SINGLE-CELL CHEMICAL TRANSCRIPTOMIC DISSECTION OF AN ESSENTIAL TRANSCRIPTION FACTOR NETWORK PROJECT SUMMARY / ABSTRACT Basic helix-loop-helix leucine zipper transcription factors (TFs) in the extended MYC network play essential roles regulating cellular growth, differentiation, and homeostasis. Seminal studies have implicated MYC and its interacting network of TFs as drivers of proliferation and metabolism in development and cancer, but how dosage of these factors encodes transcriptional state remains contentious. Here, I propose a novel chemical genomic framework to systematically determine how TF dosage, transcriptional output, and cellular state are linked. I will combine our recently published massively multiplex single-cell RNA-seq screening method (sci-Plex) with chemical genetic degradation of protein targets to examine how embryonic stem cells are transcriptionally reprogrammed following dosed degradation of TFs. I will then employ state-of-the-art computational tools to quantify the cellular state trajectories encoded by specific dosages. Finally, I will leverage this single-cell ‘perturbation atlas’ to support genomic mapping experiments to understand how reduced dosage of these factors in vivo leads to physical redistribution across the genome. These studies will i.) illuminate mechanisms by which TF dosages encode transcriptional output, ii.) elucidate how intracellular concentrations of interacting TFs maintain chromatin, transcriptional, and cellular states, and iii.) provide mechanistic insight into how a transcription factor network interacts with the epigenome to regulate mammalian pluripotency. More generally, these approaches have the potential to address long-standing gene regulatory questions of how protein dosage controls cellular state in both health and in cancer.

PROJECT NARRATIVE All cells must regulate genes in order to divide, differentiate and die. This proposal employs cutting-edge genomic techniques to better understand how single cells use MYC-network transcription factors to make these decisions in stem cell pluripotency. The results will inform our basic understanding of how cells divide and differentiate in mammalian development and ultimately help understand how these proteins can deregulate cellular growth during cancer.