Developing chemical regulators of Yeats4 to engineer cell fate plasticity

About This Grant

Conversion of somatic cells into pluripotent stem cells using the transcription factors Oct4, Sox2, Klf4 and cMyc (OSKM) has revolutionized biology and medicine. While the OSKM approach has provided a paradigm for reprogramming, a deeper understanding of cell fate plasticity could bring efficient regeneration and rejuvenation therapies within reach. Somatic cells give rise to induced pluripotent stem cells (iPSCs) infrequently and slowly, indicating that the plasticity of somatic cells is generally limited. We found that the bioactive compound KL871 promotes a cell state of remarkable potential for reprogramming: in the presence of KL871, OSKM reprogram all myeloid progenitors into iPSCs within 3 days, a process known to be slow (>10 days) and inefficient (<0.1%). To pursue the mechanistic basis underlying KL871-instigated cell fate plasticity, we synthesized a photoaffinity derivative of KL871 and found it to be a Yeats4 binder. Yeats4 is a member of the YEATS domain-containing epigenetic reader: it binds to acetylated lysines on histones (H3K27ac and H3K14ac) to recruit chromatin remodeling complexes Tip60/p400 and SRCAP that are not only histone acetyl transferases (HAT) but also deposit H2A.Z, leading to transcriptional activation. We found that KL871 promotes Yeats4-associated chromatin activities, including rapidly increasing histone acetylation as well as chromatin-associated Yeats4 and H2A.Z. Further, knocking down Yeats4 abolished the KL871-instigated reprogramming effects. We therefore hypothesize that KL871 promotes cell fate plasticity via augmenting Yeats4 function. While wide-ranging efforts have been devoted to developing inhibitors or degraders of epigenetic factors, chemical strategies to augment the function of epigenetic regulators are rare and challenging. To date, no small molecule compound is known to increase Yeats4’s reader function. We propose to capitalize on the KL871:Yeats4 relationship to understand how it promotes Yeats4 activity and determine how KL871-bound Yeats4 regulates chromatin and cell fate plasticity. With the strengths of our cross disciplinary teams in cell fate reprogramming (Dr. Shangqin Guo) and chemical biology (Dr. Craig Crews), we are at a unique position to pursue the following aims. 1) Define how KL871 binds to Yeats4; 2) Determine the chromatin consequences following KL871:Yeats4 interaction; 3) Assess cell plasticity following KL871:Yeats4 manipulation, and 4) Perform structure-activity relationship study to develop improved Yeats4-modulatory compounds. Supported by compelling preliminary data and novel tools, we propose to learn how to engineer somatic cell fate plasticity by understanding the underlying biochemical and molecular basis.