{"id":{"repo_id":"uiuc","oai_identifier":"oai:www.ideals.illinois.edu:2142/92716"},"canonical_url":"https://search.dev.ndltd.org/etd/uiuc/oai:www.ideals.illinois.edu:2142/92716","repository":{"repo_id":"uiuc","name":"University of Illinois - Urbana-Champaign","base_url":"https://www.ideals.illinois.edu/oai-pmh"},"display":{"title":"Computational analysis of upstream regulatory elements regulating plant chlorophyll degradation","abstract":"\"Chlorophyll is a vital compound in photosynthesis in plants and as such both its biosynthesis and degradation are tightly regulated. Disruption of the regulatory pathway for chlorophyll breakdown by exposure to cold temperature episodes in canola seed is the basis of the economically significant \"\"green seed problem\"\". A major controlling step in the chlorophyll degradation pathway involves the enzyme pheophorbide a oxygenase (PAO), which oxidizes the chlorophyll degradation intermediate pheide a, that is eventually converted to non-fluorescent chlorophyll catabolites (NCCs). PAO activation in maturing green seeds is known to be disrupted following freezing episodes, but the exact mechanism for this is not known. There is evidence that PAO is both transcriptionally and post transcriptionally regulated but the components involved are uncertain or unknown. First, it was hypothesized that freeze exposure will affect the expression of upstream regulatory elements, leading to modulation of PAO expression and/or PAO regulators that ultimately will slow chlorophyll degradation resulting in incomplete chlorophyll clearing of mature canola seeds. The second hypothesis was that the leaf senescence process will alter the normal expression profiles of upstream regulatory elements, leading to modulation of PAO expression that ultimately will stimulate chlorophyll degradation. Third, it was hypothesized that drought will affect upstream regulatory element expression, leading to modulation of PAO expression that ultimately will stimulate chlorophyll degradation, since cold and drought are known to share components of their upstream regulons. The goal of this research was to significantly advance our understanding of the regulation of PAO activity and in turn provide important insights into strategies to mitigate the economic impact of the canola green seed problem. To test these hypotheses, several sets of genomic and bioinformatics experiments were investigated and re-analyzed using a big-data computational approach. First, a co-expression approach was taken in which gene expression patterns were analyzed of genes correlated with PAO expression and activated in seed tissue that has undergone freeze-treatment episodes compared to control. Then their functions were investigated as candidate upstream transcription factors or other regulatory elements that may regulate PAO expression. Second, these analyses were repeated comparatively before and after the onset of leaf senescence. Third, data from drought and control conditions were cross-analyzed in a similar fashion. After analyzing the microarray data from the different experiments using statistical methods, PAO transcript expression was found to be significantly up-regulated in warm conditions, during leaf senescence, and in drought conditions, and in all three conditions significantly positively correlated with expression of ATAF1, a NAC transcription factor implicated in literature as being related to all three of these types of conditions. This analysis posits a regulatory network in which ATAF1 is triggered in response to these abiotic stresses and acts to regulate chlorophyll degradation by up-regulating PAO expression.\"","abstract_html":""Chlorophyll is a vital compound in photosynthesis in plants and as such both its biosynthesis and degradation are tightly regulated. Disruption of the regulatory pathway for chlorophyll breakdown by exposure to cold temperature episodes in canola seed is the basis of the economically significant ""green seed problem"". A major controlling step in the chlorophyll degradation pathway involves the enzyme pheophorbide a oxygenase (PAO), which oxidizes the chlorophyll degradation intermediate pheide a, that is eventually converted to non-fluorescent chlorophyll catabolites (NCCs). PAO activation in maturing green seeds is known to be disrupted following freezing episodes, but the exact mechanism for this is not known. There is evidence that PAO is both transcriptionally and post transcriptionally regulated but the components involved are uncertain or unknown. First, it was hypothesized that freeze exposure will affect the expression of upstream regulatory elements, leading to modulation of PAO expression and/or PAO regulators that ultimately will slow chlorophyll degradation resulting in incomplete chlorophyll clearing of mature canola seeds. The second hypothesis was that the leaf senescence process will alter the normal expression profiles of upstream regulatory elements, leading to modulation of PAO expression that ultimately will stimulate chlorophyll degradation. Third, it was hypothesized that drought will affect upstream regulatory element expression, leading to modulation of PAO expression that ultimately will stimulate chlorophyll degradation, since cold and drought are known to share components of their upstream regulons. The goal of this research was to significantly advance our understanding of the regulation of PAO activity and in turn provide important insights into strategies to mitigate the economic impact of the canola green seed problem. To test these hypotheses, several sets of genomic and bioinformatics experiments were investigated and re-analyzed using a big-data computational approach. First, a co-expression approach was taken in which gene expression patterns were analyzed of genes correlated with PAO expression and activated in seed tissue that has undergone freeze-treatment episodes compared to control. Then their functions were investigated as candidate upstream transcription factors or other regulatory elements that may regulate PAO expression. Second, these analyses were repeated comparatively before and after the onset of leaf senescence. Third, data from drought and control conditions were cross-analyzed in a similar fashion. After analyzing the microarray data from the different experiments using statistical methods, PAO transcript expression was found to be significantly up-regulated in warm conditions, during leaf senescence, and in drought conditions, and in all three conditions significantly positively correlated with expression of ATAF1, a NAC transcription factor implicated in literature as being related to all three of these types of conditions. This analysis posits a regulatory network in which ATAF1 is triggered in response to these abiotic stresses and acts to regulate chlorophyll degradation by up-regulating PAO expression."","abstract_has_math":false,"creators":["Ghandchi, Frederick Pejman"],"institution":"University of Illinois at Urbana-Champaign","degree_name":"Ph.D.","degree_level":"Dissertation","degree_discipline":"Crop Sciences","degree_department":null,"school":null,"contributors":["Ort, Donald R.","Caetano-Anollés, Gustavo","Ludaescher, Bertram","Clough, Steven J."],"advisors":[],"committee_chairs":[],"committee_members":[],"year":2016,"date_issued":"2016-11-10T17:49:45Z","date_published":"2016-11-10T17:49:45Z","updated_at":"2026-07-22T22:26:35Z","subjects":["Genomics","Data Science","Data Engineering","Data Analysis","Computational Analysis","Statistical Programming","Database Development","Statistical Modeling"],"languages":["en"],"rights":["Copyright 2016 Frederick Ghandchi"],"rights_urls":[],"identifier_entries":[]},"links":{"outbound_url":"http://hdl.handle.net/2142/92716","outbound_label":"Handle","outbound_source":"dc:identifier"},"metadata_groups":[{"id":"people","label":"People","entries":[{"key":"dc:contributor","label":"Contributor","values":["Ort, Donald R.","Caetano-Anollés, Gustavo","Ludaescher, Bertram","Clough, Steven J."]},{"key":"dc:creator","label":"Author","values":["Ghandchi, Frederick Pejman"]}]},{"id":"academic_context","label":"Academic Context","entries":[{"key":"dc:date","label":"Dc Date","values":["2016-11-10T17:49:45Z","2016-06-16","2016-08"]},{"key":"dc:type","label":"Dc Type","values":["text"]},{"key":"thesis:degree_discipline","label":"Discipline","values":["Crop Sciences"]},{"key":"thesis:degree_level","label":"Degree Level","values":["Dissertation"]},{"key":"thesis:degree_name","label":"Degree Name","values":["Ph.D."]},{"key":"thesis:institution_name","label":"Thesis Institution Name","values":["University of Illinois at Urbana-Champaign"]}]},{"id":"subjects_keywords","label":"Subjects and Keywords","entries":[{"key":"dc:subject","label":"Dc Subject","values":["Genomics","Data Science","Data Engineering","Data Analysis","Computational Analysis","Statistical Programming","Database Development","Statistical Modeling"]}]},{"id":"language_rights","label":"Language and Rights","entries":[{"key":"dc:language","label":"Dc Language","values":["en"]},{"key":"dc:rights","label":"Dc Rights","values":["Copyright 2016 Frederick Ghandchi"]}]},{"id":"identifiers","label":"Identifiers","entries":[{"key":"dc:identifier","label":"Identifier","values":["http://hdl.handle.net/2142/92716"]}]},{"id":"additional","label":"Additional Metadata","entries":[{"key":"dc:description","label":"Description","values":["\"Chlorophyll is a vital compound in photosynthesis in plants and as such both its biosynthesis and degradation are tightly regulated. Disruption of the regulatory pathway for chlorophyll breakdown by exposure to cold temperature episodes in canola seed is the basis of the economically significant \"\"green seed problem\"\". A major controlling step in the chlorophyll degradation pathway involves the enzyme pheophorbide a oxygenase (PAO), which oxidizes the chlorophyll degradation intermediate pheide a, that is eventually converted to non-fluorescent chlorophyll catabolites (NCCs). PAO activation in maturing green seeds is known to be disrupted following freezing episodes, but the exact mechanism for this is not known. There is evidence that PAO is both transcriptionally and post transcriptionally regulated but the components involved are uncertain or unknown. First, it was hypothesized that freeze exposure will affect the expression of upstream regulatory elements, leading to modulation of PAO expression and/or PAO regulators that ultimately will slow chlorophyll degradation resulting in incomplete chlorophyll clearing of mature canola seeds. The second hypothesis was that the leaf senescence process will alter the normal expression profiles of upstream regulatory elements, leading to modulation of PAO expression that ultimately will stimulate chlorophyll degradation. Third, it was hypothesized that drought will affect upstream regulatory element expression, leading to modulation of PAO expression that ultimately will stimulate chlorophyll degradation, since cold and drought are known to share components of their upstream regulons. The goal of this research was to significantly advance our understanding of the regulation of PAO activity and in turn provide important insights into strategies to mitigate the economic impact of the canola green seed problem. To test these hypotheses, several sets of genomic and bioinformatics experiments were investigated and re-analyzed using a big-data computational approach. First, a co-expression approach was taken in which gene expression patterns were analyzed of genes correlated with PAO expression and activated in seed tissue that has undergone freeze-treatment episodes compared to control. Then their functions were investigated as candidate upstream transcription factors or other regulatory elements that may regulate PAO expression. Second, these analyses were repeated comparatively before and after the onset of leaf senescence. Third, data from drought and control conditions were cross-analyzed in a similar fashion. After analyzing the microarray data from the different experiments using statistical methods, PAO transcript expression was found to be significantly up-regulated in warm conditions, during leaf senescence, and in drought conditions, and in all three conditions significantly positively correlated with expression of ATAF1, a NAC transcription factor implicated in literature as being related to all three of these types of conditions. This analysis posits a regulatory network in which ATAF1 is triggered in response to these abiotic stresses and acts to regulate chlorophyll degradation by up-regulating PAO expression.\"","Submission original under an indefinite embargo labeled 'Open Access'. The submission was exported from vireo on 2016-11-09 without embargo terms","The student, Frederick Ghandchi, accepted the attached license on 2016-06-13 at 17:10.","The student, Frederick Ghandchi, submitted this Dissertation for approval on 2016-06-13 at 17:46.","This Dissertation was approved for publication on 2016-06-16 at 09:51.","DSpace SAF Submission Ingestion Package generated from Vireo submission #9661 on 2016-11-09 at 10:21:10","Made available in DSpace on 2016-11-10T17:49:45Z (GMT). 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Disruption of the regulatory pathway for chlorophyll breakdown by exposure to cold temperature episodes in canola seed is the basis of the economically significant \"\"green seed problem\"\". A major controlling step in the chlorophyll degradation pathway involves the enzyme pheophorbide a oxygenase (PAO), which oxidizes the chlorophyll degradation intermediate pheide a, that is eventually converted to non-fluorescent chlorophyll catabolites (NCCs). PAO activation in maturing green seeds is known to be disrupted following freezing episodes, but the exact mechanism for this is not known. There is evidence that PAO is both transcriptionally and post transcriptionally regulated but the components involved are uncertain or unknown. First, it was hypothesized that freeze exposure will affect the expression of upstream regulatory elements, leading to modulation of PAO expression and/or PAO regulators that ultimately will slow chlorophyll degradation resulting in incomplete chlorophyll clearing of mature canola seeds. The second hypothesis was that the leaf senescence process will alter the normal expression profiles of upstream regulatory elements, leading to modulation of PAO expression that ultimately will stimulate chlorophyll degradation. Third, it was hypothesized that drought will affect upstream regulatory element expression, leading to modulation of PAO expression that ultimately will stimulate chlorophyll degradation, since cold and drought are known to share components of their upstream regulons. The goal of this research was to significantly advance our understanding of the regulation of PAO activity and in turn provide important insights into strategies to mitigate the economic impact of the canola green seed problem. To test these hypotheses, several sets of genomic and bioinformatics experiments were investigated and re-analyzed using a big-data computational approach. First, a co-expression approach was taken in which gene expression patterns were analyzed of genes correlated with PAO expression and activated in seed tissue that has undergone freeze-treatment episodes compared to control. Then their functions were investigated as candidate upstream transcription factors or other regulatory elements that may regulate PAO expression. Second, these analyses were repeated comparatively before and after the onset of leaf senescence. Third, data from drought and control conditions were cross-analyzed in a similar fashion. After analyzing the microarray data from the different experiments using statistical methods, PAO transcript expression was found to be significantly up-regulated in warm conditions, during leaf senescence, and in drought conditions, and in all three conditions significantly positively correlated with expression of ATAF1, a NAC transcription factor implicated in literature as being related to all three of these types of conditions. This analysis posits a regulatory network in which ATAF1 is triggered in response to these abiotic stresses and acts to regulate chlorophyll degradation by up-regulating PAO expression.\"","Submission original under an indefinite embargo labeled 'Open Access'. The submission was exported from vireo on 2016-11-09 without embargo terms","The student, Frederick Ghandchi, accepted the attached license on 2016-06-13 at 17:10.","The student, Frederick Ghandchi, submitted this Dissertation for approval on 2016-06-13 at 17:46.","This Dissertation was approved for publication on 2016-06-16 at 09:51.","DSpace SAF Submission Ingestion Package generated from Vireo submission #9661 on 2016-11-09 at 10:21:10","Made available in DSpace on 2016-11-10T17:49:45Z (GMT). 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