Abstract
Abstract The immune suppressive function of regulatory T (Treg) cells is governed by the Foxp3-depenent transcriptional programs that remain unclear, which constraints effective manipulation of Treg behaviors for the treatment of many autoimmune diseases and cancer. To overcome the technical barriers for addressing this issue, we developed a new method to reveal the protein components of the cis-regulatory elements (cis-proteome) in Treg cells defined by Foxp3 binding, because the interaction among these DNA elements and their associated proteins ultimately determine Treg development and function. Specifically, we projected the spatial information (PSI) of Foxp3 onto its adjacent chromatins and nuclear factors with a proximity ligation reaction and identified the labeled DNA-protein complexes with chromatin immunoprecipitation (ChIP) and quantitative mass spectrometry-based proteomics. Our Foxp3 PSI reproducibly captured majority of the open chromatins and active enhancers and promoters, representing the Treg cis-regulatory hubs, and identified 1500 proteins including many known Foxp3 interactors, crucial regulators of Treg function, and numerous novel nuclear proteins that encompass all the key steps of gene regulation. Among them 124 are highly variable in their expression levels in a cell type- or activity-dependent manner. Using a CRISPR/Cas9 approach we identified more than 50 novel nuclear factors specifically required for the induction or maintenance of Foxp3 expression. Our study thereby offers a broadly applicable strategy to investigate the proteins involved in Treg differentiation and function and will produce many mechanistic insights into the transcriptional basis of Treg-mediated immune tolerance.
Published Version
Talk to us
Join us for a 30 min session where you can share your feedback and ask us any queries you have
Schedule a call