Document Type


Date of Degree

Spring 2016

Degree Name

PhD (Doctor of Philosophy)

Degree In

Molecular and Cell Biology

First Advisor

Price, David H

First Committee Member

Musselman, Catherine A

Second Committee Member

Okeoma, Chioma M

Third Committee Member

Pufall, Miles A

Fourth Committee Member

Weeks, Daniel L


In humans, RNA polymerase II is the sole source of messenger RNAs that are ultimately translated into proteins and its transcriptional activity is highly regulated.

Mechanisms have evolved to control which, when, and to what degree genes are transcribed. Because most cells have the same genome, control of transcription is essential in maintaining cellular identity. Misregulation of Pol II transcription is a hallmark of both cancer and retroviral infection. This research investigates the regulation of Pol II transcription and related co-transcriptional mRNA capping.

Chromatin immunoprecipitation experiments were used to characterize the composition of nucleosomes and Pol II, DSIF and NELF occupancies at bidirectional promoters and enhancers. In collaboration with Alberto Bosque and Vicente Planelles, sequencing experiments were performed in a primary T cell model of HIV latency and a role for sequence-specific recruitment of STAT5 was established in HIV reactivation. In contrast, analysis of Myc binding in vitro and in cells demonstrated that transcription machinery played a major role in recruiting Myc to genomic sites. A precise method was also developed to detect polymerase-associated nascent transcripts in nuclei.

The roles of Cdk7, a subunit of TFIIH that phosphorylates Pol II during initiation, were characterized by treatment of nuclear extracts and cells with THZ1, a recently developed covalent inhibitor with anti-cancer properties. Inhibition of Cdk7 was demonstrated to cause defects in Pol II phosphorylation, co-transcriptional capping, promoter proximal pausing, and productive elongation. Capping of nascent RNAs was found to be spatially and temporally regulated in part by a previously undescribed THZ1-sensitive factor present in nuclear extract. THZ1 impacted pausing through a capping-independent block of DSIF and NELF loading. The P-TEFb-dependent transition into productive elongation was also inhibited by THZ1, likely due to misloading of DSIF.

In vitro and sequencing methods were used to describe an extremely rapid and global transcriptional response to hydrogen peroxide. During periods of oxidative stress, termination was likely inhibited and Pol II accumulated at promoters and enhancers after as few as two minutes, and clearance of these polymerases required P-TEFb. In the presence of flavopiridol, a potent P-TEFb inhibitor, non-productive elongation was observed and a potential role for P-TEFb in termination was proposed.

Public Abstract

Humans are composed of millions of cells and most of these have the same DNA, or blueprint. Different cells transcribe different RNAs, or messages, to create different proteins, which perform the work of the cell. Control of this transcription is what makes these different cells within different tissues and organs function, and breakdown of this control leads to developmental defects and cancer. HIV also hijacks this control and this makes AIDS difficult to cure. During my graduate career, I developed methods to study this control genome-wide and characterized how a potentially new HIV drug works. By using small-picture biochemistry assays to study THZ1, a new cancer drug, I also identified new ways in which transcription of these messages are controlled. Finally, I discovered rapid transcriptional response to hydrogen peroxide. Overall, this research demonstrates the importance of controlling transcription both generally and in response to cellular stress.


ChIP-Seq, mRNA Capping, Pol II, P-TEFb, THZ1


xi, 160 pages


Includes bibliographical references (pages 135-160).


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Copyright © 2016 Kyle Andrew Nilson

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