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

Abstract

Pioneer factors are transcription factors (TFs) that have the unique ability to recognise their target DNA sequences within closed chromatin. Whereas their interactions with cognate DNA is similar to other TFs, their ability to interact with chromatin remains poorly understood. Having previously defined the modalities of DNA interactions for the pioneer factor Pax7, we have now used natural isoforms of this pioneer as well as deletion and replacement mutants to investigate the Pax7 structural requirements for chromatin interaction and opening. We show that the GL+ natural isoform of Pax7 that has two extra amino acids within the DNA binding paired domain is unable to activate the melanotrope transcriptome and to fully activate a large subset of melanotrope-specific enhancers targeted for Pax7 pioneer action. This enhancer subset remains in the primed state rather than being fully activated, despite the GL+ isoform having similar intrinsic transcriptional activity as the GL– isoform. C-terminal deletions of Pax7 lead to the same loss of pioneer ability, with similar reduced recruitments of the cooperating TF Tpit and of the co-regulators Ash2 and BRG1. This suggests complex interrelations between the DNA binding and C-terminal domains of Pax7 that are crucial for its chromatin opening pioneer ability.

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

“…These observations led some authors to suggest that recruitment strength is critical for pioneer action 26,27 . We found that Pax7 isoforms or mutants that have decreased affinity fail to open subsets of targets but these analyses also revealed intrinsic target site differences that presumably reflects context-dependent chromatin heterogeneity 4,28 . Irrespective of these relations, the present work suggests a model where permissive sites of Pax7 pioneer action are in various states of compaction as reflected by the level of histone H1.…”