Embryonic and Maternal Genes have Different 5’ and 3’ Regulation Complexity

Shai Shen-Orr
Harvard University

Yitzhak Pilpel
Weizmann Institute of Science

Craig Hunter
Harvard University

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     Last modified: March 31, 2006

Abstract
Early embryonic development is a passing of the baton between maternally deposited transcripts and embryonically produced ones. Genes expressed solely in one of these two groups are subject to very different pressures. Maternal transcripts are at first expressed in the germline and deposited uniformly in the zygote and subsequently selectively degraded. In contrast, developmentally important embryonic transcripts need to be expressed at an exact time in specific cells. Using C. elegans expression data we show evidence that these differences in the requirements of expression for maternal and embryonic genes, can be seen at multiple levels of genome organization. We set rules for predicting how a transcript is regulated and whether it is expressed by the mother or the embryo. Our results allow us to explore the relationship between regulatory complexity and gene spacing. Regulatory regions associated with maternal and embryonic genes in D. melangaster have similar characteristics.