Pre-marked chromatin and transcription factor co-binding shape the pioneering activity of Foxa2.

Filippo M Cernilogar,Ida M Evenroed,Stefan Hasenöder,Gregor D Gilfillan,Heiko Lickert,Ingo Burtscher,Gunnar Schotta,Michael Sterr,Sophia Groh,Katharina Scheibner,Zeyang Wang,Pawel Smialowski

doi:10.1093/nar/gkz627

Abstract

Pioneer transcription factors (PTF) can recognize their binding sites on nucleosomal DNA and trigger chromatin opening for recruitment of other non-pioneer transcription factors. However, critical properties of PTFs are still poorly understood, such as how these transcription factors selectively recognize cell type-specific binding sites and under which conditions they can initiate chromatin remodelling. Here we show that early endoderm binding sites of the paradigm PTF Foxa2 are epigenetically primed by low levels of active chromatin modifications in embryonic stem cells (ESC). Priming of these binding sites is supported by preferential recruitment of Foxa2 to endoderm binding sites compared to lineage-inappropriate binding sites, when ectopically expressed in ESCs. We further show that binding of Foxa2 is required for chromatin opening during endoderm differentiation. However, increased chromatin accessibility was only detected on binding sites which are synergistically bound with other endoderm transcription factors. Thus, our data suggest that binding site selection of PTFs is directed by the chromatin environment and that chromatin opening requires collaboration of PTFs with additional transcription factors.

Highlights

Transcription factors (TFs) drive lineage-specific transcription programs by binding gene regulatory elements dispersed throughout the genome [1]
To study Foxa2 binding site selection and Foxa2-dependent chromatin changes we decided to investigate the transition from pluripotent embryonic stem cells (ESC) via mesendoderm (MESEND) progenitors to definitive endoderm (DE) cells using an in vitro differentiation system (Figure 1A)
This analysis suggests that transcription factors such as Foxa2, Gata4 and Eomes appear as most important to initiate endoderm differentiation (d0–d3F network), while the importance of additional TFs emerges in later stages of endoderm differentiation (d0– d5FS network)

Summary

Introduction

Transcription factors (TFs) drive lineage-specific transcription programs by binding gene regulatory elements dispersed throughout the genome [1]. Most TFs can recognize their target sequence only on nucleosome-free DNA, so-called pioneer transcription factors (PTFs) have the peculiar ability to engage their target sequence on nucleosomal DNA [4,5] Following binding to their target sites, PTFs can induce chromatin opening supporting the recruitment of non-pioneer TFs and leading to activation of the underlying gene regulatory elements [6,7]. Despite their potentially universal targeting, PTFs only bind to a subset of their potential DNA binding motif containing target sites [6,8,9]. These findings imply that additional mechanisms, such as cell-type specific cofactors [10,11] and chromatin environment [12,13,14,15] can influence binding site selection of PTFs

Methods

Results

Conclusion