Planarian Promoter Architecture

Background: Core promoters are minimal regions sufficient to direct accurate initiation of transcription and are crucial for regulation of gene expression. They are highly diverse in terms of associated core promoter motifs, underlying sequence composition and patterns of transcription initiation. Distinctive features of promoters are also seen at the chromatin level, in-cluding nucleosome positioning patterns and the presence of specific histone modifications. Freshwater planarian, Dugesia japonica and Schmidtea mediterranea have emerged as power-ful model system for studying regeneration and adult stem cell (ASC) transcriptional and chromatin biology research. Such re-search is contingent on the accurate annotation of transcription start sites (TSSs) and promoters.Materials and Methods: To characterize the cis-regulatory landscape of D. japonica as the first record of TSSs activity genome-wide, we produced a high-resolution map of the pro-moters active in D. japonica and S. mediterranea. We performed Cap Analysis of Gene Expression (CAGE) and the Identifiied TSSs were utilized to generate a first record of Planarian Pro-moter Database, as a catalog of active promoters across the surveyed samples.Results: We characterized and compared the features of pro-moters and identifiied candidate core promoter motifs for FACS sorted populations and integrated de novo motif discovery using CAGEdefiined TSSs. A comparison of promoter activities, mo-tif discovery and differential gene expression revealed insights into the properties of stem cell regulation and differentiation. Conclusion: Our planarian Promoter Database presented here provides a valuable resource for the comparative study of cis-regulatory regions, as well as a fundamental resource data for transcriptional, gene regulatory and epigenetic studies.

کلیدواژه ها:

Transcription Start Site ، Promoter ، CAGE-Seq ، Stem Cell and Regenerative Biology ، Planaria