{"id":{"repo_id":"utmb","oai_identifier":"oai:utmb-ir.tdl.org:2152.3/11146"},"canonical_url":"https://search.dev.ndltd.org/etd/utmb/oai:utmb-ir.tdl.org:2152.3/11146","repository":{"repo_id":"utmb","name":"University of Texas Medical Branch","base_url":"https://utmb-ir.tdl.org/server/oai/request"},"display":{"title":"Understanding The Repair Mechanisms at Ionizing Radiation-induced Damage in The Human Genome","abstract":"Ionizing radiation (IR) such as X-rays induce damage clusters in the genome that include DNA double-strand breaks (DSB) with unligatable dirty ends, along with more frequent oxidized bases and single-strand breaks (SSB). While nonhomologous end joining and homologous recombination are major DSB repair pathways which have been extensively characterized over the past decades, contribution of error-prone alternative end joining (Alt-EJ) at X-ray-induced DNA damage is poorly characterized and underestimated. Moreover, how repair of oxidative base lesions and DSB are coordinated at damage clusters is an important unanswered question. I used recircularization of linearized plasmid reporters to monitor repair of DSBs with 3P-blocked termini, which mimic X-ray-induced strand breaks, both in cell and in vitro, with repair complexes and measured relative efficiency of NHEJ vs. Alt-EJ based on sequence analysis of the joint site. Although NHEJ was the predominant pathway for DSB repair, Alt-EJ was significantly enhanced in pre-irradiated cells. This stimulation was dependent on XRCC1 phosphorylation by casein kinase 2 (CK2) that enhanced the interaction of XRCC1 with the end resection enzymes Mre11 and CtIP. The XRCC1 immunocomplex isolated from U2OS cells had Alt-EJ activity in vitro; this activity was significantly higher in the immunocomplex from pre-irradiated cells. Our studies thus suggest that activation of Alt-EJ proficient repair complexes after irradiation in surviving cells could contribute to radioresistance and could be therapeutically targeted. In a separate study, we showed that there is a hierarchy in repair of DSBs by NHEJ followed by base excision repair of oxidized bases at IR-induced damage clusters, coordinated by scaffold attachment factor-A (SAF-A), that is crucial to maintain genomic integrity.","abstract_html":"Ionizing radiation (IR) such as X-rays induce damage clusters in the genome that include DNA double-strand breaks (DSB) with unligatable dirty ends, along with more frequent oxidized bases and single-strand breaks (SSB). While nonhomologous end joining and homologous recombination are major DSB repair pathways which have been extensively characterized over the past decades, contribution of error-prone alternative end joining (Alt-EJ) at X-ray-induced DNA damage is poorly characterized and underestimated. Moreover, how repair of oxidative base lesions and DSB are coordinated at damage clusters is an important unanswered question. I used recircularization of linearized plasmid reporters to monitor repair of DSBs with 3P-blocked termini, which mimic X-ray-induced strand breaks, both in cell and in vitro, with repair complexes and measured relative efficiency of NHEJ vs. Alt-EJ based on sequence analysis of the joint site. Although NHEJ was the predominant pathway for DSB repair, Alt-EJ was significantly enhanced in pre-irradiated cells. This stimulation was dependent on XRCC1 phosphorylation by casein kinase 2 (CK2) that enhanced the interaction of XRCC1 with the end resection enzymes Mre11 and CtIP. The XRCC1 immunocomplex isolated from U2OS cells had Alt-EJ activity in vitro; this activity was significantly higher in the immunocomplex from pre-irradiated cells. Our studies thus suggest that activation of Alt-EJ proficient repair complexes after irradiation in surviving cells could contribute to radioresistance and could be therapeutically targeted. In a separate study, we showed that there is a hierarchy in repair of DSBs by NHEJ followed by base excision repair of oxidized bases at IR-induced damage clusters, coordinated by scaffold attachment factor-A (SAF-A), that is crucial to maintain genomic integrity.","abstract_has_math":false,"creators":["Dutta, Arijit"],"institution":"The University of Texas Medical Branch at Galveston","degree_name":"Biochemistry and Molecular Biology (Doctoral)","degree_level":"Doctoral","degree_discipline":null,"degree_department":null,"school":null,"contributors":[],"advisors":["Sowers, Lawrence C"],"committee_chairs":[],"committee_members":["Mitra, Sankar","Hegde, Muralidhar L","Hazra, Tapas","Pazdrak, Konrad","Wiederhold, Lee R","Pandita, Tej K"],"year":null,"date_issued":"","date_published":null,"updated_at":"2026-07-24T05:51:10Z","subjects":["Clustered DNA damage","Ionizing radiation","Double strand break","Non-homologous end joining","Alternative end joining","Genomic instability","Repair complex"],"languages":[],"rights":[],"rights_urls":[],"identifier_entries":[]},"links":{"outbound_url":"https://hdl.handle.net/2152.3/11146","outbound_label":"Handle","outbound_source":"dc:identifier.uri"},"metadata_groups":[{"id":"people","label":"People","entries":[{"key":"dc:contributor.advisor","label":"Advisor","values":["Sowers, Lawrence C"]},{"key":"dc:contributor.committeemember","label":"Committee Member","values":["Mitra, Sankar","Hegde, Muralidhar L","Hazra, Tapas","Pazdrak, Konrad","Wiederhold, Lee R","Pandita, Tej K"]},{"key":"dc:creator","label":"Author","values":["Dutta, Arijit"]}]},{"id":"academic_context","label":"Academic Context","entries":[{"key":"dc:date.accessioned","label":"Dc Date Accessioned","values":["2019-03-13T20:24:25Z"]},{"key":"dc:date.available","label":"Dc Date Available","values":["2019-03-13T20:24:25Z"]},{"key":"dc:type","label":"Dc Type","values":["Thesis"]},{"key":"thesis:degree_level","label":"Degree Level","values":["Doctoral"]},{"key":"thesis:degree_name","label":"Degree Name","values":["Biochemistry and Molecular Biology (Doctoral)"]},{"key":"thesis:institution_name","label":"Thesis Institution Name","values":["The University of Texas Medical Branch at Galveston"]}]},{"id":"subjects_keywords","label":"Subjects and Keywords","entries":[{"key":"dc:subject","label":"Dc Subject","values":["Clustered DNA damage","Ionizing radiation","Double strand break","Non-homologous end joining","Alternative end joining","Genomic instability","Repair complex"]}]},{"id":"identifiers","label":"Identifiers","entries":[{"key":"dc:identifier.uri","label":"Identifier URI","values":["https://hdl.handle.net/2152.3/11146"]}]},{"id":"additional","label":"Additional Metadata","entries":[{"key":"dc:description.abstract","label":"Abstract","values":["Ionizing radiation (IR) such as X-rays induce damage clusters in the genome that include DNA double-strand breaks (DSB) with unligatable dirty ends, along with more frequent oxidized bases and single-strand breaks (SSB). While nonhomologous end joining and homologous recombination are major DSB repair pathways which have been extensively characterized over the past decades, contribution of error-prone alternative end joining (Alt-EJ) at X-ray-induced DNA damage is poorly characterized and underestimated. Moreover, how repair of oxidative base lesions and DSB are coordinated at damage clusters is an important unanswered question. I used recircularization of linearized plasmid reporters to monitor repair of DSBs with 3P-blocked termini, which mimic X-ray-induced strand breaks, both in cell and in vitro, with repair complexes and measured relative efficiency of NHEJ vs. Alt-EJ based on sequence analysis of the joint site. Although NHEJ was the predominant pathway for DSB repair, Alt-EJ was significantly enhanced in pre-irradiated cells. This stimulation was dependent on XRCC1 phosphorylation by casein kinase 2 (CK2) that enhanced the interaction of XRCC1 with the end resection enzymes Mre11 and CtIP. The XRCC1 immunocomplex isolated from U2OS cells had Alt-EJ activity in vitro; this activity was significantly higher in the immunocomplex from pre-irradiated cells. Our studies thus suggest that activation of Alt-EJ proficient repair complexes after irradiation in surviving cells could contribute to radioresistance and could be therapeutically targeted. In a separate study, we showed that there is a hierarchy in repair of DSBs by NHEJ followed by base excision repair of oxidized bases at IR-induced damage clusters, coordinated by scaffold attachment factor-A (SAF-A), that is crucial to maintain genomic integrity."]},{"key":"dc:format.mimetype","label":"Dc Format Mimetype","values":["application/pdf"]},{"key":"dc:title","label":"Title","values":["Understanding The Repair Mechanisms at Ionizing Radiation-induced Damage in The Human Genome"]}]}],"canonical_facts":{"dc:contributor.advisor":["Sowers, Lawrence C"],"dc:contributor.committeemember":["Mitra, Sankar","Hegde, Muralidhar L","Hazra, Tapas","Pazdrak, Konrad","Wiederhold, Lee R","Pandita, Tej K"],"dc:creator":["Dutta, Arijit"],"dc:date.accessioned":["2019-03-13T20:24:25Z"],"dc:date.available":["2019-03-13T20:24:25Z"],"dc:description.abstract":["Ionizing radiation (IR) such as X-rays induce damage clusters in the genome that include DNA double-strand breaks (DSB) with unligatable dirty ends, along with more frequent oxidized bases and single-strand breaks (SSB). While nonhomologous end joining and homologous recombination are major DSB repair pathways which have been extensively characterized over the past decades, contribution of error-prone alternative end joining (Alt-EJ) at X-ray-induced DNA damage is poorly characterized and underestimated. Moreover, how repair of oxidative base lesions and DSB are coordinated at damage clusters is an important unanswered question. I used recircularization of linearized plasmid reporters to monitor repair of DSBs with 3P-blocked termini, which mimic X-ray-induced strand breaks, both in cell and in vitro, with repair complexes and measured relative efficiency of NHEJ vs. Alt-EJ based on sequence analysis of the joint site. Although NHEJ was the predominant pathway for DSB repair, Alt-EJ was significantly enhanced in pre-irradiated cells. This stimulation was dependent on XRCC1 phosphorylation by casein kinase 2 (CK2) that enhanced the interaction of XRCC1 with the end resection enzymes Mre11 and CtIP. The XRCC1 immunocomplex isolated from U2OS cells had Alt-EJ activity in vitro; this activity was significantly higher in the immunocomplex from pre-irradiated cells. Our studies thus suggest that activation of Alt-EJ proficient repair complexes after irradiation in surviving cells could contribute to radioresistance and could be therapeutically targeted. In a separate study, we showed that there is a hierarchy in repair of DSBs by NHEJ followed by base excision repair of oxidized bases at IR-induced damage clusters, coordinated by scaffold attachment factor-A (SAF-A), that is crucial to maintain genomic integrity."],"dc:format.mimetype":["application/pdf"],"dc:identifier.uri":["https://hdl.handle.net/2152.3/11146"],"dc:subject":["Clustered DNA damage","Ionizing radiation","Double strand break","Non-homologous end joining","Alternative end joining","Genomic instability","Repair complex"],"dc:title":["Understanding The Repair Mechanisms at Ionizing Radiation-induced Damage in The Human Genome"],"dc:type":["Thesis"],"thesis:degree_level":["Doctoral"],"thesis:degree_name":["Biochemistry and Molecular Biology (Doctoral)"],"thesis:institution_name":["The University of Texas Medical Branch at Galveston"]},"updated_at":"2026-07-24T05:51:10Z"}