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Engineering lysine demethylases to orthogonally probe cellular functions

Breski, Megan (2018) Engineering lysine demethylases to orthogonally probe cellular functions. Doctoral Dissertation, University of Pittsburgh. (Unpublished)

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Post-translational modifications (PTMs) are an essential mechanism that increases the complexity of cellular processes. Protein methylation is a common PTM that can result in structural variation altering protein-protein/protein-DNA interactions. Several enzymes have been identified that have the ability to remove methyl groups from proteins. Many of these enzymes are histone demethylases, which are vital epigenetic modifiers. Lysine demethylases (KDMs) remove methyl groups from proteins, such as histones, resulting in a transition of chromatin accessibility for transcription factors. Jumonji C (JmjC) domain containing KDMs are a family of approximately 30 2-ketoglutarate (2-KG/2-OG) dependent enzymes known to demethylate histones within the chromatin nucleosomal core structure for the regulation of gene expression. Histone demethylases have tissue specific expression patterns and are active towards particular lysine residues, which suggest they are involved in specific cellular pathways. Irregular expression of KDM4s is associated with several types of cancer, but the roles of each KDM4 member in oncogenesis or cancer progression is convoluted. It is a difficult task to study an individual epigenetic enzyme and elucidate non-histone substrates due to the redundant cofactor utilization and their functional rapidity. To orthogonally study KDM4s, a bump-and-hole activation and inhibition system was developed. To elucidate non-histone catalytic substrates of KDM4s, a photo-crosslinkable unnatural amino acid (UAA) was incorporated in the catalytic domain to induce covalent binding to substrates for subsequent identification. Elucidating the roles of individual epigenetic modifiers will greatly impact public health because it will allow for improved therapeutic interventions and diagnostic biomarkers.


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Item Type: University of Pittsburgh ETD
Status: Unpublished
CreatorsEmailPitt UsernameORCID
Breski, Meganmmb123@pitt.edummb123
ETD Committee:
TitleMemberEmail AddressPitt UsernameORCID
Committee ChairUrban, Zsolturbanz@pitt.eduurbanz
Committee MemberKammerer, Candacecmk3@pitt.educmk3
Committee MemberRoman, Bethromanb@pitt.eduromanb
Committee MemberMartinson, Jeremyjmartins@pitt.edujmartins
Date: 30 January 2018
Date Type: Publication
Defense Date: 17 November 2017
Approval Date: 30 January 2018
Submission Date: 13 December 2017
Access Restriction: 5 year -- Restrict access to University of Pittsburgh for a period of 5 years.
Number of Pages: 127
Institution: University of Pittsburgh
Schools and Programs: School of Public Health > Human Genetics
Degree: PhD - Doctor of Philosophy
Thesis Type: Doctoral Dissertation
Refereed: Yes
Uncontrolled Keywords: Genetics, Epigenetics, Histones, demethylases, 2-ketoglutarate, gene regulation, lysine demethylases, chemical biology, biochemistry, methylation, unnatural amino acid, cross linking
Date Deposited: 30 Jan 2018 22:40
Last Modified: 01 Jan 2023 06:15


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