The Role of Genomic Sequence in the Spatial and Temporal Propagation of Heterochromatin

Abstract

Characterizing how genomic sequence interacts with trans-acting regulatory factors to implement a program of gene expression in eukaryotic organisms is critical to our understanding of genome function. One means by which patterns of gene expression are achieved is through the differential packaging of DNA into distinct types of chromatin. While chromatin state exerts a major influence on gene expression, the extent to which cis-acting DNA sequences contribute to the specification of chromatin state remains incompletely understood. To address this, we have used a fission yeast sequence element (L5), known to be sufficient to nucleate heterochromatin, to establish de novo heterochromatin domains in the S. pombe genome to address the role of DNA sequence in shaping the spatial and temporal propagation of heterochromatin. In this thesis, I describe a major effect of genomic sequences in determining spatial propagation of such de novo heterochromatin domains. I demonstrate that the sequence content of a genomic region plays a significant role in shaping its response to encroaching heterochromatin and suggest a role of DNA sequence in specifying chromatin state. Despite the role of DNA sequence in the spatial propagation of chromatin domains, I demonstrate that heterochromatin, once assembled, can propagate by an epigenetic signal, entirely independent of the original nucleating sequences. While the epigenetic signal is sufficient for maintenance and transmission of the heterochromatic state, it is insufficient for reestablishment of heterochromatin following its loss. Thus, these data demonstrate uncoupling of genomic and epigenetic signals necessary for the establishment, spatial propagation, and temporal propagation of chromatin states.