Student Theses and Dissertations

Linda Molla

Date of Award

2018

Document Type

Thesis

RU Laboratory

Papavasiliou Laboratory

Abstract

APOBEC2 is a member of the AID/APOBEC cytidine deaminase family of proteins. Unlike most of AID/APOBEC, however, APOBEC2’s function remains elusive. Previous research has implicated APOBEC2 in diverse organisms and cellular processes such as muscle biology (in Mus musculus), regeneration (in Danio rerio), and development (in Xenopus laevis). APOBEC2 has also been implicated in cancer. However the enzymatic activity, substrate or physiological target(s) of APOBEC2 are unknown. For this thesis, I have combined Next Generation Sequencing (NGS) techniques with state-of-the-art molecular biology to determine the physiological targets of APOBEC2. Using a cell culture muscle differentiation system, and RNA sequencing (RNA-Seq) by polyA capture, I demonstrated that unlike the AID/APOBEC family member APOBEC1, APOBEC2 is not an RNA editor. Using the same system combined with enhanced Reduced Representation Bisulfite Sequencing (eRRBS) analyses I showed that, unlike the AID/APOBEC family member AID, APOBEC2 does not act as a 5-methyl-C deaminase. Finally, using a combination of biochemical, Chromatin Immunoprecipitation Sequencing (ChiP-Seq) and polyA RNA-Seq analyses I show that APOBEC2 is a (negative) regulator of gene expression (at least in muscle cells) and binds chromatin directly to inhibit transcription of genes involved in muscle cell differentiation. While the precise mechanism behind this activity is still a matter of investigation, this role of APOBEC2 in inhibiting genes involved in cell cycle exit, might have implications for its role in in cancer.

Comments

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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