epigenetic dynamics during erythropoiesis in mice

Open Access
Wozniak, Jacob M
Area of Honors:
Biochemistry and Molecular Biology
Bachelor of Science
Document Type:
Thesis Supervisors:
  • Ross Cameron Hardison, Thesis Supervisor
  • Teh Hui Kao, Honors Advisor
  • Scott Brian Selleck, Faculty Reader
  • Epigenetics
  • erythropoiesis
  • histones
  • dnase
  • chip-seq
  • dnase-seq
With the completion of the Human Genome project and the advancements of methods used to sequence DNA and analyze factors that control gene expression, a vast deluge of data that was not accessible before has become available. RNA-seq, ChIP-seq and DNase-seq can analyze genome-wide gene expression, transcription factor binding and histone modifications, and DNase hypersensitivity sites, respectively. Data of this proportion requires the integration of computational and statistical techniques with biochemical knowledge to effectively identify useful information amidst the immaterial background noise. A variety of epigenetic features, including transcription factor binding, histone modifications and DNase hypersensitivity sites, combine to regulate gene expression. The focus of this thesis is to advance our understanding of epigenetic dynamics as mouse cell lines go through erythropoiesis. DNase hypersensitivity sites are known to mark regions of the genome accessible to regulatory elements, thus, it is a useful starting point for annotating regulatory landscapes. Combining these sites with histone modification information and TF-binding locations, which can shed light on specific functional aspects of regulatory sites, leads to a vastly clearer view into the control of gene regulation. In addition, this report investigates the advantages of using ChromHMM to visualize many histone modifications as a single colored bar on a genome browser.