Journal: bioRxiv
Article Title: DNA-guided transcription factor cooperativity shapes face and limb mesenchyme
doi: 10.1101/2023.05.29.541540
Figure Lengend Snippet: A . Schematic of endogenous tagging TFs with the FKBP12 F36V degron and V5 epitope tag in human embryonic stem cells (hESC) followed by differentiation into cranial neural crest cells (hCNCC) and treatment with or without dTAG V -1. The ALX4 gene was instead knocked out by a frameshift mutation. B . Confirmation of TF tagging and depletion upon dTAG V -1 addition by Western blot for V5 epitope, with CTCF as a loading control. IB, immunoblot. C . Confirmation of ALX4 knockout in three independent clones by Western blot, with HSP90 as a loading control. D . Homeodomain TFs bind DNA at TWIST1-bound sites at variable occupancies. Heatmap shows promoter-distal binding sites for TWIST1 and/or AP2a. Assay indicates whether data shown is from ChIP, CUT&RUN (C&R), or ATAC, and whether an endogenous or V5 antibody was used. Rows are ranked by the sum of the homeodomain signals from undepleted cells. In the scale bar, units are reads per genome coverage, except for ATAC data, which is in signal per million reads. E . Homeodomain TFs bind the Coordinator motif. The top enriched motif (by AME) is shown for each TF, with p-values in parentheses.
Article Snippet: Antibodies used include TWIST1 (Abcam, ab50887), V5 (Abcam, ab15828), H3K27ac (Active Motif, 39133), Flag (Sigma-Aldrich, F1804), AP2a (Cell Signaling, 3215), AP2a (Novus Bio, NB100–74359).
Techniques: Mutagenesis, Western Blot, Control, Knock-Out, Clone Assay, Binding Assay