Transcriptional network orchestrating regional patterning of cortical progenitors
Athéna R. Ypsilanti, Kartik Pattabiraman, Rinaldo Catta-Preta, Olga Golonzhka, Susan Lindtner, Ke Tang, Ian Jones, Armen Abnousi, Ivan Jurić, Ming Hu, Yin Shen, Diane E. Dickel, Axel Visel, L Pennacchio, Michael Hawrylycz, Carol L. Thompson, Hongkui Zeng, Iros Barozzi, Alex S. Nord, John L.R. Rubenstein
Abstract
Significance Development of cortical areas begins in cortical stem cells through the action of morphogens controlling the graded expression of transcription factors (TFs). Here, we have systematically identified the TFs and gene regulatory elements (REs) that together control regional pattering of the cortical progenitor zone; these data have led us to propose a cortical regionalization TF network. To identify REs active in this network, we performed TF chromatin immunoprecipitation followed by sequencing (ChIP-seq) and chromatin-looping conformation experiments as well as assays for epigenomic marks and DNA accessibility in purified ventricular zone (VZ) progenitor cells in wild-type and patterning mutant mice. This integrated approach has laid the foundations to identify a TF network and cortical VZ REs involved in cortical regional patterning.