Pioneer factors: roles and their regulation in development

Abstract

Pioneer factors are a subclass of transcription factors that can bind and initiate opening of silent chromatin regions. Pioneer factors subsequently regulate lineage-specific genes and enhancers and, thus, activate the zygotic genome after fertilization, guide cell fate transitions during development, and promote various forms of human cancers. As such, pioneer factors are useful in directed cell reprogramming. In this review, we define the structural and functional characteristics of pioneer factors, how they bind and initiate opening of closed chromatin regions, and the consequences for chromatin dynamics and gene expression during cell differentiation. We also discuss emerging mechanisms that modulate pioneer factors during development.

Keywords: development; gene expression; heterochromatin; nucleosome; pioneer factor; zygotic gene activation.

Figure 1:. Pioneer factors bind silent chromatin and drive cell differentiation.

(A) Left: Pioneer factors binds closed chromatin regions. Middle: Pioneer factor induces local DNA accessibility to other transcription factors and protein complexes. Right: Pioneer factor induces chromatin reorganization and thus DNA sequence activation. Protein machineries include histone modifying complexes, the RNA polymerase transcription complex, and additional protein complexes regulating cis-regulatory elements. (B) Chromatin state of cis-regulatory elements in euchromatin regions (top) and silent chromatin regions (bottom). Unlike canonical transcription factors (TFs), pioneer factors (PFs) are able to bind silent chromatin regions. (C) Pioneer factors guide cell differentiation; their dysregulation might lead to cancer or cell reprogramming. Pioneer factors drive zygotic gene activation.

Figure 2:. Mechanism of action of Pioneer factors to induce silent chromatin opening.

(A) Unlike canonical transcription factor (TF), pioneer factors (PFs) can transiently interact with silent chromatin in order to identify their binding sites. (B) Pioneer factor interacts with nucleosomal DNA containing its DNA motif through its DNA-binding domain (DBD) and its non-DNA-binding domain. The non-DNA-binding domain establishes non-specific electrostatic interactions with nucleosomal DNA and direct contacts with nucleosome core particle, as described by Donovan et al. (2023) [51]. (C) Pioneer factor binding induces local silent chromatin opening by inducing local DNA accessibility and local chromatin decompaction.

Figure 3:. Pioneer factors drive closed chromatin reorganization and gene expression activation.

(A) In vitro, PU.1 is able to recruit the cBAF SWI/SNF nucleosome remodeling complex on H1-compacted nucleosome arrays to expand local DNA accessibility, as described by Frederick et al. (2023) [61]. (B) In vivo, a pioneer factor (PF) leads to chromatin reorganization and thus enhancer activation. Pioneer factor recruits SWI/SNF nucleosome remodeling complexes to promote nucleosome eviction and chromatin opening. Pioneer factors promote deposition of active chromatin on enhancer by recruiting MLL3/4 and p300 enzymes.

Figure 4:. Pioneer factors induce gene silencing.

(A) Pioneer factors induce passive enhancer inactivation by relocalizing protein complexes on chromatin. As described by Yang et al. (2023) [95], SOX9 recruits MLL3/4 and SWI/SNF nucleosome remodeling complex away from active epidermal enhancers during a hair follicle cell fate transition. (B) In vitro, FOXA1 increases local compaction of closed chromatin by recruiting Grg transcriptional corepressor, as described by Sekiya et al. (2007) [118]. (C) In vivo, pioneer factors directly induces enhancer inactivation. It erases active chromatin and induces chromatin closure on enhancers by recruiting histone deacetylase complex (NuRD). Pioneer factors also establish H3K27me3-marked heterochromatin by recruiting and stimulating the PRC2 complex.

Figure 5:. Pioneer binding and opening activity are modulated.

(A) Cooperative binding. A first pioneer factor binds and distorts nucleosomal DNA, leading to exposure of a second DNA motif and thus binding of a second factor. (B) Pioneer factor binding and opening activity depend on pioneer factor cofactors. As described by Zhang et al. (2019) [143], SOX2 interacts with OCT4 in embryonic stem cells, then loss its interaction with OCT4 to gain interaction with PAX6 during neural fate transition leading to SOX2 genome wide relocalization. (C) Poised pioneer factor binds closed chromatin regions but does not induce its local opening. Closed chromatin opening may occur later during development. (D) Histone modifications might favor or impede pioneer factor binding/local opening activity.