Student Theses and Dissertations

Date of Award


Document Type


RU Laboratory

Allis Laboratory


chromatin, histone H3, mouse embryonic stem cells, methyl-histone binding proteins


The association of genomic DNA with histone proteins in the three-dimensional structure known as chromatin is the central framework for “epigenetics,” which is defined as inherited phenotypes governed by differences that cannot be explained by changes in DNA sequence. In recent years, studies have shown that regulated changes in the chemical and physical properties of chromatin often lead to dynamic changes in many cellular processes, including development and differentiation, by affecting the accessibility of the genomic information stored in the DNA. The cell uses many different mechanisms to regulate chromatin in order to establish, maintain, and propagate patterns of gene expression that are necessary for proper development and differentiation. Many of these mechanisms involve the histone component of chromatin, both through chemical and structural changes of the histone proteins themselves and via complex interactions with other non-histone chromatin proteins. Here, in my thesis work, I describe how a few of these chromatin regulatory mechanisms are used during mammalian differentiation, specifically focusing on those involving histone H3. First, in Chapter 2, I describe how certain non-histone chromatin proteins that are key to development specifically interact with modified histones using biochemical, biophysical and structural approaches. Next, in Chapter 3, I describe how chromatin undergoes specific, dramatic changes as cells lose their capacity for self-renewal and proceed toward a specific lineage using a mouse embryonic stem cell model of differentiation and early embryonic development. These changes involve both the post-translational modification of histone H3 and the incorporation of different H3 variant proteins into the chromatin fiber. Finally, I describe the observation that differentiating mouse embryonic stem cells proteolytically cleave histone H3 and identify a protease that accomplishes this cleavage.


A thesis presented to the faculty of The Rockefeller University in partial fulfillment of the requirements for the degree of Doctor of Philosophy.

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