A Basis for Lineage-Determining Pioneer Factors Targeting Different Repressed Chromatin States in Cell Fate Transitions Andrew Katznelson

Format:

Book

Thesis/Dissertation

Author/Creator:

Katznelson, Andrew, author.

Contributor:

University of Pennsylvania. Cell and Molecular Biology., degree granting institution.

Language:

English

Subjects (All):

0306.

0369.

0379.

0487.

0758.

Local Subjects:

0306.

0369.

0379.

0487.

0758.

Physical Description:

1 electronic resource (239 pages)

Contained In:

Dissertations Abstracts International 87-07B

Place of Publication:

Ann Arbor : ProQuest Dissertations and Theses, 2025

Language Note:

English

Summary:

In this thesis, I present a comparative assessment of how 13 lineage-determining transcription factors target different forms of silent chromatin, a prerequisite initial step in changing cell fate, in a primary human fibroblast reprogramming cell model. I found that pioneer factors share the fundamental and definitional property to bind DNase-inaccessible and nucleosome-enriched targets. However, they vary in their abilities to target naïve, H3K9me3, and H3K27me3 heterochromatin, with different combinations of nucleosome turnover, high or low histone modification status influencing binding. By employing genomics and single molecule tracking of SOX2, FOXA1, and DBD-only truncations, I show that non-DBDs enhance chromatin scanning and nucleosome targeting. Collectively, these findings demonstrate that both pioneer factor DBD and non-DBD regions contribute to the control of cell fate, in which combinations of developmental factors with distinct chromatin targeting preferences target distinct genetic networks for activation. I used SOX2, a pioneer factor that poorly binds H3K9me3 heterochromatin, as a paradigm to devise ways to overcome the heterochromatin barrier. By depleting global H3K9me3 at the start of iPSC reprogramming, I found that SOX2 could bind many of its normal iPSC sites embedded in previously-marked H3K9me3 regions. I additionally fused non-DBD segments of pioneer factors I found to target heterochromatin onto SOX2 to generate a hybrid pioneer factor that retained SOX2 DNA motif specificity and gained heterochromatin binding capacity, demonstrating the modular nature of non-DBDs. Both strategies of perturbing heterochromatin as well as generating a hybrid SOX2 pioneer factor expanded chromatin targeting during iPSC reprogramming and enhanced pluripotent colony formation. In sum, this thesis finds that pioneer factors possess distinct chromatin targeting preferences which shape cell fate determination

Notes:

Advisors: Zaret, Kenneth S. Committee members: Blobel, Gerd A.; Philips-Cremins, Jennifer E.; Raj, Arjun; Lakadamyali, Melike

Source: Dissertations Abstracts International, Volume: 87-07, Section: B.

Ph.D. University of Pennsylvania 2025

Vendor supplied data

Local Notes:

School code: 0175

ISBN:

9798276001852

Access Restriction:

Restricted for use by site license