KDM2B links recognition of CpG islands to polycomb domain formation in vivo
<p>Mammalian genomes are characterised by global and pervasive DNA methylation and this modification is generally thought to be inhibitory to transcription. An exception to this widespread DNA modification are genomic elements called CpG islands (CGI), contiguous regions of non-methylated DNA...
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| Format: | Thesis |
| Language: | English |
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2013
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| _version_ | 1797112954174308352 |
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| author | Farcas, AM |
| author2 | Klose, RJ |
| author_facet | Klose, RJ Farcas, AM |
| author_sort | Farcas, AM |
| collection | OXFORD |
| description | <p>Mammalian genomes are characterised by global and pervasive DNA methylation and this modification is generally thought to be inhibitory to transcription. An exception to this widespread DNA modification are genomic elements called CpG islands (CGI), contiguous regions of non-methylated DNA which encompass the transcription start site of two thirds of mammalian genes. Although CGIs represent the most prominent feature of mammalian promoters, the contribution of these elements to promoter function remains unclear. Work in this study shows that the histone lysine demethylase KDM2B (FBXL10/ JHDM1B) is a nuclear protein which binds specifically to non-methylated CpG dinucleotides and associates with CGI elements genome-wide through its zinc-finger CxxC (ZF-CxxC) DNA binding domain. Furthermore, in mouse embryonic stem cells, biochemical investigation revealed that KDM2B associates with Polycomb group E3 ubiquitin ligase RING1B to form a variant Polycomb repressive complex 1 (PRC1) characterized by the PCGF1 subunit.</p> <p>Considering that KDM2B has clear DNA-binding activity and that CGIs were reported to function as nucleation sites for polycomb repressive complexes, a potential role for KDM2B in mediating PRC1 recruitment to target genes was investigated. Stable depletion studies indicated that KDM2B is required for the normal targeting of RING1B to CGIs and the regulation of expression of a subset of Polycomb-occupied genes. By taking advantage of a genetic ablation system in which the DNA binding domain of KDM2B can be conditionally deleted, results in this thesis reveal that the ability of KDM2B to recognize non-methylated DNA is essential for polycomb domain formation and normal embryonic development. Finally, through the use of a <em>de novo</em> targeting assay, an unexpected PRC2 recruitment pathway was discovered which is dependent on PRC1-mediated H2AK119ub1 deposition. Together this work uncovers a novel mechanism linking KDM2B-dependent recognition of non-methylated DNA with recruitment of Polycomb proteins and provides the framework on which to further investigate the contribution of CGIs to formation of polycomb domains.</p> |
| first_indexed | 2024-03-07T04:25:31Z |
| format | Thesis |
| id | oxford-uuid:cc773afe-703c-4b43-a792-7ee7ba333bcd |
| institution | University of Oxford |
| language | English |
| last_indexed | 2024-04-09T03:55:21Z |
| publishDate | 2013 |
| record_format | dspace |
| spelling | oxford-uuid:cc773afe-703c-4b43-a792-7ee7ba333bcd2024-03-13T12:34:18ZKDM2B links recognition of CpG islands to polycomb domain formation in vivoThesishttp://purl.org/coar/resource_type/c_db06uuid:cc773afe-703c-4b43-a792-7ee7ba333bcdBiology (medical sciences)BiochemistryGenetics (life sciences)Life SciencesBiologyEnglishOxford University Research Archive - Valet2013Farcas, AMKlose, RJ<p>Mammalian genomes are characterised by global and pervasive DNA methylation and this modification is generally thought to be inhibitory to transcription. An exception to this widespread DNA modification are genomic elements called CpG islands (CGI), contiguous regions of non-methylated DNA which encompass the transcription start site of two thirds of mammalian genes. Although CGIs represent the most prominent feature of mammalian promoters, the contribution of these elements to promoter function remains unclear. Work in this study shows that the histone lysine demethylase KDM2B (FBXL10/ JHDM1B) is a nuclear protein which binds specifically to non-methylated CpG dinucleotides and associates with CGI elements genome-wide through its zinc-finger CxxC (ZF-CxxC) DNA binding domain. Furthermore, in mouse embryonic stem cells, biochemical investigation revealed that KDM2B associates with Polycomb group E3 ubiquitin ligase RING1B to form a variant Polycomb repressive complex 1 (PRC1) characterized by the PCGF1 subunit.</p> <p>Considering that KDM2B has clear DNA-binding activity and that CGIs were reported to function as nucleation sites for polycomb repressive complexes, a potential role for KDM2B in mediating PRC1 recruitment to target genes was investigated. Stable depletion studies indicated that KDM2B is required for the normal targeting of RING1B to CGIs and the regulation of expression of a subset of Polycomb-occupied genes. By taking advantage of a genetic ablation system in which the DNA binding domain of KDM2B can be conditionally deleted, results in this thesis reveal that the ability of KDM2B to recognize non-methylated DNA is essential for polycomb domain formation and normal embryonic development. Finally, through the use of a <em>de novo</em> targeting assay, an unexpected PRC2 recruitment pathway was discovered which is dependent on PRC1-mediated H2AK119ub1 deposition. Together this work uncovers a novel mechanism linking KDM2B-dependent recognition of non-methylated DNA with recruitment of Polycomb proteins and provides the framework on which to further investigate the contribution of CGIs to formation of polycomb domains.</p> |
| spellingShingle | Biology (medical sciences) Biochemistry Genetics (life sciences) Life Sciences Biology Farcas, AM KDM2B links recognition of CpG islands to polycomb domain formation in vivo |
| title | KDM2B links recognition of CpG islands to polycomb domain formation in vivo |
| title_full | KDM2B links recognition of CpG islands to polycomb domain formation in vivo |
| title_fullStr | KDM2B links recognition of CpG islands to polycomb domain formation in vivo |
| title_full_unstemmed | KDM2B links recognition of CpG islands to polycomb domain formation in vivo |
| title_short | KDM2B links recognition of CpG islands to polycomb domain formation in vivo |
| title_sort | kdm2b links recognition of cpg islands to polycomb domain formation in vivo |
| topic | Biology (medical sciences) Biochemistry Genetics (life sciences) Life Sciences Biology |
| work_keys_str_mv | AT farcasam kdm2blinksrecognitionofcpgislandstopolycombdomainformationinvivo |