Nucleosome dynamics and organization in C. elegans gametes and embryos

Abstract

Nucleosomes act as scaffolds on which DNA is structurally organized, allowing the cell to fit meters of DNA inside a micrometer-sized nucleus. In order to access the DNA sequence and perform regulatory events, however, nucleosomes must be evicted from their binding sites. A thorough description of nucleosome biology – of where nucleosomes are localized, the post-translational modifications they contain, the stability of their DNA interaction, and how these features are inherited from one generation to the next – is critical to understanding the complicated mechanism coordinating gene regulatory events. Next Generation Sequencing, and the myriad new technologies utilizing this platform, has revolutionized our understanding of gene regulation. My thesis describes the application of these technologies to C. elegans, a fabulous genetic model organism that previously lacked comprehensive genomic characterization.

Fundamental to the study of gene regulation is a thorough list of gene locations and transcription start sites. In Chapter 2, I describe work performed with the Ahringer lab to catalogue precise transcriptional start sites genome-wide in C. elegans embryos. In Chapter 3, I describe the results of the Model Organism Encyclopedia of DNA Elements project (modENCODE), a large-scale, multi-laboratory consortium effort to detail and compare the transcription factor, histone modification, and chromatin landscape among different model organisms.

Together, these works generated hundreds of publicly available datasets that will serve as the backdrop for future studies. In Chapter 4, I further investigated the dynamic nature of nucleosome stability in C. elegans embryos genome-wide. I found destabilized nucleosomes enriched at the promoters of lowly-expressed genes, and suggest that unstable nucleosomes act to poise genes for context-specific response. Finally, in Chapter 5, together with the Strome lab I examined how nucleosomes are organized in C. elegans oocytes and sperm, and how chromatin modifications are inherited from gametes to the fertilized embryo.

Collectively, these experiments represent a significant improvement in our understanding of chromatin function and regulation in the model organism C. elegans, and how epigenetic signals are transmitted from one generation to the next. Future experiments will build on this platform to further investigate the mechanisms by which chromatin organization controls cell-type and tissue-specific events.