Extended Data Fig. 9: Identification of candidate gene regulatory elements in TBC1D7 and TSC1.
From: TSC tunes progenitor balance and upper-layer neuron generation in neocortex
(A) ATAC-seq peaks showing a candidate HGE (teal box; TBC1D7-P1) in the TBC1D7 promoter56. The black lines indicate the significantly correlated peak pairs across a population of human neural progenitors and their correlation values (r). (B) HGEs were not detected near TSC1 in ATAC-seq or Hi-C data from neurons, progenitors, or germinal zone (GZ). (C) qPCR analysis of relative TBC1D7 expression in hNPCs after lentiviral transduction with dCas9-KRAB-gRNAs targeted to the candidate TBC1D7 human-gained enhancer. No changes in TBC1D7 expression were detected. Data shown are mean ± SEM (n = 9 unique donors). Unpaired two-sided t-test p > 0.05 (0.6363 [Cntrl sg vs sg1]; 0.6559 [Cntrl sg vs sg2]; 0.0702 [Cntrl sg vs sg3]; 0.3921 [Cntrl sg vs sg4]; 0.3130 [Cntrl sg vs sg5]; 0.4876 [Cntrl sg vs sg6]).
