{"id":{"repo_id":"uiuc","oai_identifier":"oai:www.ideals.illinois.edu:2142/129695"},"canonical_url":"https://search.dev.ndltd.org/etd/uiuc/oai:www.ideals.illinois.edu:2142/129695","repository":{"repo_id":"uiuc","name":"University of Illinois - Urbana-Champaign","base_url":"https://www.ideals.illinois.edu/oai-pmh"},"display":{"title":"New insights into 3D genome architecture through improved genomic methods","abstract":"Submission published under a 24 month embargo labeled 'Closed Access', the embargo will last until 2027-05-01","abstract_html":"Submission published under a 24 month embargo labeled 'Closed Access', the embargo will last until 2027-05-01","abstract_has_math":false,"creators":["Kumar, Pradeep"],"institution":"University of Illinois Urbana-Champaign","degree_name":"Ph.D.","degree_level":"Dissertation","degree_discipline":"Cell and Developmental Biology","degree_department":null,"school":null,"contributors":["Belmont, Andrew S.","Prasanth, Kannanganattu V.","Freeman, Brian C.","Kalsotra, Auinash"],"advisors":[],"committee_chairs":[],"committee_members":[],"year":2025,"date_issued":"2025-04-28","date_published":"2025-04-28","updated_at":"2026-07-22T22:25:05Z","subjects":["3D genome organization","Nuclear compartment","Nuclear speckles","Nuclear lamina","Nucleolus"],"languages":["en","eng"],"rights":["Copyright 2025 Pradeep Kumar"],"rights_urls":[],"identifier_entries":[]},"links":{"outbound_url":"https://hdl.handle.net/2142/129695","outbound_label":"Handle","outbound_source":"dc:identifier"},"metadata_groups":[{"id":"people","label":"People","entries":[{"key":"dc:contributor","label":"Contributor","values":["Belmont, Andrew S.","Prasanth, Kannanganattu V.","Freeman, Brian C.","Kalsotra, Auinash"]},{"key":"dc:creator","label":"Author","values":["Kumar, Pradeep"]}]},{"id":"academic_context","label":"Academic Context","entries":[{"key":"dc:date","label":"Dc Date","values":["2025-04-28","2025-05"]},{"key":"dc:type","label":"Dc Type","values":["text","Thesis"]},{"key":"thesis:degree_discipline","label":"Discipline","values":["Cell and Developmental Biology"]},{"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 Urbana-Champaign"]}]},{"id":"subjects_keywords","label":"Subjects and Keywords","entries":[{"key":"dc:subject","label":"Dc Subject","values":["3D genome organization","Nuclear compartment","Nuclear speckles","Nuclear lamina","Nucleolus"]}]},{"id":"language_rights","label":"Language and Rights","entries":[{"key":"dc:language","label":"Dc Language","values":["en","eng"]},{"key":"dc:rights","label":"Dc Rights","values":["Copyright 2025 Pradeep Kumar"]}]},{"id":"identifiers","label":"Identifiers","entries":[{"key":"dc:identifier","label":"Identifier","values":["https://hdl.handle.net/2142/129695"]}]},{"id":"additional","label":"Additional Metadata","entries":[{"key":"dc:description","label":"Description","values":["Submission published under a 24 month embargo labeled 'Closed Access', the embargo will last until 2027-05-01","The student, Pradeep Kumar, accepted the attached license on 2025-04-17 at 09:19.","The student, Pradeep Kumar, submitted this Dissertation for approval on 2025-04-17 at 09:21.","This Dissertation was approved for publication on 2025-04-28 at 16:24.","DSpace SAF Submission Ingestion Package generated from Vireo submission #21810 on 2025-10-19 at 19:53:08","The eukaryotic interphase nucleus contains morphologically and functionally distinct substructures known as chromatin domains and nuclear bodies. Genome organization within the nucleus is highly nonrandom, and abnormal changes in genome organization can lead to diseases including cancer. Two widely used models in the field: the radial genome organization model and the binary division model address various aspects of genome organization. However, while these models are effective in explaining certain features, they have significant limitations, including their failure to account for the nuclear bodies and their possible influence on genome organization. Lamina-associated domains (LADs) localize not only at nuclear lamina but also localize at the nucleolus and pericentromeric heterochromatin (PCH). In Chapter 2, I present nucleolus and centromere TSA-seq methods, which were developed to map genomic regions localizing at the nucleolus and PCH. Using these methods, I made several interesting observations about genomic regions localizing at these nuclear substructures, including the identification of two distinct subsets of LADs that exhibit unique gene expression profiles and DNA replication timing, despite their differential localization at the nucleolus or nuclear lamina, depending on the cell type. Unlike previous studies in the field, Chapter 3 presents my collaborative research where we integrated multiple spatial (DamID, TSA-seq and Hi-C), functional genomic methods (16-fraction Repli-seq and RNA-seq), combined with light microscopy, to investigate genome organization in relation to various nuclear bodies across multiple cell types. This work uncovered several novel features of genome organization and challenges long-standing models in the field. Finally, the appendices of this thesis, I include several protocols for novel genomic methods. These include a new protocol for the TSA-seq nanotag (TSA-seq 3.0) method, which requires 500 times fewer cells compared to the current TSA-seq 2.0 protocol and has higher throughput. Additionally I present an improved nanotag protocol that addresses the limitations of the CUT&Tag method and is compatible with fixed cells."]},{"key":"dc:format","label":"Dc Format","values":["application/pdf"]},{"key":"dc:title","label":"Title","values":["New insights into 3D genome architecture through improved genomic methods"]}]}],"canonical_facts":{"dc:contributor":["Belmont, Andrew S.","Prasanth, Kannanganattu V.","Freeman, Brian C.","Kalsotra, Auinash"],"dc:creator":["Kumar, Pradeep"],"dc:date":["2025-04-28","2025-05"],"dc:description":["Submission published under a 24 month embargo labeled 'Closed Access', the embargo will last until 2027-05-01","The student, Pradeep Kumar, accepted the attached license on 2025-04-17 at 09:19.","The student, Pradeep Kumar, submitted this Dissertation for approval on 2025-04-17 at 09:21.","This Dissertation was approved for publication on 2025-04-28 at 16:24.","DSpace SAF Submission Ingestion Package generated from Vireo submission #21810 on 2025-10-19 at 19:53:08","The eukaryotic interphase nucleus contains morphologically and functionally distinct substructures known as chromatin domains and nuclear bodies. Genome organization within the nucleus is highly nonrandom, and abnormal changes in genome organization can lead to diseases including cancer. Two widely used models in the field: the radial genome organization model and the binary division model address various aspects of genome organization. However, while these models are effective in explaining certain features, they have significant limitations, including their failure to account for the nuclear bodies and their possible influence on genome organization. Lamina-associated domains (LADs) localize not only at nuclear lamina but also localize at the nucleolus and pericentromeric heterochromatin (PCH). In Chapter 2, I present nucleolus and centromere TSA-seq methods, which were developed to map genomic regions localizing at the nucleolus and PCH. Using these methods, I made several interesting observations about genomic regions localizing at these nuclear substructures, including the identification of two distinct subsets of LADs that exhibit unique gene expression profiles and DNA replication timing, despite their differential localization at the nucleolus or nuclear lamina, depending on the cell type. Unlike previous studies in the field, Chapter 3 presents my collaborative research where we integrated multiple spatial (DamID, TSA-seq and Hi-C), functional genomic methods (16-fraction Repli-seq and RNA-seq), combined with light microscopy, to investigate genome organization in relation to various nuclear bodies across multiple cell types. This work uncovered several novel features of genome organization and challenges long-standing models in the field. Finally, the appendices of this thesis, I include several protocols for novel genomic methods. These include a new protocol for the TSA-seq nanotag (TSA-seq 3.0) method, which requires 500 times fewer cells compared to the current TSA-seq 2.0 protocol and has higher throughput. Additionally I present an improved nanotag protocol that addresses the limitations of the CUT&Tag method and is compatible with fixed cells."],"dc:format":["application/pdf"],"dc:identifier":["https://hdl.handle.net/2142/129695"],"dc:language":["en","eng"],"dc:rights":["Copyright 2025 Pradeep Kumar"],"dc:subject":["3D genome organization","Nuclear compartment","Nuclear speckles","Nuclear lamina","Nucleolus"],"dc:title":["New insights into 3D genome architecture through improved genomic methods"],"dc:type":["text","Thesis"],"thesis:degree_discipline":["Cell and Developmental Biology"],"thesis:degree_level":["Dissertation"],"thesis:degree_name":["Ph.D."],"thesis:institution_name":["University of Illinois Urbana-Champaign"]},"updated_at":"2026-07-22T22:25:05Z"}