Date of Award

Spring 5-15-2020

Author's School

Graduate School of Arts and Sciences

Author's Department

Biology & Biomedical Sciences (Neurosciences)

Degree Name

Doctor of Philosophy (PhD)

Degree Type



Precise control of gene expression is essential for neural development and function. This control is regulated by the interplay of chromatin remodelers and transcription factors (TFs). To better understand these mechanisms involved in gene regulation, we pursue two questions: 1) what are the roles of the chromatin remodeler CHD7 in cerebellar development and 2) what are the roles of the MEF2 TF family in cerebellar function. CHD7 mutations are causative for CHARGE syndrome, a heterogeneous disorder affecting many organ systems, occurring in 1:10,000 newborns. Recent MRI studies have identified cerebellar hypoplasia and foliation defects in a large portion of CHARGE syndrome patients. To identify the how a decrease in CHD7 activity leads to cerebellar defects seen in patients, we conditionally knockout CHD7 in granule cell precursors of mouse cerebellum. Surprisingly, we see a stereotyped folding pattern along the typically smooth mediolateral axis. We then characterize cellular processes and identify a switch in the preferred axis of granule cell precursor division prior to onset of irregular folding. Upon assessing transcriptomic and epigenomic functions of CHD7, we find CHD7 to regulate gene programs implicated in human disorders of brain folding. Additionally, we show that CHD7 reduces accessibility of enhancers with corresponding reduction in enhancer activity and proximal gene expression. The recruitment of chromatin remodelers to specific regions is accomplished by multiple factors including transcription factors. Thus, TFs also play a vital role in proper gene regulation. Furthermore, transcription factors can bind accessible regions and recruit other factors important for transcription to occur. The latter part of this dissertation will address the roles of paralogous transcription factors, MEF2A and MEF2D, and their roles in cerebellar function. MEF2A and MEF2D are highly expressed in cerebellar granule cells, the most abundant neuron in the brain. Using single and double conditional knockout of MEF2 family TFs, we find that MEF2A and MEF2D play functionally redundant roles in cerebellar-dependent motor learning. Although both TFs are highly expressed in granule neurons, transcriptomic analyses show MEF2D is the predominant genomic regulator of gene expression in vivo. Strikingly, genome-wide occupancy analyses reveal upon depletion of MEF2D, MEF2A occupancy robustly increases at a subset of sites normally bound to MEF2D. Importantly, sites experiencing compensatory MEF2A occupancy are concentrated within open chromatin and undergo functional compensation for genomic activation and gene expression. Finally, motor activity induces a switch from non-compensatory to compensatory MEF2-dependent gene regulation. These studies uncover genome-wide functional interdependency between paralogous TFs in the brain. Collectively, our studies on CHD7 and MEF2 provide further understanding of the roles of two critical classes of gene regulators in cerebellar development and function. These studies have set the basis for understanding how TFs and chromatin remodelers control gene expression. Future studies will address how knockout of chromatin remodelers affect TF occupancy, and conversely, how TF depletion prevents chromatin remodeler recruitment.


English (en)

Chair and Committee

Azad Bonni

Committee Members

David Ornitz, Harrison Gabel, Kristen Kroll, Rob Mitra,