The Role of NELF in Mediating Human Gene Expression

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dc.contributor.author Daigneault, Jillian
dc.date.accessioned 2017-10-05T20:27:48Z
dc.date.available NO_RESTRICTION
dc.date.available 2017-10-05T20:27:48Z
dc.date.issued 2017
dc.date.submitted 2017
dc.identifier.uri http://hdl.handle.net/2027.42/138582
dc.description.abstract Transcription is the synthesis of RNA from a DNA template. Transcription has been shown to occur in three main steps, initiation, elongation and termination. Additional regulatory steps include a rate limiting step between initiation and elongation of RNA polymerase II (RNA Pol II) termed promoter-proximal pausing of RNA polymerase. Dysregulation at any stage of this process can lead to cancer development. There has been extensive work focusing on how drastic alterations to the transcription process contributes to cancer development; however, there has been less focus on how the fine-tuning steps of transcription regulation contribute to cancer phenotypes. Specifically, my thesis focuses on understanding the contributions of NELF-mediated pausing to cancer development. To begin, I focused on primary cells in order to better understand the function of NELF-mediated pausing in a normal context. My work has identified a global profile of paused genes in human cells. Following the completion of this profile, I wanted to identify pathways that were enriched for paused genes. I found that paused genes are involved in cancer associated pathways such as EGFR and TGFb signaling as well as general transcription and gene expression. After identifying human genes with paused RNA polymerases, I focused on studying NELF. I found that almost all genes with NELF enrichment are paused. A majority of these genes also require NELF to maintain the pause. I then wanted to investigate the biological consequences of NELF-mediated pausing. I found that the expression of more than half of NELF-mediated paused genes are regulated by NELF. These genes include those involved in the cancer-associated pathways EGFR, TGFb and VEGF signaling. I showed that besides localizing to gene promoters, NELF also targets other genomic regions. I found that approximately half of these sites are in enhancers, specifically those enhancers that are actively transcribed. We showed that the abundance of these eRNAs is dependent on NELF. Finally, we found that loss of transcription of these eRNA result in changes in expression of nearby genes. Upon identifying NELF as a key regulator of gene expression in normal cells, I investigated how this process contributed to the gene expression changes found in cancer. To begin, I identified paused genes in HT29 colorectal cancer cells. I found that many of the same pathways show pausing in both normal cells and cancer cells. I also found that most genes utilize pausing to reduce their expression in cancer cells. These genes were enriched for cellular senescence, cellular stress response and WNT signaling. My work provides insight into the role of RNA Pol II pausing in cancer development. I have shown that cancer-associated pathways, such as EGFR, are regulated by RNA Pol II pausing. I have also generated global profiles of pausing in both normal and cancer cells. In comparing these two profiles, I have identified differences in the function of pausing between normal and cancer cells. One of the key differences I identified is the mechanism by which pausing regulates gene expression in normal and cancer cells. Collectively, my work shows that NELF and NELF-mediated pausing are key regulators of gene expression that may be harnessed by cancer cells to promote tumorigenesis.
dc.language.iso en_US
dc.subject RNA Pol II Pausing
dc.subject NELF
dc.title The Role of NELF in Mediating Human Gene Expression
dc.type Thesis en_US
dc.description.thesisdegreename PHD
dc.description.thesisdegreediscipline Cancer Biology
dc.description.thesisdegreegrantor University of Michigan, Horace H. Rackham School of Graduate Studies
dc.contributor.committeemember Cheung, Vivian
dc.contributor.committeemember Sekiguchi, JoAnn M
dc.contributor.committeemember Lawrence, Theodore S
dc.contributor.committeemember Day, Mark L
dc.contributor.committeemember Fearon, Eric R
dc.contributor.committeemember Ferguson, David O
dc.subject.hlbsecondlevel Genetics
dc.subject.hlbtoplevel Health Sciences
dc.description.bitstreamurl https://deepblue.lib.umich.edu/bitstream/2027.42/138582/1/jmboden_1.pdf
dc.owningcollname Dissertations and Theses (Ph.D. and Master's)
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