Investigating the role of the BAF Complex in Human Disease and Evolution Open Access
Davis, Sona (Spring 2024)
Published
Abstract
This Honors Thesis contains two projects each addressing gaps in our current knowledge on the BAF complex. The first project (described in Chapter 2) sought to identify areas of the genome where the BAF Complex works to remodel chromatin. The second project (described in Chapter 3) sought to determine whether there are genetic variations in BAF subunit genes between modern humans, ancient humans, and non-human primates that could contribute to differences in brain development in these populations. Together, these projects deepen our understanding of the role of the BAF Complex in human evolution and disease. The results provide strong baselines for future research on BAF function, as well as intriguing insights into its implications. Moreover, they pave the way for potential therapeutic interventions and open up new avenues for exploring the intricate interplay between the BAF Complex and various biological processes.
Table of Contents
Overview of Project 1
Overview of Project 2
1.1: DNA Structure and Packaging
1.2: Chromatin-Based Regulation of Gene Expression
1.3: BRG1/BRM Associated Factor Family of Chromatin Remodeling
1.4: BAF Mutations in Human Disease
2.1: Background
2.1.2: BAF complexes are bound at cREs and required to maintain chromatin accessibility.
2.1.3: Key gap(s) in knowledge
2.1.4: Our approach
2.2: Results
2.2.1: Primer pairs and qualitative PCR assay successfully measure signal to noise ratio of ATAC-Seq Libraries.
2.2.2: ATAC-seq Libraries from K-562 cell-line have high signal to noise ratio.
2.2.3: Identifying optimal concentration to treat K-562 with BAF inhibiting drug.
2.2.5: Surprisingly, BAF Inhibition does not lead to loss of chromatin accessibility.
2.3: Methods
2.3.1: Primer Design
2.3.2: pCR
2.3.3: Gel Electrophoresis
2.3.4: qPCR
2.3.5: Drug Inhibitor Dose Escalation
2.3.6: Cell Culture and Treatment
2.3.7: ATAC-Seq
2.3.8: Next-Generation Sequencing and Analysis
2.4: Conclusions
2.4.1: The inhibition of the BAF complex in the K-562 cell line does not result in significant changes in accessibility.
2.4.2: Limitations
2.4.3: Potential Next Steps
3.1: Background
3.1.1: The BAF Complex in Brain Development
3.1.2: The Evolutionary Conservation of the BAF Complex
3.1.3: Single Nucleotide Polymorphisms and Missense Mutations
3.1.4: Non-Human Primates
3.1.5: Neanderthals
3.2: Results
3.2.1: Identifying variants in BAF Protein subunits’ genes.
3.2.2: Predicting the impact of genetic variants on BAF protein structure and function.
3.2.3: Identifying variants predicted to be “Damaging”by all three computational tools.
3.3.7: Determining variants’ presence in the human population.
3.3: Methods
3.3.1: Obtaining variants between the human genome and Neanderthal/Non-Human Primate Genomes
3.3.2: Filtering for Coding Sequences within Exons
3.3.3: Bedtools Intersect
3.3.4: CADD
3.3.5: SIFT
3.3.6: PolyPhen-2
3.4: Conclusions
3.4.1: Eight individuals of the non-human primates analyzed in my study have a genetic variant in SMARCE1 that is predicted to cause NDD in humans.
3.4.2: Limitations
3.4.3: Potential Next Steps
Works Cited
About this Honors Thesis
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