Mechanism of nucleosome targeting by pioneer transcription factors / Meilin M. Fernandez Garcia.

Format:

Book

Thesis/Dissertation

Author/Creator:

Fernandez Garcia, Meilin M., author.

Contributor:

University of Pennsylvania. Department of Biochemistry and Molecular Biophysics, degree granting institution.

Zaret, Kenneth S., degree supervisor.

Language:

English

Subjects (All):

Biochemistry.

Biophysics.

Biochemistry and Molecular Biophysics--Penn dissertations.

Penn dissertations--Biochemistry and Molecular Biophysics.

Local Subjects:

Biochemistry.

Biophysics.

Biochemistry and Molecular Biophysics--Penn dissertations.

Penn dissertations--Biochemistry and Molecular Biophysics.

Genre:

Academic theses.

Physical Description:

1 online resource (226 pages)

Contained In:

Dissertations Abstracts International 81-07B.

Place of Publication:

[Philadelphia, Pennsylvania] : University of Pennsylvania ; Ann Arbor : ProQuest Dissertations & Theses, 2019.

Language Note:

English

System Details:

Mode of access: World Wide Web.

text file

Summary:

Transcription factors (TFs) forage the genome to instruct cell plasticity, identity, and differentiation. These developmental processes are elicited through TF engagement with chromatin. Yet, how and which TFs can engage with chromatin and thus, nucleosomes, remains largely unexplored. Pioneer TFs are TF that display a high affinity for nucleosomes. Extensive genetic and biochemical studies on the pioneer TF FOXA, a driver of fibroblast to hepatocyte reprogramming, revealed its nucleosome binding ability and chromatin targeting lead to chromatin accessibility and subsequent cooperative binding of TFs. Similarly, a number of reprogramming TFs have been suggested to have pioneering activity due to their ability to target compact chromatin and increase accessibility and enhancer formation in vivo. But whether these factors directly interact with nucleosomes remains to be assessed. Here we test the nucleosome binding ability of the cell reprogramming TFs, Oct4, Sox2, Klf4 and cMyc, that are required for the generation of induced pluripotent stem cells. In addition, we also test neuronal and macrophage reprogramming TFs. Our study shows that reprogramming TFs bind nucleosomes with a range of nucleosome binding affinities, indicating that although specific cocktails of TFs are required for reprogramming, mechanistically these TFs show differential nucleosome interacting behaviors. These results allowed us to assess differential features between TFs nucleosome binding ability and to correlate their binding with reprogramming potential. To determine how general is nucleosome binding we extended our analysis to screen 593 of the 2,000 predicted human TFs in the genome for potential nucleosome binding and validated their binding in solution. Based on 3D structural analysis, we proposed that strong nucleosome binders anchor DNA through short -helixes and have a flexible and adaptable DNA binding domain while weak nucleosome binders use -sheets or unstructured regions and have a higher rigidity within their DNA binding domain. Through the experiments presented in this dissertation we present the first study revealing the shared structural features contributing to nucleosome binding potential of pioneer TFs and thus allow for predication of novel pioneer TFs with cell reprogramming potential.

Notes:

Source: Dissertations Abstracts International, Volume: 81-07, Section: B.

Includes supplementary digital materials.

Advisors: Zaret, Kenneth S.; Committee members: Ronen Marmorstein; Ben Black; Doris Wagner; Marisa Bartolomei.

Department: Biochemistry and Molecular Biophysics.

Ph.D. University of Pennsylvania 2019.

Local Notes:

School code: 0175

ISBN:

9781392891988

Access Restriction:

Restricted for use by site license.

This item is not available from ProQuest Dissertations & Theses.

This item must not be sold to any third party vendors.