Pioneer factor Pax7 initiates two-step cell-cycle dependent chromatin opening

Abstract

Pioneer transcription factors direct cell differentiation by deploying new enhancer repertoires through their unique ability to target and initiate remodelling of closed chromatin. The initial steps of their action remain undefined although pioneers were shown to interact with nucleosomal target DNA and with some chromatin remodelling complexes. We now define the sequence of events that provide pioneers with their unique abilities. Chromatin condensation exerted by linker histone H1 is the first constraint on pioneer recruitment, and this establishes the initial speed of chromatin remodelling. The first step of pioneer action involves recruitment of the LSD1 H3K9me2 demethylase for removal of this repressive mark, as well as recruitment of the MLL complex for deposition of the H3K4me1 mark. Further progression of pioneer action requires passage through cell division, and this involves dissociation of pioneer targets from perinuclear lamins. Only then, the SWI/SNF remodeling complex and the coactivator p300 are recruited, leading to nucleosome displacement and enhancer activation. Thus, the unique features of pioneer actions are those occurring in the lamin-associated compartment of the nucleus. This model is consistent with much prior work that showed a dependence on cell division for establishment of new cell fates.

Chromatin opening ability of pioneer factor Pax7 depends on unique isoform and C-terminal domain

“…Also, the apparent Pax7 ChIP recruitment signal intensity in itself is not well correlated with chromatin opening ability. A similar conclusion was reached by analysis of initial recruitments at different Pax7 pioneer sites where initial recruitment strength is inversely correlated with the levels of linker histone H1 (2). But it could be a combination of DNA and chromatin interaction strengths, together with ability to recruit the cooperating TF Tpit (as discussed below), that ultimately determine chromatin modification and opening.…”

“…going through the first step of chromatin opening but failing to undergo the second cell-cycle dependent step that involves nucleosome displacement and recruitment of the SWI/SNF complex (2). We also showed that this second step requires the cooperating nonpioneer factor Tpit in addition to cell replication (2).…”

“…The loss of Tpit recruitment at the GL-sensitive and Pax465Ala 459-461 subsets of impaired pioneer sites is similar (Figure 6f) and hence this is a reasonable explanation. And indeed, the subset of sites that are only primed by Pax7 in AtT-20 cells does not recruit Tpit (2,8) and knockout of the Tpit gene results in failure of Pax7 pioneer capacity in the mouse pituitary (18). Further, Pax3 behaves very similarly to the GL+ Pax7 isoform in pituitary cells despite Pax3 being GL-and it also shows reduced Tpit recruitment (Figure 6f).…”

“…Pioneer transcription factors are unique in their ability to recognise and bind their target DNA sequences in closed chromatin (1). Their action initiates chromatin opening by a process that has received recent insight (2). This unique property has endowed this class of transcription factors with the power to direct new cell fates in development (3,4).…”