Supporting data for “ Evaluating the capabilities of POU (Pit-Oct-Unc) transcription factors to engage epigenetically silenced chromatin”

This is the dataset used for the PhD thesis entitled “Evaluating the capabilities of POU (Pit-Oct-Unc) transcription factors to engage epigenetically silenced chromatin”.

Pioneer transcription factors (TFs) bind to and activate epigenetically silenced chromatin, making them critical regulators of cell fate. Oct4 of the Pit-Oct-Unc (POU) TF family is essential to establishing and maintaining pluripotency. Oct4 binds to silenced chromatin, such as methylated DNA or DNA compacted by nucleosome core particles (NCPs). Significant gaps remain to accurately define the unique traits of pioneer TFs to differentiate them from collaborating non-pioneering TFs. Furthermore, the mechanism behind how Oct4 asserts its function on methylated DNA remains elusive. Here, Oct4's interaction with a methylated DNA element called “CpGpal” was examined. We then compared Oct4 and Brn2's binding to methylated DNA and nucleosome core particles (NCPs) through biochemical and structural analyses. Through this comparison, we aim to uncover whether differential engagement with methylated DNA and NCPs could contribute to their contrasting biological functions.

Furthermore, the evaluation of POU factors and their partners was further explored from a molecular evolution perspective. POU and their interactions with Sox factors are crucial to regulating stemness in mammals. To investigate the evolutionary conservation of biochemical properties in unicellular relatives of animals, we compared Sox and POU TFs from choanoflagellates and filastereans to their mammalian counterparts.