In few systems is it possible to analyze the global cis-regulatory structure of developmental transcription networks. One system where this is in principle possible is segmentation in Drosophila melanogaster, although to date such an undertaking has not been attempted. Here using computational algorithms to analyze the transcriptional regulatory regions of genes of the gap and pair rule classes such an analysis is carried out. Computational analysis, transgenic reporter element assays, site directed mutagenesis, genetics, and time courses of in situ hybridizations of central genes in carefully staged embryos are combined to understand how the cis-elements function together to achieve patterning of the anterior posterior axis. The transition from the non-periodic gap patterns to the seven striped periodic patterns of the pair rule genes is analyzed in detail. This step in the genetic hierarchy is of particular interest as it generates the segmental pattern that underlies the Drosophila body plan. The analysis clarifies the primary and secondary pair rule classification system and suggests certain organizational principles in pair rule cis-regulation.
","abstract_html":"<p>In few systems is it possible to analyze the global cis-regulatory structure of developmental transcription networks. One system where this is in principle possible is segmentation in Drosophila melanogaster, although to date such an undertaking has not been attempted. Here using computational algorithms to analyze the transcriptional regulatory regions of genes of the gap and pair rule classes such an analysis is carried out. Computational analysis, transgenic reporter element assays, site directed mutagenesis, genetics, and time courses of in situ hybridizations of central genes in carefully staged embryos are combined to understand how the cis-elements function together to achieve patterning of the anterior posterior axis. The transition from the non-periodic gap patterns to the seven striped periodic patterns of the pair rule genes is analyzed in detail. This step in the genetic hierarchy is of particular interest as it generates the segmental pattern that underlies the Drosophila body plan. The analysis clarifies the primary and secondary pair rule classification system and suggests certain organizational principles in pair rule cis-regulation.</p>","abstract_has_math":false,"creators":["Schroeder, Mark David"],"institution":null,"degree_name":"Doctor of Philosophy (PhD)","degree_level":"Thesis","degree_discipline":null,"degree_department":null,"school":null,"contributors":["Ulrike Gaul"],"advisors":[],"committee_chairs":[],"committee_members":[],"year":2009,"date_issued":"2009-01-01T08:00:00Z","date_published":"2009-01-01T08:00:00Z","updated_at":"2026-07-24T04:10:53Z","subjects":["CIS-regulation","Drosophila melanogaster","segmentation hierarchy","pair rule hierarchy","Life Sciences"],"languages":[],"rights":[],"rights_urls":[],"identifier_entries":[]},"links":{"outbound_url":"https://digitalcommons.rockefeller.edu/student_theses_and_dissertations/126","outbound_label":"Repository record","outbound_source":"dc:identifier"},"metadata_groups":[{"id":"people","label":"People","entries":[{"key":"dc:contributor","label":"Contributor","values":["Ulrike Gaul"]},{"key":"dc:creator","label":"Author","values":["Schroeder, Mark David"]}]},{"id":"academic_context","label":"Academic Context","entries":[{"key":"thesis:degree_level","label":"Degree Level","values":["Thesis"]},{"key":"thesis:degree_name","label":"Degree Name","values":["Doctor of Philosophy (PhD)"]}]},{"id":"subjects_keywords","label":"Subjects and Keywords","entries":[{"key":"dc:subject","label":"Dc Subject","values":["CIS-regulation","Drosophila melanogaster","segmentation hierarchy","pair rule hierarchy","Life Sciences"]}]},{"id":"identifiers","label":"Identifiers","entries":[{"key":"dc:identifier","label":"Identifier","values":["https://digitalcommons.rockefeller.edu/student_theses_and_dissertations/126"]}]},{"id":"additional","label":"Additional Metadata","entries":[{"key":"dc:description.abstract","label":"Abstract","values":["In few systems is it possible to analyze the global cis-regulatory structure of developmental transcription networks. One system where this is in principle possible is segmentation in Drosophila melanogaster, although to date such an undertaking has not been attempted. Here using computational algorithms to analyze the transcriptional regulatory regions of genes of the gap and pair rule classes such an analysis is carried out. Computational analysis, transgenic reporter element assays, site directed mutagenesis, genetics, and time courses of in situ hybridizations of central genes in carefully staged embryos are combined to understand how the cis-elements function together to achieve patterning of the anterior posterior axis. The transition from the non-periodic gap patterns to the seven striped periodic patterns of the pair rule genes is analyzed in detail. This step in the genetic hierarchy is of particular interest as it generates the segmental pattern that underlies the Drosophila body plan. The analysis clarifies the primary and secondary pair rule classification system and suggests certain organizational principles in pair rule cis-regulation.
"]},{"key":"dc:title","label":"Title","values":["Hierarchy and CIS-Regulation in Drosophila Segmentation: Rules for Pattern Formation and Clues to Evolution"]}]}],"canonical_facts":{"dc:contributor":["Ulrike Gaul"],"dc:creator":["Schroeder, Mark David"],"dc:description.abstract":["In few systems is it possible to analyze the global cis-regulatory structure of developmental transcription networks. One system where this is in principle possible is segmentation in Drosophila melanogaster, although to date such an undertaking has not been attempted. Here using computational algorithms to analyze the transcriptional regulatory regions of genes of the gap and pair rule classes such an analysis is carried out. Computational analysis, transgenic reporter element assays, site directed mutagenesis, genetics, and time courses of in situ hybridizations of central genes in carefully staged embryos are combined to understand how the cis-elements function together to achieve patterning of the anterior posterior axis. The transition from the non-periodic gap patterns to the seven striped periodic patterns of the pair rule genes is analyzed in detail. This step in the genetic hierarchy is of particular interest as it generates the segmental pattern that underlies the Drosophila body plan. The analysis clarifies the primary and secondary pair rule classification system and suggests certain organizational principles in pair rule cis-regulation.
"],"dc:identifier":["https://digitalcommons.rockefeller.edu/student_theses_and_dissertations/126"],"dc:subject":["CIS-regulation","Drosophila melanogaster","segmentation hierarchy","pair rule hierarchy","Life Sciences"],"dc:title":["Hierarchy and CIS-Regulation in Drosophila Segmentation: Rules for Pattern Formation and Clues to Evolution"],"thesis:degree_level":["Thesis"],"thesis:degree_name":["Doctor of Philosophy (PhD)"]},"updated_at":"2026-07-24T04:10:53Z"}