{"id":{"repo_id":"cambridge","oai_identifier":"oai:www.repository.cam.ac.uk:1810/372364"},"canonical_url":"https://search.dev.ndltd.org/etd/cambridge/oai:www.repository.cam.ac.uk:1810/372364","repository":{"repo_id":"cambridge","name":"Cambridge University","base_url":"https://api.repository.cam.ac.uk/server/oai/request"},"display":{"title":"A TRIM28 centric strategy to efficiently uncover the contribution of KZFPs to the evolution of gene regulatory networks","abstract":"The family of KRAB zinc-finger proteins (KZFPs) is the largest group of DNA-binding factors in tetrapods and is rapidly evolving, with >350 protein-coding members in humans. While the individual roles of most human KZFPs is poorly characterized, it is known that their primary role is to epigenetically silence transposable elements (TEs). KZFPs bind TEs in a sequence specific manner and recruit TRIM28 which interacts with other proteins to add H3K9me3, inducing silencing-associated heterochromatin. Interestingly, it was discovered following a large-scale survey of their binding sites that most human KZFPs target evolutionary conserved transposable elements that have long lost their transposition potential. This suggests additional selection pressures aside from their role in preventing transposition of young mobile elements. To explain the long-term conservation of KZFPs and the remnants of their TE targets, it was hypothesized that KZFPs participate in the domestication process of TEs. As they have varied expression patterns, KZFPs were theorized to serve as have a role in the regulation of domesticated TEs in a cell-context specific way. We have recently been accumulating evidence in favour of this model; for example, ZNF808 has recently been identified as an essential primate-specific regulator of pancreas development via the regulation of MER11 elements which, when derepressed, are able to trigger a liver cell fate program. Here I present a new large-scale strategy to uncover links between KZFPs, TEs and gene regulation. We leverage the shared ability of most KZFPs to recruit TRIM28, which is essential for their role as epigenetic silencers. Targeting TRIM28 allows for the indirect capture of the global activity of KZFPs active in a particular context. First, I have produced genome-wide maps of TRIM28 binding using ChIP-exo in multiple different cell types to understand which elements are differentially silenced between cellular contexts. Second, I demonstrate that endogenously tagged TRIM28 with an inducible protein degradation tag allows us to quantify early transcriptomic events unfolding after its depletion. Together these strategies provide evidence that TRIM28 and KZFPs have cell type specific patterns of binding which contribute to gene regulation by controlling the epigenetic accessibility of cis-regulatory elements and allow us to pinpoint promising individual KZFPs for future studies. This system is amenable to be scaled to multiple cell types and contexts and will allow for a global understanding of the contribution of domesticated TEs regulated by KZFPs to human health and biology.","abstract_html":"The family of KRAB zinc-finger proteins (KZFPs) is the largest group of DNA-binding factors in tetrapods and is rapidly evolving, with >350 protein-coding members in humans. While the individual roles of most human KZFPs is poorly characterized, it is known that their primary role is to epigenetically silence transposable elements (TEs). KZFPs bind TEs in a sequence specific manner and recruit TRIM28 which interacts with other proteins to add H3K9me3, inducing silencing-associated heterochromatin. Interestingly, it was discovered following a large-scale survey of their binding sites that most human KZFPs target evolutionary conserved transposable elements that have long lost their transposition potential. This suggests additional selection pressures aside from their role in preventing transposition of young mobile elements. To explain the long-term conservation of KZFPs and the remnants of their TE targets, it was hypothesized that KZFPs participate in the domestication process of TEs. As they have varied expression patterns, KZFPs were theorized to serve as have a role in the regulation of domesticated TEs in a cell-context specific way. We have recently been accumulating evidence in favour of this model; for example, ZNF808 has recently been identified as an essential primate-specific regulator of pancreas development via the regulation of MER11 elements which, when derepressed, are able to trigger a liver cell fate program. Here I present a new large-scale strategy to uncover links between KZFPs, TEs and gene regulation. We leverage the shared ability of most KZFPs to recruit TRIM28, which is essential for their role as epigenetic silencers. Targeting TRIM28 allows for the indirect capture of the global activity of KZFPs active in a particular context. First, I have produced genome-wide maps of TRIM28 binding using ChIP-exo in multiple different cell types to understand which elements are differentially silenced between cellular contexts. Second, I demonstrate that endogenously tagged TRIM28 with an inducible protein degradation tag allows us to quantify early transcriptomic events unfolding after its depletion. Together these strategies provide evidence that TRIM28 and KZFPs have cell type specific patterns of binding which contribute to gene regulation by controlling the epigenetic accessibility of cis-regulatory elements and allow us to pinpoint promising individual KZFPs for future studies. This system is amenable to be scaled to multiple cell types and contexts and will allow for a global understanding of the contribution of domesticated TEs regulated by KZFPs to human health and biology.","abstract_has_math":false,"creators":["Davis, Juliette"],"institution":"University of Cambridge","degree_name":"Doctor of Philosophy (PhD)","degree_level":"Doctoral","degree_discipline":null,"degree_department":null,"school":null,"contributors":[],"advisors":["Imbeault, Michael"],"committee_chairs":[],"committee_members":[],"year":2024,"date_issued":"2024-01-19","date_published":"2024-01-19","updated_at":"2026-07-22T22:24:21Z","subjects":["Epigenetics","Gene regulation","KAP1","KRAB-ZFP","KZFP","Transposable element","TRIM28"],"languages":["eng"],"rights":[],"rights_urls":["https://apollo8-f-pro.lib.cam.ac.uk/bitstreams/6cfb8a7d-acd0-4f2c-9741-604edcbf36c6/download","https://www.rioxx.net/licenses/all-rights-reserved/"],"identifier_entries":[]},"links":{"outbound_url":"https://doi.org/10.17863/CAM.111229","outbound_label":"DOI","outbound_source":"dc:identifier.doi"},"metadata_groups":[{"id":"people","label":"People","entries":[{"key":"dc:contributor.advisor","label":"Advisor","values":["Imbeault, Michael"]},{"key":"dc:creator","label":"Author","values":["Davis, Juliette"]}]},{"id":"academic_context","label":"Academic Context","entries":[{"key":"dc:date.issued","label":"Date","values":["2024-01-19"]},{"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/1810/372364"]},{"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":["Epigenetics","Gene regulation","KAP1","KRAB-ZFP","KZFP","Transposable element","TRIM28"]}]},{"id":"language_rights","label":"Language and Rights","entries":[{"key":"dc:language","label":"Dc Language","values":["eng"]},{"key":"dc:rights","label":"Dc Rights","values":["https://apollo8-f-pro.lib.cam.ac.uk/bitstreams/6cfb8a7d-acd0-4f2c-9741-604edcbf36c6/download","https://www.rioxx.net/licenses/all-rights-reserved/"]}]},{"id":"identifiers","label":"Identifiers","entries":[{"key":"dc:identifier.doi","label":"DOI","values":["https://doi.org/10.17863/CAM.111229"]},{"key":"dc:identifier.uri","label":"Identifier URI","values":["https://apollo8-f-pro.lib.cam.ac.uk/bitstreams/bf7c3bfe-0d27-40c6-949f-bf40296ef31b/download"]}]},{"id":"additional","label":"Additional Metadata","entries":[{"key":"dc:description.abstract","label":"Abstract","values":["The family of KRAB zinc-finger proteins (KZFPs) is the largest group of DNA-binding factors in tetrapods and is rapidly evolving, with >350 protein-coding members in humans. While the individual roles of most human KZFPs is poorly characterized, it is known that their primary role is to epigenetically silence transposable elements (TEs). KZFPs bind TEs in a sequence specific manner and recruit TRIM28 which interacts with other proteins to add H3K9me3, inducing silencing-associated heterochromatin. Interestingly, it was discovered following a large-scale survey of their binding sites that most human KZFPs target evolutionary conserved transposable elements that have long lost their transposition potential. This suggests additional selection pressures aside from their role in preventing transposition of young mobile elements. To explain the long-term conservation of KZFPs and the remnants of their TE targets, it was hypothesized that KZFPs participate in the domestication process of TEs. As they have varied expression patterns, KZFPs were theorized to serve as have a role in the regulation of domesticated TEs in a cell-context specific way. We have recently been accumulating evidence in favour of this model; for example, ZNF808 has recently been identified as an essential primate-specific regulator of pancreas development via the regulation of MER11 elements which, when derepressed, are able to trigger a liver cell fate program. Here I present a new large-scale strategy to uncover links between KZFPs, TEs and gene regulation. We leverage the shared ability of most KZFPs to recruit TRIM28, which is essential for their role as epigenetic silencers. Targeting TRIM28 allows for the indirect capture of the global activity of KZFPs active in a particular context. First, I have produced genome-wide maps of TRIM28 binding using ChIP-exo in multiple different cell types to understand which elements are differentially silenced between cellular contexts. Second, I demonstrate that endogenously tagged TRIM28 with an inducible protein degradation tag allows us to quantify early transcriptomic events unfolding after its depletion. Together these strategies provide evidence that TRIM28 and KZFPs have cell type specific patterns of binding which contribute to gene regulation by controlling the epigenetic accessibility of cis-regulatory elements and allow us to pinpoint promising individual KZFPs for future studies. This system is amenable to be scaled to multiple cell types and contexts and will allow for a global understanding of the contribution of domesticated TEs regulated by KZFPs to human health and biology."]},{"key":"dc:format.checksum.md5","label":"Dc Format Checksum Md5","values":["17eb58d3bdd323e976f212146b4951d0","87eda9de84448d1f82354d60eee3eb5f"]},{"key":"dc:title","label":"Title","values":["A TRIM28 centric strategy to efficiently uncover the contribution of KZFPs to the evolution of gene regulatory networks"]}]}],"canonical_facts":{"dc:contributor.advisor":["Imbeault, Michael"],"dc:creator":["Davis, Juliette"],"dc:date.issued":["2024-01-19"],"dc:description.abstract":["The family of KRAB zinc-finger proteins (KZFPs) is the largest group of DNA-binding factors in tetrapods and is rapidly evolving, with >350 protein-coding members in humans. While the individual roles of most human KZFPs is poorly characterized, it is known that their primary role is to epigenetically silence transposable elements (TEs). KZFPs bind TEs in a sequence specific manner and recruit TRIM28 which interacts with other proteins to add H3K9me3, inducing silencing-associated heterochromatin. Interestingly, it was discovered following a large-scale survey of their binding sites that most human KZFPs target evolutionary conserved transposable elements that have long lost their transposition potential. This suggests additional selection pressures aside from their role in preventing transposition of young mobile elements. To explain the long-term conservation of KZFPs and the remnants of their TE targets, it was hypothesized that KZFPs participate in the domestication process of TEs. As they have varied expression patterns, KZFPs were theorized to serve as have a role in the regulation of domesticated TEs in a cell-context specific way. We have recently been accumulating evidence in favour of this model; for example, ZNF808 has recently been identified as an essential primate-specific regulator of pancreas development via the regulation of MER11 elements which, when derepressed, are able to trigger a liver cell fate program. Here I present a new large-scale strategy to uncover links between KZFPs, TEs and gene regulation. We leverage the shared ability of most KZFPs to recruit TRIM28, which is essential for their role as epigenetic silencers. Targeting TRIM28 allows for the indirect capture of the global activity of KZFPs active in a particular context. First, I have produced genome-wide maps of TRIM28 binding using ChIP-exo in multiple different cell types to understand which elements are differentially silenced between cellular contexts. Second, I demonstrate that endogenously tagged TRIM28 with an inducible protein degradation tag allows us to quantify early transcriptomic events unfolding after its depletion. Together these strategies provide evidence that TRIM28 and KZFPs have cell type specific patterns of binding which contribute to gene regulation by controlling the epigenetic accessibility of cis-regulatory elements and allow us to pinpoint promising individual KZFPs for future studies. This system is amenable to be scaled to multiple cell types and contexts and will allow for a global understanding of the contribution of domesticated TEs regulated by KZFPs to human health and biology."],"dc:format.checksum.md5":["17eb58d3bdd323e976f212146b4951d0","87eda9de84448d1f82354d60eee3eb5f"],"dc:identifier.doi":["https://doi.org/10.17863/CAM.111229"],"dc:identifier.uri":["https://apollo8-f-pro.lib.cam.ac.uk/bitstreams/bf7c3bfe-0d27-40c6-949f-bf40296ef31b/download"],"dc:language":["eng"],"dc:publisher.institution":["University of Cambridge"],"dc:relation.isreferencedby.uri":["https://www.repository.cam.ac.uk/handle/1810/372364"],"dc:rights":["https://apollo8-f-pro.lib.cam.ac.uk/bitstreams/6cfb8a7d-acd0-4f2c-9741-604edcbf36c6/download","https://www.rioxx.net/licenses/all-rights-reserved/"],"dc:subject":["Epigenetics","Gene regulation","KAP1","KRAB-ZFP","KZFP","Transposable element","TRIM28"],"dc:title":["A TRIM28 centric strategy to efficiently uncover the contribution of KZFPs to the evolution of gene regulatory networks"],"dc:type":["Thesis"],"dc:type.qualificationlevel":["Doctoral"],"dc:type.qualificationname":["Doctor of Philosophy (PhD)"]},"updated_at":"2026-07-22T22:24:21Z"}