Faculty

Peggy Farnham, PhD
Peggy Farnham, PhD
Chair and Professor of Biochemistry & Molecular Medicine;W.M. Keck Chair in Biochemistry
Biochemistry and Molecular Medicine
NRT 511 B 1450 Biggy Street Health Sciences Campus Los Angeles
Dr. Farnham is the William M. Keck Professor of Biochemistry and the Chair of the Department of Biochemistry and Molecular Biology at the Keck School of Medicine at the University of Southern California in Los Angeles, California. Dr. Farnham received her bachelor’s degree from Rice University, her Ph.D. from Yale University, and performed her post-doctoral training at Stanford University. Dr. Farnham previously held Professorships at the McArdle Laboratory for Cancer Research at the University of Wisconsin-Madison and at the University of California-Davis where she was the Associate Director of the UC Davis Genome Center. Dr. Farnham is an international leader in the study of chromatin regulation and its control of transcription factor binding and function. She is a member of an international consortia of genomic scientists working on the ENCODE (Encyclopedia of DNA elements) Project and a member of an NIH Roadmap Reference Epigenome Mapping Center. Based on her contributions to biomedical research, she was elected as a fellow of AAAS in 2010 and in 2012 she received the ASBMB Herbert A Sober Award, which recognizes outstanding biochemical and molecular biological research with particular emphasis on the development of methods and techniques to aid in research.

Research Interests: transcriptional genomics, genomic technologies
Diseases Models: cancer cells and tissues, cultured neuroepithelial cells
Consortia: ENCODE, Roadmap Epigenome Mapping Centers, PsychENCODE

: ASBMB Herbert A. Sober Award , 2012

: Ooops. Something went wrong., 2012

: AAAS Fellow, 2010

: Ooops. Something went wrong., 2010

CRISPR-mediated deletion of prostate cancer risk-associated CTCF loop anchors identifies repressive chromatin loops Genome Biol. 2018 Oct 08; 19(1):160. . View in PubMed

CRISPR-mediated deletion of prostate cancer risk-associated CTCF loop anchors identifies repressive chromatin loops Genome Biol. 2018 10 08; 19(1):160. . View in PubMed

Defining Regulatory Elements in the Human Genome Using Nucleosome Occupancy and Methylome Sequencing (NOMe-Seq) Methods Mol Biol. 2018; 1766:209-229. . View in PubMed

A Prostate Cancer Risk Element Functions as a Repressive Loop that Regulates HOXA13 Cell Rep. 2017 Nov 07; 21(6):1411-1417. . View in PubMed

dCas9-based epigenome editing suggests acquisition of histone methylation is not sufficient for target gene repression Nucleic Acids Res. 2017 Sep 29; 45(17):9901-9916. . View in PubMed

4C-seq revealed long-range interactions of a functional enhancer at the 8q24 prostate cancer risk locus Sci Rep. 2016 Mar 03; 6:22462. . View in PubMed

Identification of activated enhancers and linked transcription factors in breast, prostate, and kidney tumors by tracing enhancer networks using epigenetic traits Epigenetics Chromatin. 2016; 9:50. . View in PubMed

Effects on the transcriptome upon deletion of a distal element cannot be predicted by the size of the H3K27Ac peak in human cells Nucleic Acids Res. 2016 05 19; 44(9):4123-33. . View in PubMed

Inferring regulatory element landscapes and transcription factor networks from cancer methylomes Genome Biol. 2015 May 21; 16:105. . View in PubMed

Integrative analysis of 111 reference human epigenomes Nature. 2015 Feb 19; 518(7539):317-30. . View in PubMed

Intermediate DNA methylation is a conserved signature of genome regulation Nat Commun. 2015 Feb 18; 6:6363. . View in PubMed

Epigenetic and transcriptional determinants of the human breast Nat Commun. 2015 Feb 18; 6:6351. . View in PubMed

Demystifying the secret mission of enhancers: linking distal regulatory elements to target genes Crit Rev Biochem Mol Biol. 2015; 50(6):550-73. . View in PubMed

Altering cancer transcriptomes using epigenomic inhibitors Epigenetics Chromatin. 2015; 8:9. . View in PubMed

Functional annotation of colon cancer risk SNPs Nat Commun. 2014 Sep 30; 5:5114. . View in PubMed

Global loss of DNA methylation uncovers intronic enhancers in genes showing expression changes Genome Biol. 2014 Sep 20; 15(9):469. . View in PubMed

Global analysis of ZNF217 chromatin occupancy in the breast cancer cell genome reveals an association with ERalpha BMC Genomics. 2014 Jun 24; 15:520. . View in PubMed

Defining functional DNA elements in the human genome Proc Natl Acad Sci U S A. 2014 Apr 29; 111(17):6131-8. . View in PubMed

Comprehensive functional annotation of 77 prostate cancer risk loci PLoS Genet. 2014 Jan; 10(1):e1004102. . View in PubMed

Analysis of an artificial zinc finger epigenetic modulator: widespread binding but limited regulation Nucleic Acids Res. 2014; 42(16):10856-68. . View in PubMed

Can genome engineering be used to target cancer-associated enhancers? Epigenomics. 2014; 6(5):493-501.. View in PubMed

Cross-talk between site-specific transcription factors and DNA methylation states J Biol Chem. 2013 Nov 29; 288(48):34287-94. . View in PubMed

Functional DNA methylation differences between tissues, cell types, and across individuals discovered using the M&M algorithm Genome Res. 2013 Sep; 23(9):1522-40. . View in PubMed

DNA hypomethylation within specific transposable element families associates with tissue-specific enhancer landscape Nat Genet. 2013 Jul; 45(7):836-41. . View in PubMed

Cell type-specific binding patterns reveal that TCF7L2 can be tethered to the genome by association with GATA3 Genome Biol. 2012 Sep 26; 13(9):R52. . View in PubMed

Architecture of the human regulatory network derived from ENCODE data Nature. 2012 Sep 06; 489(7414):91-100. . View in PubMed

An integrated encyclopedia of DNA elements in the human genome Nature. 2012 Sep 06; 489(7414):57-74. . View in PubMed

ChIP-seq guidelines and practices of the ENCODE and modENCODE consortia Genome Res. 2012 Sep; 22(9):1813-31. . View in PubMed

Integration of Hi-C and ChIP-seq data reveals distinct types of chromatin linkages Nucleic Acids Res. 2012 Sep; 40(16):7690-704. . View in PubMed

Human ESC self-renewal promoting microRNAs induce epithelial-mesenchymal transition in hepatocytes by controlling the PTEN and TGFß tumor suppressor signaling pathways Mol Cancer Res. 2012 Jul; 10(7):979-91. . View in PubMed

Autophagy driven by a master regulator of hematopoiesis Mol Cell Biol. 2012 Jan; 32(1):226-39. . View in PubMed

Genetic framework for GATA factor function in vascular biology Proc Natl Acad Sci U S A. 2011 Aug 16; 108(33):13641-6. . View in PubMed

Functional analysis of KAP1 genomic recruitment Mol Cell Biol. 2011 May; 31(9):1833-47. . View in PubMed

Genome-wide analysis of transcription factor E2F1 mutant proteins reveals that N- and C-terminal protein interaction domains do not participate in targeting E2F1 to the human genome J Biol Chem. 2011 Apr 08; 286(14):11985-96. . View in PubMed

A user's guide to the encyclopedia of DNA elements (ENCODE) PLoS Biol. 2011 Apr; 9(4):e1001046. . View in PubMed

Characterization of the contradictory chromatin signatures at the 3' exons of zinc finger genes PLoS One. 2011 Feb 15; 6(2):e17121. . View in PubMed

Epigenetic modulation of miR-122 facilitates human embryonic stem cell self-renewal and hepatocellular carcinoma proliferation PLoS One. 2011; 6(11):e27740. . View in PubMed

Genome-wide binding of the orphan nuclear receptor TR4 suggests its general role in fundamental biological processes BMC Genomics. 2010 Dec 02; 11:689. . View in PubMed

Comparison of sequencing-based methods to profile DNA methylation and identification of monoallelic epigenetic modifications Nat Biotechnol. 2010 Oct; 28(10):1097-105. . View in PubMed

5-azacytidine treatment reorganizes genomic histone modification patterns Epigenetics. 2010 Apr; 5(3):229-40. . View in PubMed

Genomic targets of the KRAB and SCAN domain-containing zinc finger protein 263 J Biol Chem. 2010 Jan 08; 285(2):1393-403. . View in PubMed

Discovering hematopoietic mechanisms through genome-wide analysis of GATA factor chromatin occupancy Mol Cell. 2009 Nov 25; 36(4):667-81. . View in PubMed

Insights from genomic profiling of transcription factors Nat Rev Genet. 2009 Sep; 10(9):605-16. . View in PubMed

E2F in vivo binding specificity: comparison of consensus versus nonconsensus binding sites Genome Res. 2008 Nov; 18(11):1763-77. . View in PubMed

Analysis of the mechanisms mediating tumor-specific changes in gene expression in human liver tumors Cancer Res. 2008 Apr 15; 68(8):2641-51. . View in PubMed

Integrated epigenomic analyses of neuronal MeCP2 reveal a role for long-range interaction with active genes Proc Natl Acad Sci U S A. 2007 Dec 04; 104(49):19416-21. . View in PubMed

Genome-scale ChIP-chip analysis using 10,000 human cells Biotechniques. 2007 Dec; 43(6):791-7. . View in PubMed

A comprehensive ChIP-chip analysis of E2F1, E2F4, and E2F6 in normal and tumor cells reveals interchangeable roles of E2F family members Genome Res. 2007 Nov; 17(11):1550-61. . View in PubMed

Functional demarcation of active and silent chromatin domains in human HOX loci by noncoding RNAs Cell. 2007 Jun 29; 129(7):1311-23. . View in PubMed

Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project Nature. 2007 Jun 14; 447(7146):799-816. . View in PubMed

Genome-wide analysis of KAP1 binding suggests autoregulation of KRAB-ZNFs PLoS Genet. 2007 Jun; 3(6):e89. . View in PubMed

Identification of an OCT4 and SRY regulatory module using integrated computational and experimental genomics approaches Genome Res. 2007 Jun; 17(6):807-17. . View in PubMed

Identification of genes directly regulated by the oncogene ZNF217 using chromatin immunoprecipitation (ChIP)-chip assays J Biol Chem. 2007 Mar 30; 282(13):9703-12. . View in PubMed

A computational genomics approach to identify cis-regulatory modules from chromatin immunoprecipitation microarray data--a case study using E2F1 Genome Res. 2006 Dec; 16(12):1585-95. . View in PubMed

Comparison of sample preparation methods for ChIP-chip assays Biotechniques. 2006 Nov; 41(5):577-80. . View in PubMed

Composition and histone substrates of polycomb repressive group complexes change during cellular differentiation Proc Natl Acad Sci U S A. 2005 Feb 08; 102(6):1859-64. . View in PubMed

CpG Island microarray probe sequences derived from a physical library are representative of CpG Islands annotated on the human genome Nucleic Acids Res. 2005; 33(9):2952-61. . View in PubMed

Genomic approaches that aid in the identification of transcription factor target genes Exp Biol Med (Maywood). 2004 Sep; 229(8):705-21. . View in PubMed

High-throughput screening of chromatin immunoprecipitates using CpG-island microarrays Methods Enzymol. 2004; 376:315-34. . View in PubMed

E2F6 negatively regulates BRCA1 in human cancer cells without methylation of histone H3 on lysine 9 J Biol Chem. 2003 Oct 24; 278(43):42466-76. . View in PubMed

Analysis of Myc bound loci identified by CpG island arrays shows that Max is essential for Myc-dependent repression Curr Biol. 2003 May 13; 13(10):882-6. . View in PubMed

Identification and characterization of CRG-L2, a new marker for liver tumor development Oncogene. 2003 Mar 20; 22(11):1730-6. . View in PubMed

Identification of novel pRb binding sites using CpG microarrays suggests that E2F recruits pRb to specific genomic sites during S phase Oncogene. 2003 Mar 13; 22(10):1445-60. . View in PubMed

Identification of the polycomb group protein SU(Z)12 as a potential molecular target for human cancer therapy Mol Cancer Ther. 2003 Jan; 2(1):113-21. . View in PubMed

In vivo assays to examine transcription factor localization and target gene specificity Methods. 2002 Jan; 26(1):1-2. . View in PubMed

Characterizing transcription factor binding sites using formaldehyde crosslinking and immunoprecipitation Methods. 2002 Jan; 26(1):48-56. . View in PubMed

Identification of unknown target genes of human transcription factors using chromatin immunoprecipitation Methods. 2002 Jan; 26(1):37-47. . View in PubMed

c-Myc mediates activation of the cad promoter via a post-RNA polymerase II recruitment mechanism J Biol Chem. 2001 Dec 21; 276(51):48562-71. . View in PubMed

Computer-assisted identification of cell cycle-related genes: new targets for E2F transcription factors J Mol Biol. 2001 May 25; 309(1):99-120. . View in PubMed

Expression profiling and identification of novel genes in hepatocellular carcinomas Oncogene. 2001 May 10; 20(21):2704-12. . View in PubMed

Direct examination of histone acetylation on Myc target genes using chromatin immunoprecipitation J Biol Chem. 2000 Oct 27; 275(43):33798-805. . View in PubMed

Direct recruitment of N-myc to target gene promoters Mol Carcinog. 2000 Oct; 29(2):76-86. . View in PubMed

Exogenous E2F expression is growth inhibitory before, during, and after cellular transformation Oncogene. 2000 Apr 27; 19(18):2257-68. . View in PubMed

CAD, a c-Myc target gene, is not deregulated in Burkitt's lymphoma cell lines Mol Carcinog. 2000 Feb; 27(2):84-96. . View in PubMed

Coexamination of site-specific transcription factor binding and promoter activity in living cells Mol Cell Biol. 1999 Dec; 19(12):8393-9. . View in PubMed

Context-dependent transcriptional regulation J Biol Chem. 1999 Oct 15; 274(42):29583-6. . View in PubMed

Identification of target genes of oncogenic transcription factors Proc Soc Exp Biol Med. 1999 Oct; 222(1):9-28. . View in PubMed

Activation of the murine dihydrofolate reductase promoter by E2F1A requirement for CBP recruitment. J Biol Chem. 1999 May 28; 274(22):15883-91. . View in PubMed

Characterization of the 3' untranslated region of mouse E2F1 mRNA Gene. 1998 Nov 26; 223(1-2):355-60. . View in PubMed

c-Myc target gene specificity is determined by a post-DNAbinding mechanism Proc Natl Acad Sci U S A. 1998 Nov 10; 95(23):13887-92. . View in PubMed

E2F-mediated growth regulation requires transcription factor cooperation J Biol Chem. 1997 Jul 18; 272(29):18367-74. . View in PubMed

Conclusions and future directions Curr Top Microbiol Immunol. 1996; 208:129-37. . View in PubMed

An E-box-mediated increase in cad transcription at the G1/S-phase boundary is suppressed by inhibitory c-Myc mutants Mol Cell Biol. 1995 May; 15(5):2527-35. . View in PubMed

Identification of cis-acting elements that can obviate a requirement for the C-terminal domain of RNA polymerase II J Biol Chem. 1995 Mar 24; 270(12):6798-807. . View in PubMed

Inappropriate transcription from the 5' end of the murine dihydrofolate reductase gene masks transcriptional regulation Nucleic Acids Res. 1994 Aug 11; 22(15):3061-8. . View in PubMed

Cloning, chromosomal location, and characterization of mouse E2F1 Mol Cell Biol. 1994 Mar; 14(3):1861-9. . View in PubMed

An inhibitory Raf-1 mutant suppresses expression of a subset of v-raf-activated genes J Biol Chem. 1993 Jul 25; 268(21):15674-80. . View in PubMed

A protein synthesis-dependent increase in E2F1 mRNA correlates with growth regulation of the dihydrofolate reductase promoter Mol Cell Biol. 1993 Mar; 13(3):1610-8. . View in PubMed

Expression cloning of a cDNA encoding a retinoblastoma-binding protein with E2F-like properties Cell. 1992 Jul 24; 70(2):351-64. . View in PubMed

Heat sensitivity and Sp1 activation of complex formation at the Syrian hamster carbamoyl-phosphate synthase (glutamine-hydrolyzing)/aspartate carbamoyltransferase/dihydroorotase promoter in vitro J Biol Chem. 1992 Jan 05; 267(1):385-91. . View in PubMed

Cell cycle analysis of Krox-20, c-fos, and JE expression in proliferating NIH3T3 fibroblasts Cell Growth Differ. 1991 Sep; 2(9):465-73. . View in PubMed

Identification of the serum-responsive transcription initiation site of the zinc finger gene Krox-20 Mol Cell Biol. 1990 Jul; 10(7):3788-91. . View in PubMed

Characterization of the 5' end of the growth-regulated Syrian hamster CAD gene Cell Growth Differ. 1990 Apr; 1(4):179-89. . View in PubMed

Identification of a new promoter upstream of the murine dihydrofolate reductase gene Mol Cell Biol. 1989 Oct; 9(10):4568-70. . View in PubMed

In vitro transcription and delimitation of promoter elements of the murine dihydrofolate reductase gene Mol Cell Biol. 1986 Jul; 6(7):2392-401. . View in PubMed

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Effects of DNA base analogs on transcription termination at the tryptophan operon attenuator of EScherichia coli Proc Natl Acad Sci U S A. 1982 Feb; 79(4):998-1002. . View in PubMed

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