Date of Graduation


Document Type

Dissertation (PhD)

Program Affiliation

Genes and Development

Degree Name

Doctor of Philosophy (PhD)

Advisor/Committee Chair

Dr. Michelle Craig Barton

Committee Member

Dr. Sharon R.Y. Dent

Committee Member

Dr. Wei Li

Committee Member

Dr. Pierre D. McCrea

Committee Member

Dr. Nicholas Navin



Zeynep Hande Coban Akdemir, B.S.,M.A.

Advisory Professor: Michelle Craig Barton, Ph.D.

p53 is a tumor suppressor that has been well studied in tumor-derived, cultured cells. However, its functions in normal proliferating cells and tissues are generally overlooked. We propose that p53 functions during the G1-S transition can be studied in normal, differentiated cells during surgery-induced liver regeneration. Two-thirds partial hepatectomy (PH) of mouse liver offers a unique model to compare p53 functions in regenerating versus sham (control) cells. My hypothesis is that intersection of global expression analyses (microarray and RNA sequencing) and profiling of p53 interactions with chromatin (ChIP sequencing) at the G1-S transition of normal cell cycle, corresponding to 24h post-PH in mice liver regeneration, will reveal p53 functions during cell cycle regulation in normal cells and during tissue regeneration.

Combining chromatin immunoprecipitation with next generation sequencing technology (ChIP-Seq) allowed detection of genome-wide binding of p53 to target genes in liver. We found 5074 de novo p53 target genes, 92% of which participate in non-canonical p53 functions, mainly developmental processes. Integration of ChIP-Seq findings with global expression profiling (RNA-Seq) of both normal and p53-null liver allowed us to identify functional p53 target genes. Intriguingly, our data analysis revealed that a specific subset of p53-activated target genes is involved in liver-enriched functions such as lipid biosynthetic process, steroid metabolic process, circadian rhythm, and drug detoxification. These findings suggested that the loss of p53-chromatin interactions in regenerating liver may result in a decreased activity of differentiation-specific cellular processes and in attenuation of hepatic cell identity. Remarkably, p53 cooperates with the master regulator of hepatocyte differentiation, HNF4α, to induce 78% of these genes, including a number of liver-enriched transcription factors such as CCAAT/enhancer binding protein beta (CEBPβ), hepatocyte nuclear factor 6 alpha (HNF6α), hepatocyte nuclear factor 6 beta (HNF6β). Thus, p53 acts in concert with HNF4α to promote the maintenance of liver functions during the G1àS transition of the cell cycle of normal proliferating livers cells.


p53, liver regeneration, hepatic identity, chromatin interactions, gene expression, genome-wide profiling, HNF4α



To view the content in your browser, please download Adobe Reader or, alternately,
you may Download the file to your hard drive.

NOTE: The latest versions of Adobe Reader do not support viewing PDF files within Firefox on Mac OS and if you are using a modern (Intel) Mac, there is no official plugin for viewing PDF files within the browser window.