{"id":{"repo_id":"cambridge","oai_identifier":"oai:www.repository.cam.ac.uk:1810/395327"},"canonical_url":"https://search.dev.ndltd.org/etd/cambridge/oai:www.repository.cam.ac.uk:1810/395327","repository":{"repo_id":"cambridge","name":"Cambridge University","base_url":"https://api.repository.cam.ac.uk/server/oai/request"},"display":{"title":"Exploiting Lentiviral Integrations to Profile Chromatin","abstract":"Current methods for profiling histone modifications and protein localisation along chromatin suffer from critical limitations: the gold standard, ChIP-seq, relies on high-quality antibodies, while other antibody-free techniques like DamID are limited by the availability of specific DNA sequences. Here, I describe the development of ChILI-seq (Chromatin Interactions by Lentiviral Integration Sequencing), an antibody-free and sequence-independent method to profile the genomic localisation of proteins, as well as DNA and histone modifications. ChILI-seq exploits the dependency of the lentiviral integrase on LEDGF (Lens Epithelium-Derived Growth Factor). By fusing LEDGF to a chromatin-binding protein of interest, lentiviral integrations are redirected to the genomic targets of that protein, and can be identified through integration site mapping and next-generation sequencing. To validate ChILI-seq, I demonstrate its utility to profile histone and DNA modifications using known chromatin reader domains. I show that ChILI-seq is a cost-effective alternative to traditional techniques, providing superior resolution and signal-to-noise ratios. I then go on to show that ChILI-seq can reveal the binding preferences of many chromatin reader domains, allowing us to dissect the recruitment requirements of key epigenetic modifiers, including BRD4 and the HUSH complex. Finally, I utilise a high-throughput screening approach to identify chromatin-binding domains of unknown specificities and exploit ChILI-seq to reveal their binding preferences. This screen suggested an intriguing new role for the KAT14 acetyltransferase in LINE-1 element regulation. In summary, ChILI-seq expands our chromatin profiling toolkit, offering a versatile, antibody-free and sequence-independent method to probe interactions between epigenetic modifiers and chromatin.","abstract_html":"Current methods for profiling histone modifications and protein localisation along chromatin suffer from critical limitations: the gold standard, ChIP-seq, relies on high-quality antibodies, while other antibody-free techniques like DamID are limited by the availability of specific DNA sequences. Here, I describe the development of ChILI-seq (Chromatin Interactions by Lentiviral Integration Sequencing), an antibody-free and sequence-independent method to profile the genomic localisation of proteins, as well as DNA and histone modifications. ChILI-seq exploits the dependency of the lentiviral integrase on LEDGF (Lens Epithelium-Derived Growth Factor). By fusing LEDGF to a chromatin-binding protein of interest, lentiviral integrations are redirected to the genomic targets of that protein, and can be identified through integration site mapping and next-generation sequencing. To validate ChILI-seq, I demonstrate its utility to profile histone and DNA modifications using known chromatin reader domains. I show that ChILI-seq is a cost-effective alternative to traditional techniques, providing superior resolution and signal-to-noise ratios. I then go on to show that ChILI-seq can reveal the binding preferences of many chromatin reader domains, allowing us to dissect the recruitment requirements of key epigenetic modifiers, including BRD4 and the HUSH complex. Finally, I utilise a high-throughput screening approach to identify chromatin-binding domains of unknown specificities and exploit ChILI-seq to reveal their binding preferences. This screen suggested an intriguing new role for the KAT14 acetyltransferase in LINE-1 element regulation. In summary, ChILI-seq expands our chromatin profiling toolkit, offering a versatile, antibody-free and sequence-independent method to probe interactions between epigenetic modifiers and chromatin.","abstract_has_math":false,"creators":["Qin, Chuyan"],"institution":"University of Cambridge","degree_name":"Doctor of Philosophy (PhD)","degree_level":"Doctoral","degree_discipline":null,"degree_department":null,"school":null,"contributors":[],"advisors":["Tchasovnikarova, Iva"],"committee_chairs":[],"committee_members":[],"year":2025,"date_issued":"2025-07-20","date_published":"2025-07-20","updated_at":"2026-07-22T22:23:59Z","subjects":["ChILI-seq","Chromatin Profiling","LEDGF","Lentiviral Integration"],"languages":["eng"],"rights":[],"rights_urls":["https://www.repository.cam.ac.uk/bitstreams/6fa7a778-abbc-4655-9af3-1aa3148c8785/download","http://purl.org/NET/rdflicense/allrightsreserved"],"identifier_entries":[]},"links":{"outbound_url":"https://doi.org/10.17863/CAM.124872","outbound_label":"DOI","outbound_source":"dc:identifier.doi"},"metadata_groups":[{"id":"people","label":"People","entries":[{"key":"dc:contributor.advisor","label":"Advisor","values":["Tchasovnikarova, Iva"]},{"key":"dc:creator","label":"Author","values":["Qin, Chuyan"]}]},{"id":"academic_context","label":"Academic Context","entries":[{"key":"dc:date.issued","label":"Date","values":["2025-07-20"]},{"key":"dc:publisher.institution","label":"Dc Publisher Institution","values":["University of Cambridge"]},{"key":"dc:relation.isreferencedby.uri","label":"Dc Relation Isreferencedby URI","values":["https://www.repository.cam.ac.uk/handle/1810/395327"]},{"key":"dc:type","label":"Dc Type","values":["Thesis"]},{"key":"dc:type.qualificationlevel","label":"Dc Type Qualificationlevel","values":["Doctoral"]},{"key":"dc:type.qualificationname","label":"Dc Type Qualificationname","values":["Doctor of Philosophy (PhD)"]}]},{"id":"subjects_keywords","label":"Subjects and Keywords","entries":[{"key":"dc:subject","label":"Dc Subject","values":["ChILI-seq","Chromatin Profiling","LEDGF","Lentiviral Integration"]}]},{"id":"language_rights","label":"Language and Rights","entries":[{"key":"dc:language","label":"Dc Language","values":["eng"]},{"key":"dc:rights","label":"Dc Rights","values":["https://www.repository.cam.ac.uk/bitstreams/6fa7a778-abbc-4655-9af3-1aa3148c8785/download","http://purl.org/NET/rdflicense/allrightsreserved"]}]},{"id":"identifiers","label":"Identifiers","entries":[{"key":"dc:identifier.doi","label":"DOI","values":["https://doi.org/10.17863/CAM.124872"]},{"key":"dc:identifier.uri","label":"Identifier URI","values":["https://www.repository.cam.ac.uk/bitstreams/a1c55360-1169-4152-b2cd-56a1291e8e8f/download"]}]},{"id":"additional","label":"Additional Metadata","entries":[{"key":"dc:description.abstract","label":"Abstract","values":["Current methods for profiling histone modifications and protein localisation along chromatin suffer from critical limitations: the gold standard, ChIP-seq, relies on high-quality antibodies, while other antibody-free techniques like DamID are limited by the availability of specific DNA sequences. 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I then go on to show that ChILI-seq can reveal the binding preferences of many chromatin reader domains, allowing us to dissect the recruitment requirements of key epigenetic modifiers, including BRD4 and the HUSH complex. Finally, I utilise a high-throughput screening approach to identify chromatin-binding domains of unknown specificities and exploit ChILI-seq to reveal their binding preferences. This screen suggested an intriguing new role for the KAT14 acetyltransferase in LINE-1 element regulation. 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