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Temporal Bioinformatic Analysis of Epigenetics through Histone Modifications

  • Author(s): West, Robert
  • Advisor(s): Downing, Timothy
  • et al.
Creative Commons Attribution 4.0 International Public License
Abstract

Gathering information on DNA activity during development remains problematic as DNA regulation continues to periodically change, creating unknown downstream variations in final cell heterogeneity. The fluidity and complexity create extreme difficulty and impedes understanding of the process of epigenetics. Enormous amounts of modifications happen within DNA replication; current research only begins to realize the significance of histone modifications, the role they play in mRNA expression and epigenetics of cell fate. With approximately 3 billion base pairs, histone modifications are nearly endless, each one can change the regulation of DNA in diverse ways, silencing or enhancing the expression of the DNA. With current analyses, such as Chromatin immunoprecipitation sequencing (ChIP-Seq), the ability to utilize high-powered computing and differing downstream analysis techniques, insightful observations can help realize the complexities of epigenetics and reprogramming. We converted raw ChIP-seq data from Cacchiarelli, et al. into heatmaps and developed computing techniques to analyze six histone modifications through reprogramming with different sets of transcription factors. Heatmaps were generated and sorted two dissimilar ways for visualization. Some histone modifications depicted their typical roles while we saw some interesting clusters that developed over time. We were also able to discover which genes had the biggest peak enrichment differential. With insight into how each histone modification acts on the DNA over time and how certain promoters change expression, methods for mechanisms and stimulus affecting the expression and speed of reprogramming can be determined. This can then lessen reprogramming time and further enhance the importance of epigenetics in cell fate.

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