DNA-binding pluripotency factors and DNA demethylases can cooperate to maintain pluripotent stem cell identity even in the absence of Brd4 [ATAC-seq]

The relative contributions of sequence-specific transcription factors and DNA/histone modifications to stem cell maintenance remains controversial. For example, the acetyllysine reader Brd4 has been implicated in stem cell maintenance, but how absolute the role of Brd4 is in maintaining pluripotency remains unclear. Here we show that Brd4 is dispensable for the proliferation, self-renewal and pluripotency of embryonic stem cells. In naive, ground state pluripotent stem cells, Mediator recruitment and transcription factor binding to stem cell-specific genes are maintained in the absence of Brd4 function or expression. Even in metastable embryonic stem cells poised for differentiation, Brd4 independence can be maintained by overexpression of pluripotency transcription factors so long as the DNA methylcytosine oxidases, Tet1 and Tet2, are present to facilitate chromatin accessibility. These data reveal that Brd4 is not essential for self-renewal of embryonic stem cells. Rather, Brd4 contributes to stem cell maintenance only under conditions where the expression of pluripotency transcription factors and/or DNA demethylation machinery is compromised.