Peggy Farnham
A5083201945- Genomics and Chromatin Dynamics
- Epigenetics and DNA Methylation
- RNA modifications and cancer
- Gene expression and cancer classification
- RNA Research and Splicing
- Cancer-related Molecular Pathways
- Cancer-related gene regulation
- RNA and protein synthesis mechanisms
- Bioinformatics and Genomic Networks
- CRISPR and Genetic Engineering
- Cancer-related molecular mechanisms research
- Virus-based gene therapy research
- MicroRNA in disease regulation
- Endoplasmic Reticulum Stress and Disease
- Genetics and Neurodevelopmental Disorders
- DNA Repair Mechanisms
- Ubiquitin and proteasome pathways
- Genetic Associations and Epidemiology
- PARP inhibition in cancer therapy
- Nuclear Receptors and Signaling
- Molecular Biology Techniques and Applications
- Chromosomal and Genetic Variations
- Advanced biosensing and bioanalysis techniques
- Genomics and Rare Diseases
- Biochemical and Molecular Research
University of Southern California
2014-2024
Keck Hospital of USC
2023
Southern California University for Professional Studies
2011-2022
University of California, Davis
2005-2015
University of Wisconsin–Madison
1997-2012
University of California Davis Medical Center
2012
University of California, San Francisco
2012
University of Pennsylvania
2012
USC Norris Comprehensive Cancer Center
2011
University of Memphis
2009
The reference human genome sequence set the stage for studies of genetic variation and its association with disease, but epigenomic lack a similar reference. To address this need, NIH Roadmap Epigenomics Consortium generated largest collection so far epigenomes primary cells tissues. Here we describe integrative analysis 111 as part programme, profiled histone modification patterns, DNA accessibility, methylation RNA expression. We establish global maps regulatory elements, define modules...
Chromatin immunoprecipitation (ChIP) followed by high-throughput DNA sequencing (ChIP-seq) has become a valuable and widely used approach for mapping the genomic location of transcription-factor binding histone modifications in living cells. Despite its widespread use, there are considerable differences how these experiments conducted, results scored evaluated quality, data metadata archived public use. These practices affect quality utility any global ChIP experiment. Through our experience...
Transcription factors bind in a combinatorial fashion to specify the on-and-off states of genes; ensemble these binding events forms regulatory network, constituting wiring diagram for cell. To examine principles human transcriptional we determined genomic information 119 transcription-related over 450 distinct experiments. We found combinatorial, co-association transcription be highly context specific: combinations at specific locations. In particular, there are significant differences...
Genes overlap across psychiatric disease Many genome-wide studies have examined genes associated with a range of neuropsychiatric disorders. However, the degree to which genetic underpinnings these diseases differ or is unknown. Gandal et al. performed meta-analyses transcriptomic covering five major disorders and compared cases controls identify coexpressed gene modules. From this, they found that some share global expression patterns. This in polygenic traits may allow for better diagnosis...
Polycomb group (PcG) complexes 2 and 3 are involved in transcriptional silencing. These contain a histone lysine methyltransferase (HKMT) activity that targets different residues on histones H1 or H3 vitro. However, it is not known if these methylation vivo because the human PRC2/3 have been studied context of natural promoter lack target genes. Here we report use RNA expression arrays CpG-island DNA to identify characterize Using oligonucleotide arrays, first identified cohort genes whose...
Previously, identification of promoters regulated by mammalian transcription factors has relied upon overexpression studies. Here we present the a large set that are bound E2F in physiological conditions. Probing human CpG microarray with chromatin immunoprecipitated using an antibody to E2F4, have identified 68 unique target loci; 15% bidirectional and 25% recruit via mechanism distinct from defined consensus site. Interestingly, although been shown previously regulate genes involved cell...
Changes in the substrate specificities of factors that irreversibly modify histone components chromatin are expected to have a profound effect on gene expression through epigenetics. Ezh2 is histone-lysine methyltransferase with activity dependent its association other Polycomb Repressive Complexes 2 and 3 (PRC2/3). levels increasingly elevated during prostate cancer progression. Other PRC2/3 also cells. Overexpression tissue culture promotes formation previously undescribed PRC complex,...
Mutations in MECP2 cause the autism-spectrum disorder Rett syndrome. MeCP2 is predicted to bind methylated promoters and silence transcription. However, first large-scale mapping of neuronal MeCP2-binding sites on 26.3 Mb imprinted nonimprinted loci revealed that 59% are outside genes only 6% CpG islands. Integrated genome-wide promoter analysis binding, methylation, gene expression 63% MeCP2-bound actively expressed highly methylated. These results indicate primary function not silencing promoters.
Suz12 is a component of the Polycomb group complexes 2, 3, and 4 (PRC 2/3/4). These are critical for proper embryonic development, but very few target genes have been identified in either mouse or human cells. Using variety ChIP-chip approaches, we large set five different cell lines. Interestingly, found that promoters type specific, with transcription factors homeobox proteins predominating embryonal cells glycoproteins immunoglobulin-related adult tumors. We also characterized...
Genes implicated in neuropsychiatric disorders are active human fetal brain, yet difficult to study a longitudinal fashion. We demonstrate that organoids from pluripotent cells model cerebral cortical development on the molecular level before 16 weeks postconception. A multiomics analysis revealed differentially genes and enhancers, with greatest changes occurring at transition stem progenitors. Networks of converging gene enhancer modules were assembled into six four global patterns...
Distinct epigenomic profiles of histone marks have been associated with gene expression, but questions regarding the causal relationship remain. Here we investigated activity a broad collection genomically targeted epigenetic regulators that could write repressed chromatin state (G9A, SUV39H1, Krüppel-associated box (KRAB), DNMT3A as well first targetable versions Ezh2 and Friend GATA-1 (FOG1)). dCas9 fusions produced target repression over range 0- to 10-fold varied by locus cell type....