the requirement for the C-terminal domain of RNA polymerase II. J. Biol. Chem. 270: 6798-6807, 1995.
Slansky, J.E. and Farnham, P.J. The Role of the transcription factor E2F in the growth regulation of DHFR. The Cell Cycle: Regulators, targets and clinical applications. XIIIth Washington International Spring Symposium, 1994.
Schilling, L.J. and Farnham, P.J. Inappropriate transcription from the 5' end of the dhfr gene obscures growth regulation. Nucleic Acids Res.15: 3061-3068, 1994.
Hsiao, K.-M., McMahon, S.L., and Farnham, P.J. Multiple DNA elements are required for the growth regulation of the mouse E2F1 promoter. Genes Dev. 8: 1526-1537, 1994.
Li, Y., Slansky, J.E., Myers, D.J., Drinkwater, N.R., Kaelin, W.G., and Farnham, P.J. Cloning, chromosomal location, and characterization of mouse E2F1, Mol. Cell. Biol.14: 1861-1869, 1994.
Kollmar, R., Sukow, K.A., Sponagle, S.K., and Farnham, P.J. Start-site selection at the TATA-less carbamoyl-phosphate synthase (glutamine-hydrolyzing)/aspartate carbamoyltransferase/dihydroorotase promoter, J. Biol. Chem. 269: 2252-2257, 1994.
Schilling, L.J. and Farnham, P.J. Transcriptional Regulation of the DHFR/REP-2 Locus. Critical Reviews in Eukaryotic Gene Expression 4: 19-53, 1994.
Farnham, P.J., Slansky, J.E., and Kollmar, R. The role of E2F in the mammalian cell cycle. Biochem. Biophys. Acta, 1155: 125-131, 1993.
Kollmar, R. and Farnham, P.J. Site-specific initiation of transcription by RNA polymerase II. Proc. Soc. Exp. Biol. Med. 203: 127-139, 1993.
Miltenberger, R.J., Cortner, J. and Farnham, P.J. Raf-1 mutant suppresses expression of a subset of v-raf activated promoters, J. Biol. Chem. 268: 15674-15680, 1993.
Slansky, J.E., Li, Y., Kaelin, W.G., and Farnham, P.J. A protein synthesis-dependent increase in E2F1 mRNA correlates with growth regulation of the dihydrofolate reductase promoter. Mol. Cell. Biol. 13: 1610-1618, 1993.
Kaelin, W.G., Krek, W., Seller, W.R., DeCaprio, J.A., Ajchenbaum, R., Fuchs, C.S., Chittenden, T., Li, Y., Farnham, P.J., Blanar, M.A., Livingston, D.M., and Flemington, E.K. Expressing cloning of a cDNA encoding a retinoblastoma-binding protein with E2F-like properties. Cell 70: 351-364, 1992.
Buermeyer, A.B., Thompson, N.E., Strasheim, L.A., Burgess, R.R., and Farnham, P.J. The HIP1 initiator element plays a role in determining the in vitro requirement of the DHFR promoter for the C-terminal domain of RNA polymerase II. Mol. Cell. Biol. 12: 2250-2259, 1992.
Mack, K.J., Cortner, J. Mack, P., and Farnham, P.J. Krox 20 messenger RNA and protein expression in the adult central nervous system. Molecular Brain Research, 14:117-123, 1992.
Means, A. L., Slansky, J. E., McMahon, S. L., Knuth, M. W., and Farnham, P. J. The HIP1 binding site is required for growth regulation of the DHFR promoter. Mol. Cell. Biol. 12: 1054-1063, 1992.
Kollmar, R., Lindstrom, M., and Farnham, P.J. Heat sensitivity and Sp1 activation of complex formation at the syrian hamster CAD promoter in vitro. J. Biol. Chem. 267:385-391, 1992.
Cortner, J. and Farnham, P.J. Cell cycle analysis of Krox-20, c-fos, and JE expression in proliferating NIH 3T3 fibroblasts. Cell Growth and Diff. 2: 465-473, 1991.
Farnham, P.J. and Cornwell, M.M. Sp1 activation of RNA polymerase II transcription complexes involves a heat-labile DNA-binding component. Gene Express. 1: 137-148, 1991.
Cortner, J. and Farnham, P.J. Identification of the serum-responsive transcription initiation site of the zinc finger gene, Krox-20. Mol. Cell. Biol. 10:3788-3791, 1990.
Farnham, P.J. and Kollmar, R. Characterization of the 5' end of the growth-regulated syrian hamster CAD gene. Cell Growth and Diff. 1:179-189, 1990.
Farnham, P.J. and Means, A.L. Sequences downstream of the transcription initiation site modulate the activity of the murine dihydrofolate reductase promoter. Mol. Cell. Biol. 10:1390-1398, 1990.
Means, A.L. and Farnham, P.J. Transcription Initiation from the dihydrofolate reductase promoter is positioned by HIP1 binding at the initiation site. Mol. Cell. Biol. 10:653-661, 1990.
Schilling, L.J. and Farnham, P.J. Identification of a new promoter upstream of the murine dihydrofolate reductase gene. Mol. Cell. Biol. 9:4568-4570, 1989.
Farnham, P.J. and Schimke, R.T. In vitro transcription and delimitation of promoter elements of the dihydrofolate reductase gene. Mol. Cell. Biol. 6: 2392-2401, 1986.
Farnham, P.J. and Schimke, R.T. Murine dihydrofolate reductase transcripts through the cell cycle. Mol. Cell. Biol. 6: 365-371, 1986.
Farnham, P.J., Abrams, J.A., and Schimke, R.T. Opposite strand RNAs from the 5' flanking region of the mouse dihydrofolate reductase gene. Proc. Natl. Acad. Sci. USA 82: 3978-3982, 1985.
Farnham, P.J. and Schimke, R.T. Transcriptional regulation of mouse dihydrofolate reductase in the cell cycle. J. Biol. Chem. 260: 7675-7680, 1985.
McGrogan, M., Simonsen, C.C., Smouse, D.T., Farnham, P.J., and Schimke, R.T. Heterogeneity at the 5' termini of mouse dihydrofolate reductase mRNAs. J. Biol. Chem. 260: 2307-2314, 1985.
Hamkalo, B.A., Farnham, P.J., Johnston, R., and Schimke, R.T. Ultra-structural features of minute chromosomes in a methotrexate-resistant mouse 3T3 cell line. Proc. Natl. Acad. Sci. USA 82: 1126-1130, 1985.
Price, J., Farnham, P.J., and Korn. L.J. A protein factor regulates transcription of the Xenopus 5S ribosomal RNA genes in a positive fashion. In Gene Expression, UCLA Symposia on Molecular and Cellular Biology, New Series Volume III, 273-281, 1983.
Platt, T., Horowitz, H., and Farnham, P.J. A kinetic view of transcription termination. Microbiology 83: 21-25, 1983.
Farnham, P.J., Greenblatt, J., and Platt, T. Effects of nusA protein on transcription termination in the tryptophan operon of E. coli. Cell 29: 945-951, 1982.
Farnham, P.J. and Platt, T. Effects of DNA analogs on transcription termination at the tryptophan operon attenuator of E. coli. Proc. Natl. Acad. Sci. USA 79: 998-1002, 1982.
Christie, G.E., Farnham, P.J., and Platt, T. Synthetic sites for transcription termination and a functional comparison with tryptophan operon termination sites in vitro. Proc. Natl. Acad. Sci. USA 78: 4180-4184, 1981.
Farnham, P.J. and Platt, T. Rho-independent termination: Dyad symmetry in DNA causes RNA polymerase to pause during transcription in vitro. Nucl. Acids Res. 9: 563-577, 1981.
Farnham, P.J. and Platt, T. A model for transcription termination suggested by studies on the trp attenuator in vitro using base analogs. Cell 20: 739-748,1980.
Farnham, P.J., Novak, R. A., and McAdoo, D.J. A reexamination of the distributions of octopamine and phenylethanolamine in the Aplysia nervous system. J. Neurochem. 30: 1173-1176, 1978.
Asch, H.L. and Farnham, P.J. Effects of gentamicin on trypsin, chymotrypsin, and collagenase. J. Infect. Dis. 138: 257-259, 1978.
Research Interests:
My laboratory has been a leader in developing the technique of chromatin immunoprecipitation (ChIP) to study the function of mammalian transcription factors. Recently, we 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). We began by developing the ChIP-CpG approach, in which we used microarrays containing ~10,000 human or mouse CpG islands. More recently, we have worked in close collaboration with NimbleGen Systems, Inc (Madison, WI) to develop protocols that allow the use of high-density oligonucleotide microarrays for ChIP-chip studies. These new arrays allow a comprehensive analysis of transcription factor binding sites and chromatin modifications on a genome-wide scale. Current projects in the Farnham lab include the analysis of changes in chromatin structure as embryonic stem cells differentiate or as normal cells transform to tumor cells and 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), and the E2F/Rb family (key regulators of cell cycle progression). In addition to our bench work, we are also developing programs to assist in the analysis of genome-scale ChIP-chip data and to derive consensus motifs from experimentally identified binding sites.
Laboratory Personnel:
Farnham Laboratory/4617 GBSF - Henny O'Geen (project scientist) Victor Jin (postdoc) Seth Frietze (postdoc) Luis Acevedo (grad student) Alina Rabinovich (grad student) Vitalina Komashko (grad student) Sushma Iyengar (grad student) Kim Blahnik (grad student) Shally Xu (research specialist)
http://genomics.ucdavis.edu/farnham/