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Gene Expression in the Vertebrate Retina

In December 2013, during Dr. Ray Enke’s first year at JMU, 4-VA awarded him a mini-grant called Establishing a collaborative undergraduate research program: Characterizing epigenetic regulation of gene expression during development of the vertebrate retina. Launched as a collaboration to use a laser dissection microscope (LCM) at GMU, the project brought together three investigators with complementary areas of expertise. Dr. Enke focused on mechanisms of gene regulation in the vertebrate retina while Dr. Lance Liotta and Dr. Virginia Espina developed specialized techniques for analyzing retinal histology and laser capture microdissection of retinal tissue.

In 2014, access to the LCM allowed student Emily Grunwald to collect valuable tissue so the team could conduct experiments to demonstrate cell-specific patterns of epigenetic modification in the genomes of retinal neurons.

In December 2014, 4-VA awarded Dr. Enke a second mini-grant called Gene expression analysis in the developing vertebrate retina using next generation sequencing to work with Dr. Stephen Turner at UVA. Complementing his first 4-VA project, this bioinformatics collaboration is focused on analyzing several large genome-wide sequencing data sets generated in his lab as well as previously published public domain data. The plan is to streamline bioinformatics protocols for students to use in the research lab as well as in upper division biology course labs.

Dr. Ray Enke
Assistant Professor of Biology

Dr. Lance Liotta
Co-Director & Co-Founder of the Center for Applied Proteomics and Molecular Medicine (CAPMM)

Dr. Virginia Espina
Research Associate Professor and Director of the CAP accredited clinical proteomics laboratory in the CAPMM

Dr. Stephen Turner
Assistant Professor of Public Health
Director of the School of Medicine’s Bioinformatics Core

Grant Info

  • 2013 – 4-VA awarded JMU and GMU $5,000 for Establishing a collaborative undergraduate research program: Characterizing epigenetic regulation of gene expression during development of the vertebrate retina.

  • 2014 –4-VA awarded JMU and UVA $5,000 for Gene expression analysis in the
    developing vertebrate retina using next generation sequencing.

  • 2014 – JMU awarded Dr. Enke a College of Science and Mathematics Summer Research Faculty Assistance Grant of $4,000 for his project Characterizing epigenetic mechanisms of gene regulation in the vertebrate retina.

  • 2015 – Dr. Enke hosted the CGEMS Summer Training Workshop in Genomics, Proteomics & Bioinformatics for Beginners & Beyond with support from 4-VA.

  • 2015 – Dr. Enke received a $200,000 grant from the Commonwealth Health Research Board for his proposal entitled Molecular and bioinformatic analysis of epigenetic gene regulation in the normal and diseased retina: Characterizing pathways for diagnosing and treating macular degeneration.

  • 2015 – In collaboration with Dr. Elizabeth Doyle and Dr. Oliver Hyman, Dr. Enke was awarded a JMU Geospatial Mini-grant of $500 for the proposal entitled Integration of GIS and DNA Sequence Data to Characterize Biological Diversity in the Edith J. Carrier Arboretum.

  • 2016

    • Dr. Enke hosted the second CGEMS Summer Training Workshop in Genomics, Proteomics & Bioinformatics for Beginners & Beyond with support from 4-VA.
    • They also used 4-VA funding to support a biology faculty working group tasked with the redesign of the entire first year biology core curriculum, in collaboration with the Cold Spring Harbor Laboratory DNA Learning Center (DNALC) in New York.

  • 2016-2017

    CGEMS began focusing a portion of their annual summer bioinformatics workshops—which were also supported by 4-VA—on DNA Barcoding using the DNA Subway bioinformatics tools developed by the DNALC. This is what planted the seed for the idea to spread the JMU DNA Barcoding CURE (course-based undergraduate research experience) model using DNALC-developed bioinformatics tools to other educators around the country.

  • $1.97 Million Grant

    2018

    The NSF awarded Ray Enke and Oliver Hyman from JMU $1,973,924 to collaborate with their Co-PIs at the DNALC to further develop their barcoding CURE (course-based undergraduate research experience) courses at JMU and help other undergraduate educators around the U.S. learn and implement similar versions at their home institutions.

Benefits To The Commonwealth

Demonstrated Virginia’s impact on health and medical research

Developed new models for teaching and learning

Contributed to medical solutions for retinal diseases

Shared lab equipment and maximized university resources

The biology course redesign was so successful, the team was awarded a $1.97 million grant to expand it!

Student Researchers

  • Emily Grunwald
  • Morgan Hedden
  • Nicholas Dunham
  • Annamarie Meinsen
  • Courtney Stout
  • Sraavya Polisetti
  • Christophe Langouet-Astrie

Student Impact

  • Unique access to a highly specialized piece of equipment in the Liotta Lab at GMU
  • Developed computational bioinformatics protocols
7

Student Researchers

5

Conferences & Workshops

6

Publications

1.97 Million

External Funding

Conferences & Workshops

  1. 2015 Association for Research in Vision and Ophthalmology (ARVO) Conference (Denver, CO)
  2. 2015 Infrastructure & Training to Bring Next-Gen Sequence Analysis into Undergraduate Education Workshop (Bowie, MD)
  3. 2016 Association for Research in Vision and Ophthalmology (ARVO) Conference (Seattle, WA)
  4. 2016 Plant & Animal Genome Conference (San Diego, CA)
  5. 2016 Infrastructure & Training to Bring Next-Gen Sequence Analysis into Undergraduate Education Workshop (Cold Spring Harbor, NY)

Publications

  1. Berndsen CE, *Young BH, *McCormick QJ, Enke RA. Connecting common genetic polymorphisms to protein function: A modular project sequence for lecture or lab. Biochem Mol Biol Educ. 2016 Nov 12;44(6):526-536. Available from: http://onlinelibrary.wiley.com/doi/10.1002/bmb.20976/abstract
  2. *Langouet-Astrie CJ, Yang Z, *Polisetti SM, Welsbie DS, Hauswirth WW, Zack DJ, Merbs SL, Enke RA. Characterization of intravitreally delivered capsid mutant AAV2-Cre vector to induce tissue-specific mutations in murine retinal ganglion cells. Exp Eye Res. 2016 Jul 30;151:61-67. Available from: http://www.sciencedirect.com/science/article/pii/S001448351630210X?via=ihub
  3. Singh RK, Mallela RK, Hayes A, *Dunham NR, *Hedden ME, Enke RA, Fariss RN, Sternberg H, West MD, Nasonkin IO. Dnmt1, Dnmt3a and Dnmt3b cooperate in photoreceptor and outer plexiform layer development in the mammalian retina. Exp Eye Res. 2016 Nov 16. pii: S0014-4835(16)30469-9. Available from: http://www.sciencedirect.com/science/article/pii/S0014483516304699?via=ihub
  4. *Langouet-Astrie CJ, *Meinsen AL, *Grunwald ER, Turner SD, Enke RA. RNA sequencing analysis of the developing chicken retina. Sci Data. 2016 Dec 20;3:160117. doi: 10.1038/sdata. 2016.117. Available from: https://www.nature.com/articles/sdata2016117
  5. *Hossain RA, *Dunham NR, *Harris ME, *Hutchinson TL, *Kidd JM, *Kohler LR, *Salamon GJ, *Schmidt AL, *Thomas MD, Enke RA and Berndsen CE.  Modeling of Epigenetic Modification-Induced Changes in CRX-dependent Genes cis-Regulatory Elements. bioRxiv  179523 [Preprint] Posted August 22, 2017. Available from: https://doi.org/10.1101/179523
  6. Lee I, ^Rasoul BA, *Holub AS, Lejeune A, Enke RA, Timp W. Whole genome DNA methylation sequencing of the chicken retina, cornea, and brain. Sci Data, 2017 Oct 10;4:170148.10.1038/sdata.2017.148 Available from: https://www.nature.com/articles/sdata2017148

*Undergraduate student coauthors
^Graduate student coauthors