Abstract

There are about 20,000 genes in the human genome. The lowly nematode worm, C. elegans, has about the same number of genes. How could two organisms that are so different arise from a similar number of genes? The answer is epigenetics, or the factors that help control when and where genes are expressed. There are many layers that comprise the epigenetic control of genes. One of which is the structure or architecture of chromatin. Chromatin is a complex of DNA and proteins. Histone proteins with DNA wrapped around them form the fundamental component of chromatin, the nucleosome. Chromatin exists in two forms, euchromatin and heterochromatin. Euchromatin is made of loosely packed nucleosomes while in heterochromatin nucleosomes are tightly packed. Genome elements are not accessible in heterochromatin but are in euchromatin. In this way chromatin architecture provides a layer of control of genetic expression. Where nucleosome form is a function of several factors including the underlying DNA sequence, and binding competition between histones and other DNA binding proteins. Here we test the ability of various DNA sequences to position and repel histone proteins in C. elegans worms. We find that the 601sequence can position nucleosomes and that the PRS-322 sequence does repel nucleosomes in vivo. Assessing chromatin architecture requires sequences to be aligned to a reference genome, however, there are numerous programs with which to do this. Each program performs this task in a different way. These differences can have a large impact on the downstream analysis of the results. To this end, we have tested various alignment programs to assess how well they align reads to a reference genome. Here we have found that Bowtie2, BWA, and Chromap perform alignments accurately and we suggest using them. As an organism develops its genetic expression changes. This change in expression is often the result of temporally specific genomic elements such as enhancers. Understanding when enhancers are accessible during development can lead to a better understanding of the genetic control needed for development. Here we utilize data gathered at specific developmental stages in C. elegans to elucidate enhancer accessibility. In this work we have furthered the understanding of epigenetic control of expression by quantifying positioning and repelling sequences, testing read mapping programs for accuracy and identifying temporally specific enhancers in developing worms.

Degree

PhD

College and Department

Life Sciences; Microbiology and Molecular Biology

Rights

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