Nicole C. Riddle headshot.

Assistant Professor This email address is being protected from spambots. You need JavaScript enabled to view it.
Campbell Hall 109A
(205) 975-4049

Research and Teaching Interests: Epigenetics and chromatin

Office Hours: By appointment

Education:

  • B.S., University of Missouri Columbia, Biology (with Honors)
  • Ph.D., Washington University in St. Louis, Evolutionary and Population Biology

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’s increasing appreciation for the influence of epigenetics on other aspects of biology.

Research Opportunities
We are looking for talented, motivated individuals to join our research group. If you are interested in joining the Riddle lab as a Ph.D. student or post-doctoral researcher, please send me an email at This email address is being protected from spambots. You need JavaScript enabled to view it.. It should include your curriculum vitae (including the names of three references) as well as a description of your research interests.

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.

Research Interests

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.

Recent Courses

  • CLOne – Chromatin Laboratory 1
  • Genetics
  • Epigenetics
  • Epigenetics Discussion/Journal Club

Graduate Students

Alumni

  • Christine McBride
  • Mina Momeni
  • Andy Thomas
  • Benjamin B. Mills
  • Tandy Dolin-Petrov

Select Publications

For a full list of publications, please visit Dr. Riddle's PubMed entry.

Book chapter:

  • Mills BB, McBride CL, and Riddle NC, "Epigenetic inheritance," in Epigenetic Gene Expression and Regulation, Huang S, Litt M, & Blakey CA, ed. (Elsevier AP, 2016):183-208.
  • Petrov TD, and Riddle NC, "The evolution of new technologies and methods in clinical epigenetic research," accepted to appear in Epigenetic biomarkers and diagnostics, JL Garcia-Gimenez, ed. (Elsevier AP).

Articles:

  • Mills BB, Thomas AD, and Riddle NC. HP1B is a euchromatic Drosophila HP1 homolog with links to metabolism. Posted on bioRxiv (doi:https://doi.org/10.1101/372094) and in revision for PLoSOne.
  • Watanabe LP, and Riddle NC. Measuring Exercise Levels in Drosophila melanogaster Using the Rotating Exercise Quantification System (REQS) (2018) J. Vis. Exp. (135), e57751.
  • Watanabe LP, and Riddle NC. Characterization of the Rotating Exercise Quantification System (REQS), a novel Drosophila exercise quantification apparatus (2017) PLoS One 12(10):e0185090.
  • Fischer KE and Riddle NC, "Sex differences in aging: Genomic instability," Journal of Gerontology A: Biological Sciences (2017).
  • Mendez S, Watanabe LP, Hill R, Owens M, Moraczewski J, Rowe GC, Riddle NC, and Reed LK, "The TreadWheel: A novel apparatus to measure genetic variation in response to gently induced exercise for Drosophila," PLoS One 11 (No. 10, 2016):e0164706.
  • Huisinga KL, Riddle NC, Leung W, Shimonovich S, McDaniel S, Figueroa-Clarevega A, and Elgin SCR, "Targeting of P element reporters to heterochromatic domains by transposable element 1360 in Drosophila melanogaster," Genetics 202 (No. 2, 2016):565-582.
  • Gentry EG, Henderson BW, Arrant AE, Gearing M, Feng Y, Riddle NC, and Herskowitz JH, "Rho Kinase Inhibition as a Therapeutic for Progressive Supranuclear Palsy and Corticobasal Degeneration," Journal of Neuroscience 36 (No. 4, 2016):1316-1323.
  • Leung W, Shaffer CD, …, Riddle NC, Buhler J, Mardis ER, and Elgin SCR, "Drosophila Muller F elements maintain a distinct set of genomic properties over 40 million years of evolution," G3 5 (No. 5, 2015):719-40.
  • Ho JWK, Jung YL, Liu T, Alver BH*, Lee S*, Ikegami K*, Sohn K-A*, Minoda A*, Tolstorukov MY*, Appert A*, Parker SCJ*, Gu T*, Kundaje A*, Riddle NC*, Bishop E*, Egelhofer TA*, Hu SS*, Alekseyenko AA*, Rechtsteiner A*, Schwartz YB*, Asker D, Belsky JA, Bowman SK, Chen QB, Chen RA-J, Day DS, Dong Y, Dose AC, Duan X, Epstein CB, Ercan S, Feingold EA, Ferrari F, Garrigues JM, Gehlenborg N, Good PJ, Haseley P, He D, Herrmann M, Hoffman MM, Jeffers TE, Kharchenko PV, Kolasinska-Zwierz P, Kotwaliwale CV, Kumar N, Langley SA, Larschan EN, Latorre I, Libbrecht MW, Lin X, Park R, Pazin MJ, Pham HN, Plachetka A, Qin B, Shoresh N, Stempor P, Vielle A, Wang C, Whittle CM, Xue H, Kingston RE, Kim JH, Bernstein BE, Dernburg AF, Pirrotta V, Kuroda MI, Noble WS, Tullius TD, Kellis M, MacAlpine DM, Strome S, Elgin SCR, Liu XS, Lieb JD, Ahringer J, Karpen GH, and Park PJ, "Comparative analysis of metazoan chromatin organization," Nature 512 (2014):449-52. *Co-second authors
  • Riddle NC, Jung YL, Gu T, Alekseyenko AA, Asker D, Gui H, Kharchenko PV, Minoda A, Plachetka A, Schwartz YB, Tolstorukov MY, Kuroda MI, Pirrotta V, Karpen GH, Park PJ, and Elgin SCR, "Enrichment of HP1a on Drosophila chromosome 4 genes creates an alternate chromatin structure critical for regulation in this heterochromatic domain," PLoS Genetics 8 (No. 9, 2012):e1002954.

Academic Distinctions and Professional Societies

  • Named New Investigator for the UAB Nutrition Obesity Research Center (NORC), 2015
  • Provost's Award for Faculty Excellence in Academic Engagement and Global Citizenship, 2014
  • American Association for the Advancement of Science
  • The Genetics Society of America
  • UAB Sigma Xi – President-Elect (2017-2018); President (2018-2019)
  • 2016 The John R Durant Award for Excellence in Cancer Research, 1st Place, Junior Faculty Category at the UAB Comprehensive Cancer Center 18th Annual Research Retreat and Research Competition
  • 2013 The John R Durant Award for Excellence in Cancer Research, 2nd Place, Junior Faculty Category at the UAB Comprehensive Cancer Center 16th Annual Research Retreat and Research Competition

Student Groups

  • UAB Genetics Club

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