Connections between RNA Polymerase II transcriptional regulation, nucleosome arrangement and DNA damage
<p>Transcription by RNA polymerase II (RNAPII) is a central process in gene expression and so subject to many layers of regulation: post-translational modifications of the RNAPII C-terminal domain (CTD), transcription factor association, chromatin compaction and the control of polymerase acces...
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| Materyal Türü: | Tez |
| Dil: | English |
| Baskı/Yayın Bilgisi: |
2017
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| _version_ | 1826314003851247616 |
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| author | Foxwell, J |
| author_facet | Foxwell, J |
| author_sort | Foxwell, J |
| collection | OXFORD |
| description | <p>Transcription by RNA polymerase II (RNAPII) is a central process in gene expression and so subject to many layers of regulation: post-translational modifications of the RNAPII C-terminal domain (CTD), transcription factor association, chromatin compaction and the control of polymerase access to DNA. Transcription can also be altered when DNA damage is encountered.</p>
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<p>My thesis addressed different aspects of these regulatory mechanisms. Firstly I studied the role of RNA:DNA hybrids (R-loops) in pause-type termination, and assessed whether data based on the <em>β-actin</em> gene could be extended to further genes. I also investigated whether DNA damage repair (DDR) factor Rad51 is present over R-loop associated pause regions. Secondly I studied the roles of tyrosine and threonine phosphorylation (Y1P and T4P) of the RNAPII CTD, by testing their association with DDR and transcription termination respectively. I also developed a modified MNase-seq protocol using mNET-seq isolation conditions to allow close comparison between chromatin configuration and the nascent RNA signal.</p>
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<p>The outcome of my research was that I found the <em>PKM</em> gene exhibits the same basic characteristics of pause-type termination, including R-loop formation. However, little evidence for heterochromatin formation as observed for <em>β-actin</em> termination was identified. I also showed that Rad51 accumulates at R-loop regions in pause-type termination, but does not appear to induce R-loops. More likely Rad51 is recruited by downstream DDR factors. Y1P is associated with factors involved in UV DDR. My studies showed that UV damage causes a global RNAPII elongation defect with altered chromatin associated histone marks and defective recruitment of elongation factors including the PAF1 complex and SPT6 to the polymerase. Finally my studies on T4P-associated termination cis-elements indicated that positions of cleavage-independent termination are formed relative to mRNA 3’ ends but not based on specific DNA sequence. Also cleavage factor depletion increased mononucleosome signals in these termination regions.</p> |
| first_indexed | 2024-09-25T04:24:27Z |
| format | Thesis |
| id | oxford-uuid:20b27dec-2f01-41e5-b22e-dc7a8d281dce |
| institution | University of Oxford |
| language | English |
| last_indexed | 2024-09-25T04:24:27Z |
| publishDate | 2017 |
| record_format | dspace |
| spelling | oxford-uuid:20b27dec-2f01-41e5-b22e-dc7a8d281dce2024-08-22T16:45:17ZConnections between RNA Polymerase II transcriptional regulation, nucleosome arrangement and DNA damageThesishttp://purl.org/coar/resource_type/c_db06uuid:20b27dec-2f01-41e5-b22e-dc7a8d281dceDNA damageChromatinRNA polymerasesEnglishHyrax Deposit2017Foxwell, J<p>Transcription by RNA polymerase II (RNAPII) is a central process in gene expression and so subject to many layers of regulation: post-translational modifications of the RNAPII C-terminal domain (CTD), transcription factor association, chromatin compaction and the control of polymerase access to DNA. Transcription can also be altered when DNA damage is encountered.</p> <br> <p>My thesis addressed different aspects of these regulatory mechanisms. Firstly I studied the role of RNA:DNA hybrids (R-loops) in pause-type termination, and assessed whether data based on the <em>β-actin</em> gene could be extended to further genes. I also investigated whether DNA damage repair (DDR) factor Rad51 is present over R-loop associated pause regions. Secondly I studied the roles of tyrosine and threonine phosphorylation (Y1P and T4P) of the RNAPII CTD, by testing their association with DDR and transcription termination respectively. I also developed a modified MNase-seq protocol using mNET-seq isolation conditions to allow close comparison between chromatin configuration and the nascent RNA signal.</p> <br> <p>The outcome of my research was that I found the <em>PKM</em> gene exhibits the same basic characteristics of pause-type termination, including R-loop formation. However, little evidence for heterochromatin formation as observed for <em>β-actin</em> termination was identified. I also showed that Rad51 accumulates at R-loop regions in pause-type termination, but does not appear to induce R-loops. More likely Rad51 is recruited by downstream DDR factors. Y1P is associated with factors involved in UV DDR. My studies showed that UV damage causes a global RNAPII elongation defect with altered chromatin associated histone marks and defective recruitment of elongation factors including the PAF1 complex and SPT6 to the polymerase. Finally my studies on T4P-associated termination cis-elements indicated that positions of cleavage-independent termination are formed relative to mRNA 3’ ends but not based on specific DNA sequence. Also cleavage factor depletion increased mononucleosome signals in these termination regions.</p> |
| spellingShingle | DNA damage Chromatin RNA polymerases Foxwell, J Connections between RNA Polymerase II transcriptional regulation, nucleosome arrangement and DNA damage |
| title | Connections between RNA Polymerase II transcriptional regulation, nucleosome arrangement and DNA damage |
| title_full | Connections between RNA Polymerase II transcriptional regulation, nucleosome arrangement and DNA damage |
| title_fullStr | Connections between RNA Polymerase II transcriptional regulation, nucleosome arrangement and DNA damage |
| title_full_unstemmed | Connections between RNA Polymerase II transcriptional regulation, nucleosome arrangement and DNA damage |
| title_short | Connections between RNA Polymerase II transcriptional regulation, nucleosome arrangement and DNA damage |
| title_sort | connections between rna polymerase ii transcriptional regulation nucleosome arrangement and dna damage |
| topic | DNA damage Chromatin RNA polymerases |
| work_keys_str_mv | AT foxwellj connectionsbetweenrnapolymeraseiitranscriptionalregulationnucleosomearrangementanddnadamage |