Date of Award


Degree Type


Degree Name

Doctor of Philosophy (PhD)




Meilssa Pepling

Second Advisor

R. Craig Albertson


CHARGE Syndrome, chd7, development, RNA-Seq, spinal deformity, zebrafish

Subject Categories



The Chromodomain Helicase DNA Binding Protein (CHD) family consists of a group of nine known proteins that function in controlling DNA dynamics and transcription. The CHD family member of interest in this work, Chromodomain helicase DNA-binding protein 7 (chd7), has been implicated in human CHARGE (coloboma of the eye, heart defects, atresia of the choanae, retardation of growth and/or development, genital and/or urinary abnormalities, and ear abnormalities and deafness) Syndrome and Idiopathic Scoliosis, however little is known about the roles this gene plays during development.

Using zebrafish as a model system, morpholino antisense technology, whole mount in situ hybridization (WISH), and a relatively new protocol, RNA-Seq, we provide evidence of several developmental defects resulting from Chd7 knockdown as well as describe several genes that exhibit significant differential expression upon Chd7 knockdown. We provide evidence that zebrafish embryos highly express chd7 in the retina, brain and somite boundaries. We demonstrate that a reduction in Chd7 synthesis results in laterality defects in the expression of somitogenesis genes, consistent with the hypothesis that this chromatin remodeler is necessary for the proper development of the long axis of the body and may be involved in the onset of human scoliosis. We show that the presence of Chd7 is crucial for proper neural, retinal and vertebral development in zebrafish and that loss of function of Chd7 resulted in several morphological defects similar to those observed in human patients with CHARGE syndrome.

Finally, this work is the first transcriptome-wide study analyzing genetic changes in response to knockdown of a member of the Chromodomain Helicase DNA Binding Protein family. Using RNA-Seq we were able to identify and quantify differentially expressed genes in chd7 morphant zebrafish embryos compared to control morphant zebrafish embryos. These data were consistent with our knockdown experiments as well as with putative roles for Chd7 in human diseases.

In an effort to make a broader impact, we extended the use of zebrafish beyond scientific research and described several different methods of using zebrafish in the undergraduate laboratory classroom. First, we described the use of WISH in the classroom to help students form connections between molecular and organismal biology and then described the use of two model organisms, zebrafish and C. elegans, in the classroom to help students understand how genes and the environment interact to affect organismal development.

Cumulatively, this work is an example of interdisciplinary study both in the research laboratory as well as in the classroom. It involves the intensive study of a chromatin remodeler, Chd7, and makes important connections between Chd7 knockdown in zebrafish and human diseases. It also describes the pedagogical advantages of model organisms with respect to providing a rich and integrative experience for undergraduate biology majors.


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