Understanding prion-mediated transcriptional modifications and cellular phenotypes: insights into the role of Swi1 prion and prion-like behaviors of BAF proteins

The term "prion" was originally coined to describe the agent responsible for neurodegenerative diseases associated with the prion protein, PrP. This concept has now broadened to encompass a wide range of proteins in various organisms, linked to crucial cellular functions or diseases. For example, human pathogenic proteins

like Aβ, tau, α-synuclein and p53 in cancer and neurodegeneration have been proposed to follow prion-like mechanisms. However, the precise role of prions in these proteinopathies remains unclear. Yeast is a valuable platform for prion research, with several prion proteins acting as transcription modulators. One notable example

is [SWI+], the prion form of Swi1, a component of the chromatin remodeling complex SWI/SNF. Despite clear evidence of [SWI+] significantly impacting transcription, the underlying mechanism remains elusive. Moreover, whether Swi1 orthologs or other components of the human SWI/SNF (also termed BAF) complexes can undergo

prion-like conformational changes has yet to be investigated. Understanding this is vital because SWI/SNF complexes play a crucial role in transcription regulation, and BAF mutations are implicated in over 20% of tumor cases and numerous neurological diseases. The long-term goal of our research is to uncover the link between

prions and BAF complexes and contribute to novel therapeutic strategies for related diseases. Specifically, this project aims to determine if [SWI+] exists in "variants" that produce distinct transcriptomic and phenotypic effects. Additionally, we aim to understand how [SWI+] alters the structure and activities of SWI/SNF, and induces

abnormal protein interactions and heterotypic protein aggregation, ultimately leading to transcriptomic and phenotypic changes. Furthermore, we aim to investigate whether any BAF proteins or their mutants exhibit prion- like behaviors. Our studies have far-reaching implications for other prion-based models and are highly relevant

to human health. To achieve our research goals, we will employ a range of techniques. For Aim 1, we will use classical genetic and biochemical manipulations, RNA-seq, and functional assays to characterize [SWI+] variants. For Aim 2, we will utilize immunopurification, quantitative mass spectrometry (MS), ATPase assays, ChIP-seq,

and reChIP-seq to examine the impact of [SWI+] on SWI/SNF architecture and functions. Meanwhile, we will employ differential centrifugation combined with MS to identify the [SWI+] aggregome and perform genetic and cellular assays to investigate the interaction mechanism among the aggregomic components. For Aim 3, we will

examine prion-like domains (PrLDs) of BAF proteins for fibrillization in vitro and prionogenicity in yeast. We will also develop human cell lines with EGFP-based prion reporters to screen for prions of full-length BAF proteins and their mutants and investigate whether their prion conversion can be promoted by the generated in vitro fibrils

and yeast prion lysates originating from PrLDs. In summary, the outcome of this project will not only underscore the link of the prion phenomenon with SWI/SNF (BAF) complexes but also will advance our understanding of prion-mediated cellular activities and diseases in general.