{"id":{"repo_id":"mit","oai_identifier":"oai:dspace.mit.edu:1721.1/76563"},"canonical_url":"https://search.dev.ndltd.org/etd/mit/oai:dspace.mit.edu:1721.1/76563","repository":{"repo_id":"mit","name":"MIT","base_url":"https://dspace.mit.edu/oai/request"},"display":{"title":"A regulatory role for repeated decoy transcription factor binding sites in target gene expression","abstract":"Repetitive DNA sequences are prevalent in both prokaryote and eukaryote genomes and the majority of repeats are concentrated in intergenic regions. These tandem repeats (TRs) are highly variable as the number of repeated units changes frequently due to recombination events and/or polymerase slippage during replication. While TRs have been traditionally regarded as non-functional 'junk' DNA, variability in the number of TRs present within or close to genes is known to lead to gross phenotypic changes and disease. However, whether intergenic TRs have a functional role is less understood. Recent studies reveal that many intergenic TRs contain transcription factor (TF) binding sites and that several TRs of TF binding sites indeed influence gene expression. A possible mechanism is that TRs serve as TF decoys, competing with a promoter for TF binding. We utilized a synthetic system in budding yeast to examine if repeated binding sites serve as decoys, and alter the expression of genes regulated by the sequestered TF. Combining experiments with kinetic modeling suggests that repeated decoy binding sites sequester activators more strongly than a promoter binding site although both binding sites are identical in sequence. This strong binding converts a graded dose-response between activator and promoter to a sigmoidal-like response. We further find that the tight activatordecoy interaction becomes weaker with increasing activator levels, suggesting that the activator binding at the repeated decoy site array might be anti-cooperative. Finally, we show that the high affinity of repeated decoy sites qualitatively changes the behavior of a transcriptional positive feedback loop from a graded to bimodal, all-or-none response. Taken together, repeated TF binding sites play an unappreciated role as a gene regulator. Since repeated decoy sites are hypervariable in number, this variability can lead to qualitative changes in gene expression and potentially phenotypic variation over short evolutionary time scales.","abstract_html":"Repetitive DNA sequences are prevalent in both prokaryote and eukaryote genomes and the majority of repeats are concentrated in intergenic regions. These tandem repeats (TRs) are highly variable as the number of repeated units changes frequently due to recombination events and/or polymerase slippage during replication. While TRs have been traditionally regarded as non-functional 'junk' DNA, variability in the number of TRs present within or close to genes is known to lead to gross phenotypic changes and disease. However, whether intergenic TRs have a functional role is less understood. Recent studies reveal that many intergenic TRs contain transcription factor (TF) binding sites and that several TRs of TF binding sites indeed influence gene expression. A possible mechanism is that TRs serve as TF decoys, competing with a promoter for TF binding. We utilized a synthetic system in budding yeast to examine if repeated binding sites serve as decoys, and alter the expression of genes regulated by the sequestered TF. Combining experiments with kinetic modeling suggests that repeated decoy binding sites sequester activators more strongly than a promoter binding site although both binding sites are identical in sequence. This strong binding converts a graded dose-response between activator and promoter to a sigmoidal-like response. We further find that the tight activatordecoy interaction becomes weaker with increasing activator levels, suggesting that the activator binding at the repeated decoy site array might be anti-cooperative. Finally, we show that the high affinity of repeated decoy sites qualitatively changes the behavior of a transcriptional positive feedback loop from a graded to bimodal, all-or-none response. Taken together, repeated TF binding sites play an unappreciated role as a gene regulator. Since repeated decoy sites are hypervariable in number, this variability can lead to qualitative changes in gene expression and potentially phenotypic variation over short evolutionary time scales.","abstract_has_math":false,"creators":["Lee, Tek Hyung"],"institution":"Massachusetts Institute of Technology","degree_name":null,"degree_level":null,"degree_discipline":null,"degree_department":"Massachusetts Institute of Technology. Dept. of Chemical Engineering.","school":null,"contributors":[],"advisors":["Narendra Maheshri."],"committee_chairs":[],"committee_members":[],"year":2012,"date_issued":"2012","date_published":"2012","updated_at":"2026-07-22T22:22:02Z","subjects":["Chemical Engineering."],"languages":["eng"],"rights":["M.I.T. theses are protected by copyright. They may be viewed from this source for any purpose, but reproduction or distribution in any format is prohibited without written permission. See provided URL for inquiries about permission."],"rights_urls":["http://dspace.mit.edu/handle/1721.1/7582"],"identifier_entries":[]},"links":{"outbound_url":"http://hdl.handle.net/1721.1/76563","outbound_label":"Handle","outbound_source":"dc:identifier.uri"},"metadata_groups":[{"id":"people","label":"People","entries":[{"key":"dc:contributor.advisor","label":"Advisor","values":["Narendra Maheshri."]},{"key":"dc:contributor.department","label":"Department","values":["Massachusetts Institute of Technology. Dept. of Chemical Engineering."]},{"key":"dc:contributor.other","label":"Dc Contributor Other","values":["Massachusetts Institute of Technology. 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They may be viewed from this source for any purpose, but reproduction or distribution in any format is prohibited without written permission. See provided URL for inquiries about permission."]},{"key":"dc:rights.uri","label":"Rights URI","values":["http://dspace.mit.edu/handle/1721.1/7582"]}]},{"id":"identifiers","label":"Identifiers","entries":[{"key":"dc:identifier.uri","label":"Identifier URI","values":["http://hdl.handle.net/1721.1/76563"]}]},{"id":"additional","label":"Additional Metadata","entries":[{"key":"dc:description","label":"Description","values":["Thesis (Ph. D.)--Massachusetts Institute of Technology, Dept. of Chemical Engineering, 2012.","Cataloged from PDF version of thesis.","Includes bibliographical references."]},{"key":"dc:description.abstract","label":"Abstract","values":["Repetitive DNA sequences are prevalent in both prokaryote and eukaryote genomes and the majority of repeats are concentrated in intergenic regions. These tandem repeats (TRs) are highly variable as the number of repeated units changes frequently due to recombination events and/or polymerase slippage during replication. While TRs have been traditionally regarded as non-functional 'junk' DNA, variability in the number of TRs present within or close to genes is known to lead to gross phenotypic changes and disease. However, whether intergenic TRs have a functional role is less understood. Recent studies reveal that many intergenic TRs contain transcription factor (TF) binding sites and that several TRs of TF binding sites indeed influence gene expression. A possible mechanism is that TRs serve as TF decoys, competing with a promoter for TF binding. We utilized a synthetic system in budding yeast to examine if repeated binding sites serve as decoys, and alter the expression of genes regulated by the sequestered TF. Combining experiments with kinetic modeling suggests that repeated decoy binding sites sequester activators more strongly than a promoter binding site although both binding sites are identical in sequence. This strong binding converts a graded dose-response between activator and promoter to a sigmoidal-like response. We further find that the tight activatordecoy interaction becomes weaker with increasing activator levels, suggesting that the activator binding at the repeated decoy site array might be anti-cooperative. Finally, we show that the high affinity of repeated decoy sites qualitatively changes the behavior of a transcriptional positive feedback loop from a graded to bimodal, all-or-none response. Taken together, repeated TF binding sites play an unappreciated role as a gene regulator. Since repeated decoy sites are hypervariable in number, this variability can lead to qualitative changes in gene expression and potentially phenotypic variation over short evolutionary time scales."]},{"key":"dc:description.degree","label":"Dc Description Degree","values":["Ph.D."]},{"key":"dc:title","label":"Title","values":["A regulatory role for repeated decoy transcription factor binding sites in target gene expression"]}]}],"canonical_facts":{"dc:contributor.advisor":["Narendra Maheshri."],"dc:contributor.department":["Massachusetts Institute of Technology. Dept. of Chemical Engineering."],"dc:contributor.other":["Massachusetts Institute of Technology. Dept. of Chemical Engineering."],"dc:creator":["Lee, Tek Hyung"],"dc:date.accessioned":["2013-01-23T20:22:27Z"],"dc:date.available":["2013-01-23T20:22:27Z"],"dc:date.issued":["2012"],"dc:description":["Thesis (Ph. D.)--Massachusetts Institute of Technology, Dept. of Chemical Engineering, 2012.","Cataloged from PDF version of thesis.","Includes bibliographical references."],"dc:description.abstract":["Repetitive DNA sequences are prevalent in both prokaryote and eukaryote genomes and the majority of repeats are concentrated in intergenic regions. These tandem repeats (TRs) are highly variable as the number of repeated units changes frequently due to recombination events and/or polymerase slippage during replication. While TRs have been traditionally regarded as non-functional 'junk' DNA, variability in the number of TRs present within or close to genes is known to lead to gross phenotypic changes and disease. However, whether intergenic TRs have a functional role is less understood. Recent studies reveal that many intergenic TRs contain transcription factor (TF) binding sites and that several TRs of TF binding sites indeed influence gene expression. A possible mechanism is that TRs serve as TF decoys, competing with a promoter for TF binding. We utilized a synthetic system in budding yeast to examine if repeated binding sites serve as decoys, and alter the expression of genes regulated by the sequestered TF. Combining experiments with kinetic modeling suggests that repeated decoy binding sites sequester activators more strongly than a promoter binding site although both binding sites are identical in sequence. This strong binding converts a graded dose-response between activator and promoter to a sigmoidal-like response. We further find that the tight activatordecoy interaction becomes weaker with increasing activator levels, suggesting that the activator binding at the repeated decoy site array might be anti-cooperative. Finally, we show that the high affinity of repeated decoy sites qualitatively changes the behavior of a transcriptional positive feedback loop from a graded to bimodal, all-or-none response. Taken together, repeated TF binding sites play an unappreciated role as a gene regulator. Since repeated decoy sites are hypervariable in number, this variability can lead to qualitative changes in gene expression and potentially phenotypic variation over short evolutionary time scales."],"dc:description.degree":["Ph.D."],"dc:identifier.uri":["http://hdl.handle.net/1721.1/76563"],"dc:language.iso":["eng"],"dc:publisher":["Massachusetts Institute of Technology"],"dc:rights":["M.I.T. theses are protected by copyright. They may be viewed from this source for any purpose, but reproduction or distribution in any format is prohibited without written permission. See provided URL for inquiries about permission."],"dc:rights.uri":["http://dspace.mit.edu/handle/1721.1/7582"],"dc:subject":["Chemical Engineering."],"dc:title":["A regulatory role for repeated decoy transcription factor binding sites in target gene expression"],"dc:type":["Thesis"]},"updated_at":"2026-07-22T22:22:02Z"}