Positions

Overview

  • Dr. Riddle obtained her undergraduate degree from the University of Missouri in Columbia, carrying out research in a maize lab. During her graduate work at Washington University in St. Louis, she first learned about epigenetics, a research field that focuses on heritable changes in phenotypes that are not associated with changes in the DNA. At the time, epigenetics was poorly understood, and her fascination with this field has grown with the scientific community‚Äôs increasing appreciation for the influence of epigenetics on other aspects of biology. In her scientific career, Dr. Riddle has studied various aspects of epigenetics in plants and animals. Her lab at UAB utilizes a classical genetics model system, the fruit fly Drosophila melanogaster, to study various open questions in the area of epigenetics and chromatin.
  • Selected Publications

    Academic Article

    Year Title Altmetric
    2018 The Drosophila Dot Chromosome: Where Genes Flourish Amidst Repeats.Genetics.  210:757-772. 2018
    2018 Genetic networks underlying natural variation in basal and induced activity levels in Drosophila melanogaster 2018
    2018 HP1B is a euchromatic Drosophila HP1 homolog with links to metabolism 2018
    2018 HP1B is a euchromatic Drosophila HP1 homolog with links to metabolism.PLoS ONE.  13:e0205867. 2018
    2017 Sex Differences in Aging: Genomic Instability.Journals of Gerontology, Series A.  73:166-174. 2017
    2017 Characterization of the Rotating Exercise Quantification System (REQS), a novel Drosophila exercise quantification apparatus.PLoS ONE.  12:e0185090. 2017
    2017 The role of epigenetics in maintaining genome stabilityBiochemist.  39:12-15. 2017
    2016 Targeting of P-Element Reporters to Heterochromatic Domains by Transposable Element 1360 in Drosophila melanogaster.Genetics.  202:565-582. 2016
    2016 Rho Kinase Inhibition as a Therapeutic for Progressive Supranuclear Palsy and Corticobasal Degeneration.Journal of Neuroscience.  36:1316-1323. 2016
    2016 The TreadWheel: A Novel Apparatus to Measure Genetic Variation in Response to Gently Induced Exercise for Drosophila.PLoS ONE.  11:e0164706. 2016
    2015 Drosophila muller f elements maintain a distinct set of genomic properties over 40 million years of evolution.G3 : Genes, Genomes, Genetics.  5:719-740. 2015
    2014 Comparative analysis of metazoan chromatin organization.Nature.  512:449-452. 2014
    2013 Erratum: Nature and function of insulator protein binding sites in the Drosophila genome (Genome Research (2012) 22 (2188-2198))PCR methods and applications.  23:409. 2013
    2012 Nature and function of insulator protein binding sites in the Drosophila genome.PCR methods and applications.  22:2188-2198. 2012
    2012 Enrichment of HP1a on Drosophila chromosome 4 genes creates an alternate chromatin structure critical for regulation in this heterochromatic domain.PLoS Genetics.  8:e1002954. 2012
    2012 Sequence-specific targeting of dosage compensation in Drosophila favors an active chromatin context.PLoS Genetics.  8:e1002646. 2012
    2011 Comprehensive analysis of the chromatin landscape in Drosophila melanogaster.Nature.  471:480-485. 2011
    2011 Plasticity in patterns of histone modifications and chromosomal proteins in Drosophila heterochromatin.PCR methods and applications.  21:147-163. 2011
    2011 An assessment of histone-modification antibody quality.Nature Structural Biology.  18:91-93. 2011
    2010 Identification of functional elements and regulatory circuits by Drosophila modENCODE.Science.  330:1787-1797. 2010
    2010 Gene expression analysis at the intersection of ploidy and hybridity in maize.TAG Theoretical and Applied Genetics.  120:341-353. 2010
    2009 Multiple SET methyltransferases are required to maintain normal heterochromatin domains in the genome of Drosophila melanogaster.Genetics.  181:1303-1319. 2009
    2009 A lot about a little dot - lessons learned from Drosophila melanogaster chromosome 4.Biochemistry and Cell Biology.  87:229-241. 2009
    2008 An investigation of heterochromatin domains on the fourth chromosome of Drosophila melanogaster.Genetics.  178:1177-1191. 2008
    2008 Comparative analysis of inbred and hybrid maize at the diploid and tetraploid levels.TAG Theoretical and Applied Genetics.  116:563-576. 2008
    2008 A role for RNAi in heterochromatin formation in Drosophila.Current Topics in Microbiology and Immunology.  320:185-209. 2008
    2007 Localization and transcription of a retrotransposon-derived element on the maize B chromosome.Chromosome Research.  15:383-398. 2007
    2006 Genetic variation for the response to ploidy change in Zea mays L.TAG Theoretical and Applied Genetics.  114:101-111. 2006
    2006 The dot chromosome of Drosophila: insights into chromatin states and their change over evolutionary time.Chromosome Research.  14:405-416. 2006
    2005 Dosage balance in gene regulation: biological implicationsTrends in Genetics.  21:219-226. 2005
    2005 Dosage balance in gene regulation: biological implications.Trends in Genetics.  21:219-226. 2005
    2005 Genetic variation in epigenetic inheritance of ribosomal RNA gene methylation in Arabidopsis.Plant Journal.  41:524-532. 2005
    2004 Induced and natural epigenetic variation.Cold Spring Harbor Symposia on Quantitative Biology.  69:155-159. 2004
    2003 Effects of reunited diverged regulatory hierarchies in allopolyploids and species hybrids.Trends in Genetics.  19:597-600. 2003
    2003 In search of the molecular basis of heterosis.Plant Cell.  15:2236-2239. 2003
    2003 Arabidopsis MET1 cytosine methyltransferase mutants.Genetics.  163:1109-1122. 2003
    2002 The control of natural variation in cytosine methylation in Arabidopsis.Genetics.  162:355-363. 2002
    Measuring Exercise Levels in Drosophila melanogaster Using the Rotating Exercise Quantification System (REQS).Journal of Visualized Experiments

    Chapter

    Year Title Altmetric
    2015 Interindividual Variability of DNA Methylation.  17-53. 2015
    2015 Epigenetic inheritance.  183-208. 2015
    2015 The Evolution of New Technologies and Methods in Clinical Epigenetics Research.  67-89. 2015
    2014 Heritable Generational Epigenetic Effects through RNA.  105-119. 2014

    Research Overview

  • My research focuses on understanding the mechanisms establishing and regulating epigenetic information, and how epigenetic systems ultimately contribute to gene regulation, disease, and other phenotypes. In addition to the genetic information encoded within the DNA, other forms of information exist in the cell. Epigenetic information is heritable, affects gene expression states and phenotypes, but is independent of DNA sequence. Examples of epigenetic systems include DNA methylation, histone modifications, and chromatin structure. These epigenetic systems play vital roles in gene regulation, and defects in epigenetic regulation have been implicated in a variety of human diseases including cancer. My lab uses the fruit fly Drosophila melanogaster as a model system to investigate epigenetic systems and their influence on development and gene regulation. Currently, there are three on-going projects in the lab: The HP1 protein family: Heterochromatin protein 1a (HP1a) was discovered as the first heterochromatin-associated protein. Its binding characterizes the heterochromatic regions of the fly genome, and homologs have been identified in species ranging from yeast to humans. The HP1a protein contains two conserved domains, the chromo domain, and the chromo-shadow domain. Based on this domain structure, four additional HP1 family proteins have been identified in Drosophila melanogaster. Of these, HP1B and HP1C, like HP1a, are ubiquitously expressed, while HP1D/RHINO and HP1E are restricted to the germline in females and males respectively. While HP1a binds large domains in heterochromatin, it also shows binding to active transcription start sites, where it is generally found in the company of HP1B and/or HP1C. We are using molecular genetic and genomics approaches to understand the relationship between HP1a, HP1B, and HP1C, and their effect on gene regulation. The role of epigenetics in exercise response: Exercise is a common form of treatment recommended to combat the increasing obesity problem observed in many countries. How individuals respond to exercise is highly variable, and the source of this variation is not well understood. We are using the fruit fly Drosophila melanogaster as a model for exercise biology. Taking advantage of the genetics resources available in Drosophila, our experiments are designed to determine the relative importance of genetics and epigenetics in generating the variability in exercise response. The regulation of H3K9 methylation: H3K9 methylation is a histone mark generally associated with silent regions of the genome and heterochromatin. In many eukaryotes including Drosophila, H3K9 methylation is generated by three classes of SET domain containing histone methyltransferases. In Drosophila, the action of SU(VAR)3-9, EGG, and G9a produces the genome-wide H3K9 methylation patters. However, how the three enzymes are coordinated and what their individual roles are is poorly understood. We are using molecular genetic, biochemical, and genomics approaches to answer these questions. Epigenetics and chromatin
  • Education And Training

  • Doctor of Philosophy in Evolutionary Biology, Washington University/St. Louis
  • Full Name

  • Nicole Riddle
  • Blazerid

  • riddlenc