MUII Comprehensive Exam- Saad Khan

Comparison of histone modifications across species

A cell’s identity is determined by distinct sets of genes that are expressed at a given point of time. An important factor in determining which set of genes are expressed is the cells epigenome. Epigenomes are known to play an important role across all eukaryotic species in gene regulation, genome integrity, dosage compensation and development. Histone modifications are an important component of the epigenome. These histone marks are post translational modifications that take place on the n-terminal tails of histone proteins. The growth of complex and heterogeneous epigenomic data sets has led to the development of “Comparative Epigenomics”. Comparative epigenomics has three dimensions namely ‘comparison of the epigenome of same individual over a period of time or different tissue types’, ‘comparison between different individuals of the same species’, and ‘comparison of epigenomes of different species’. Comparison of histone modification across time-points, individuals or species is crucial in understanding how epigenomes evolve over time. In this work we propose informatics approaches to address three specific aims: 1) Understand how histone modifications evolve between species and across different tissues. 2) Study the factors that contribute/drive change in epigenome across species. 3) How epigenomes change across various cancer subtypes and what factors drive that change. Lastly, we will use comparative epigenomic features to better predict enhancer promoter looping. A better understanding of how these histone modifications co-appear and evolve with respect to sequence across species would help in coming up with better models of transcriptional network evolution.