Alissa Cullen

Program: Molecular Genetics and Genomics

Current advisor: Jason J. Yi, PhD

Undergraduate university: Ohio State University-Columbus, 2017

Enrollment year: 2018

Research summary
Modeling clinical missense mutations in the DNA-binding factor CTCF to unravel the CTCF code in neural development.

The 3-dimensional organization of the mammalian genome in the nucleus is critical for proper gene regulation and organismal development. In eukaryotic cells, chromosomes occupy specific chromosomal territories within the nuclei. In recent years, intrachromosomal, as well as interchromosomal, interactions have been identified that regulate the spatial organization of chromatin and regulate gene expression within these territories. Furthermore, chromosomes have been observed to be further organized into topologically associated domains (TADs), which are highly structured loops that are conserved across different cell types. These large, looped domains are generated and regulated by the cohesin complex and CCCTC-binding factor (CTCF). CTCF is an 11-zinc finger DNA binding protein that utilizes zinc finger sub-domains in a combinatorial fashion to bind a range of DNA sequences. The specificity with which CTCF binds to the genome is poorly understood and the physiological consequences of aberrant binding remains largely unexplored. Multiple clinical studies have shown that precise mutations in CTCF, and in particular, missense mutations located within the zinc finger domain, lead to a heterogenous neurological disorder that displays intellectual disability, microcephaly, and a range of behavioral abnormalities. In particular, a missense mutation was identified that leads to the replacement of an arginine critical for proper DNA binding with a tryptophan located within the protein’s last zinc finger (R567W). Given the combinatorial nature of CTCF zinc finger binding and the neurological-specific phenotypes in patients with CTCF mutations, I hypothesize that the R567W mutation in CTCF alters a neuron-specific CTCF binding profile, leading to misregulation of the neuronal genome structure and improper gene expression. Here, I propose to model the R567W mutation in mice to elucidate the molecular and developmental consequences of this mutation as well as elucidate the neuronal-specific nature of CTCF dysfunction. I propose to characterize the behavioral phenotypes associated with this model and utilize ChIP-sequencing to elucidate the altered CTCF binding profile in the cortex and hippocampus of these mice. In tandem, I will perform Hi-C and RNA-sequencing in order to understand how this mutation alters the 3-dimensional organization of the genome and influences gene expression. This study will provide new insights into the specificity of CTCF binding to the genome and provide novel mechanistic information about the role of CTCF dysfunction in neurodevelopmental disease.

Graduate publications