Date of Award


Document Type


Degree Name

Doctor of Philosophy (PhD)


Cellular, Molecular and Biomedical Sciences

First Advisor

Seth Frietze

Second Advisor

Eyal Amiel


IKAROS is expressed throughout the entire hematopoietic system and is required for lymphoid commitment and subsequent differentiation towards the B-lymphoid fate. If absent, progenitor and mature B-cell subsets are not expressed. IKAROS (encoded by IKZF1) is a zinc-finger transcription factor shown to regulate gene expression either directly or through the recruitment of chromatin remodeling complexes. The epigenetic gene regulatory mechanisms, including the posttranslational modification to histone proteins, as well as the expression of noncoding RNAs (ncRNAs) are important to control as perturbations in these processes contribute to the manifestation of human diseases. If left unregulated, uncontrolled growth, aberrant cell activation, and altered signaling cascades can arise. In this dissertation, I utilize functional genomic approaches to characterize the genome-wide chromatin and epigenetic patterns regulated by IKAROS in the context of two B-cell-related disorders. In the first part of this dissertation, patient-derived xenograft cell models were used to study the tumor-suppressor mechanism of IKAROS. The dominant negative-IK6 isoform is highly expressed in a B-cell lineage subtype of acute lymphoblastic leukemia (ALL) with an especially poor prognosis called precursor-B ALL (pre-B ALL). To restore wildtype IKAROS expression (IK1) in human pre-B ALL cells that expressed the IK6 isoform, we used a doxycycline inducible (DOX) expression system. We then set out to study the global transcriptional patterns of DN-IK6 pre-B ALL cells in response to IK1-induction. Overall, our results show that one potential mechanism in which IKAROS regulates growth suppression in pre-B ALL is by regulating the expression of ncRNAs.

In the second part of this dissertation, I investigate the role of Ikaros in regulating an epigenetic program required for the proper activation of naïve B-cells. Ikaros and other Ikaros family members have been linked to autoimmune diseases, but the molecular mechanisms have yet to be described. Here, I characterize the global chromatin and transcriptional landscape of B-cells isolated from mice containing a targeted deletion in the Ikzf1 zinc finger domain (Ikzf1DF4/DF4). This murine model contains mature B-cells which require only the first signal to become activated and proliferate, thus having a hyper-reactive response and break in central tolerance. Taken together, we offer two separate epigenetic mechanisms by which Ikaros regulates gene-expression programs ultimately leading to a break in B-cell tolerance. The first is through the regulation of active enhancers, and the second is through a developmental mechanism of silencing via regulation of H3K27me3 and H3K4me3 signal.

In total, this dissertation provides further insight into the epigenetic and chromatin regulation of B-cells at two separate stages of development and provides insight into the mechanisms underlying the Ikaros tumor suppressor function and its role to maintain an epigenetic landscape required for proper B-cell activation.



Number of Pages

188 p.