REGISTER HERE

Direct lineage reprogramming involves the remarkable conversion of cellular identity. Single-cell technologies aid in deconstructing the considerable heterogeneity in transcriptional states that typically arise during lineage conversion. However, lineage relationships are lost during cell processing, limiting accurate trajectory reconstruction. We previously developed ‘CellTagging’, a combinatorial cell indexing methodology, permitting the parallel capture of clonal history and cell identity, where sequential rounds of cell labeling enable the construction of multi-level lineage trees. CellTagging and longitudinal tracking of fibroblast to induced endoderm progenitor (iEP) reprogramming reveals two distinct trajectories: one leading to successfully reprogrammed cells, and one leading to a dead-end state. Here, I present two new methods to enable the molecular mechanisms underlying reprogramming outcome to be dissected. The first is an experimental method, 'Calling Cards', enabling transcription factor binding to be recorded, in individual cells, in the earliest stages of reprogramming. The second method is a new computational platform, called 'CellOracle', that uses single-cell transcriptome and chromatin accessibly data to reconstruct changes in GRN configurations across the reprogramming process. Together, these tools provide new mechanistic insights into how transcription factors can drive changes in cell identity, and help reveal new factors to enhance the efficiency and fidelity of reprogramming.