The study of DNA methylation anomalies in chronic lymphocytic leukaemia
Many haematological malignancies are associated with widespread alterations of the transcriptional and epigenetic programmes. Changes in DNA methylation provide the clearest example of epigenetic changes, but the mechanism(s) underlying such changes is unknown. To investigate this I studied DNA me...
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| Format: | Thesis |
| Language: | English |
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2011
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| _version_ | 1797088863252905984 |
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| author | Roy, NBA |
| author2 | Higgs, D |
| author_facet | Higgs, D Roy, NBA |
| author_sort | Roy, NBA |
| collection | OXFORD |
| description | Many haematological malignancies are associated with widespread alterations of the transcriptional and epigenetic programmes. Changes in DNA methylation provide the clearest example of epigenetic changes, but the mechanism(s) underlying such changes is unknown. To investigate this I studied DNA methylation across an ~80kb segment of the genome which is not known to be mutated in haematological malignancies. Methylation was perturbed in 35-100% of samples of DNA from individuals with a wide range of haematological malignancies but not in non-malignant haematological disorders. DNA methylation was comprehensively assessed by Southern blot analysis, classical bisulphite sequencing and using a newly developed capture bisulphite sequencing protocol. The results were also compared with analysis by MeDIP, an immunoprecipitation-based technique. These analyses provide methylation status at various levels including individual CpG resolution. This showed both gain and loss of methylation at CpG dinucleotides. Of interest, hypomethylation was most frequently seen in intergenic regions corresponding to transcription factor binding sites and areas of increased chromosome accessibility. These observations suggested that hypomethylation of the genome in haematological malignancies could arise from aberrantly expressed DNA binding proteins which, recruited to sequences in regions of open chromatin, would protect the underlying CpG dinucleotides from the methylation machinery. This, in turn, could lead to passive demethylation accumulating with increasing cell divisions. This hypothesis was tested with electrophoretic mobility shift assays using oligonucleotides representing the DNA underlying one such region. This showed that, compared to nuclear extracts from the lymphocytes of normal individuals, those from patients with CLL were enriched for a protein which binds to oligonucleotides containing the underlying sequence. Using a mass spectrometry approach, I identified a variety of proteins that may bind such regions and account for their passive demethylation in haematological malignancies. |
| first_indexed | 2024-03-07T02:56:12Z |
| format | Thesis |
| id | oxford-uuid:af6091aa-3d00-4436-b2b7-5dfe439b5c05 |
| institution | University of Oxford |
| language | English |
| last_indexed | 2024-03-07T02:56:12Z |
| publishDate | 2011 |
| record_format | dspace |
| spelling | oxford-uuid:af6091aa-3d00-4436-b2b7-5dfe439b5c052022-03-27T03:49:08ZThe study of DNA methylation anomalies in chronic lymphocytic leukaemiaThesishttp://purl.org/coar/resource_type/c_db06uuid:af6091aa-3d00-4436-b2b7-5dfe439b5c05Molecular haematologyEnglishOxford University Research Archive - Valet2011Roy, NBAHiggs, DGibbons, RMany haematological malignancies are associated with widespread alterations of the transcriptional and epigenetic programmes. Changes in DNA methylation provide the clearest example of epigenetic changes, but the mechanism(s) underlying such changes is unknown. To investigate this I studied DNA methylation across an ~80kb segment of the genome which is not known to be mutated in haematological malignancies. Methylation was perturbed in 35-100% of samples of DNA from individuals with a wide range of haematological malignancies but not in non-malignant haematological disorders. DNA methylation was comprehensively assessed by Southern blot analysis, classical bisulphite sequencing and using a newly developed capture bisulphite sequencing protocol. The results were also compared with analysis by MeDIP, an immunoprecipitation-based technique. These analyses provide methylation status at various levels including individual CpG resolution. This showed both gain and loss of methylation at CpG dinucleotides. Of interest, hypomethylation was most frequently seen in intergenic regions corresponding to transcription factor binding sites and areas of increased chromosome accessibility. These observations suggested that hypomethylation of the genome in haematological malignancies could arise from aberrantly expressed DNA binding proteins which, recruited to sequences in regions of open chromatin, would protect the underlying CpG dinucleotides from the methylation machinery. This, in turn, could lead to passive demethylation accumulating with increasing cell divisions. This hypothesis was tested with electrophoretic mobility shift assays using oligonucleotides representing the DNA underlying one such region. This showed that, compared to nuclear extracts from the lymphocytes of normal individuals, those from patients with CLL were enriched for a protein which binds to oligonucleotides containing the underlying sequence. Using a mass spectrometry approach, I identified a variety of proteins that may bind such regions and account for their passive demethylation in haematological malignancies. |
| spellingShingle | Molecular haematology Roy, NBA The study of DNA methylation anomalies in chronic lymphocytic leukaemia |
| title | The study of DNA methylation anomalies in chronic lymphocytic leukaemia |
| title_full | The study of DNA methylation anomalies in chronic lymphocytic leukaemia |
| title_fullStr | The study of DNA methylation anomalies in chronic lymphocytic leukaemia |
| title_full_unstemmed | The study of DNA methylation anomalies in chronic lymphocytic leukaemia |
| title_short | The study of DNA methylation anomalies in chronic lymphocytic leukaemia |
| title_sort | study of dna methylation anomalies in chronic lymphocytic leukaemia |
| topic | Molecular haematology |
| work_keys_str_mv | AT roynba thestudyofdnamethylationanomaliesinchroniclymphocyticleukaemia AT roynba studyofdnamethylationanomaliesinchroniclymphocyticleukaemia |