A transcription factor atlas of directed differentiation

• Published in: Cell 2023-01, Vol.186 (1), p.209-229.e26
• Main Authors: Joung, Julia, Ma, Sai, Tay, Tristan, Geiger-Schuller, Kathryn R., Kirchgatterer, Paul C., Verdine, Vanessa K., Guo, Baolin, Arias-Garcia, Mario A., Allen, William E., Singh, Ankita, Kuksenko, Olena, Abudayyeh, Omar O., Gootenberg, Jonathan S., Fu, Zhanyan, Macrae, Rhiannon K., Buenrostro, Jason D., Regev, Aviv, Zhang, Feng
• Format: Article
• Language: English
• Subjects: Atlases as Topic; Cell Differentiation; cell engineering; cellular disease modeling; Chromatin; combinatorial perturbation; Gene Expression Regulation; gene regulation; genetic screening; Human Embryonic Stem Cells - metabolism; Humans; neural progenitor; ORF overexpression; pluripotent stem cell; single cell profiling; transcription factor; Transcription Factors - metabolism
• ISSN: 0092-8674; 1097-4172
• DOI: 10.1016/j.cell.2022.11.026

Transcription factors (TFs) regulate gene programs, thereby controlling diverse cellular processes and cell states. To comprehensively understand TFs and the programs they control, we created a barcoded library of all annotated human TF splice isoforms (>3,500) and applied it to build a TF Atlas charting expression profiles of human embryonic stem cells (hESCs) overexpressing each TF at single-cell resolution. We mapped TF-induced expression profiles to reference cell types and validated candidate TFs for generation of diverse cell types, spanning all three germ layers and trophoblasts. Targeted screens with subsets of the library allowed us to create a tailored cellular disease model and integrate mRNA expression and chromatin accessibility data to identify downstream regulators. Finally, we characterized the effects of combinatorial TF overexpression by developing and validating a strategy for predicting combinations of TFs that produce target expression profiles matching reference cell types to accelerate cellular engineering efforts. [Display omitted] •Barcoded ORF library of all 3,548 human TF splice isoforms•Applied to human stem cells to build a TF Atlas of resulting expression profiles•Mapping of TFs that produce cell types from all three germ layers and trophoblasts•Prediction of TF combinations to produce target cell types Generation of a comprehensive human transcription factor (TF) barcoded ORF library and further application to embryonic stem cells to build a TF Atlas of resulting expression profiles, which enabled identification of individual and combinations of TFs that produce target cell types and, thus, accelerate cellular engineering efforts.