Date of Award


Document Type

Restricted Thesis

Terms of Use

© 2020 Jack D. Rubien. All rights reserved. Access to this work is restricted to users within the Swarthmore College network and may only be used for non-commercial, educational, and research purposes. Sharing with users outside of the Swarthmore College network is expressly prohibited. For all other uses, including reproduction and distribution, please contact the copyright holder.

Degree Name

Bachelor of Arts


Biology Department

First Advisor

Dawn M. Carone


As the study of genome regulation is moving to understand the essential functions performed by long non-coding RNAs (lncRNAs), once written off as “junk”, and biophysical studies are revealing the role of phase-separated condensates in nuclear organization, Human Satellite II (HSATII) RNAs present an advantageous opportunity to synthesize these complementary approaches. HSATII DNA, found on the heterochromatic pericentromeres of many human chromosomes, is transcriptionally repressed in normal cells, but misregulation of these genomic regions in a variety of cancer cell lines allows for their aberrant transcription. These highly repetitive HSATII RNAs aggregate into large focal accumulations immediately adjacent to their sites of transcription and bind to gene expression regulatory proteins such as methyl-CpG binding protein 2, MeCP2. Here, I present evidence that HSATII RNAs possess folded secondary structures which allow them to self-assemble into spherical droplets via liquid-liquid phase separation in vitro. Further, I show how these structures can be disrupted in vivo, providing a platform for testing key hypotheses regarding HSATII RNA droplet structure and their ability to sequester nuclear proteins such as MeCP2. Future work on HSATII RNA folding and their ability to form multivalent RNA-RNA, RNA-protein interactions in vivo will build upon a growing understanding of lncRNAs’ regulatory capacity and their role as organizers of liquid-like nuclear compartments.