ARID4B is critical for mouse embryonic stem cell differentiation towards mesoderm and endoderm, linking epigenetics to pluripotency exit

Nihal Terzi Cizmecioglu,Jialiang Huang,Ezgi G Keskin,Xiaofeng Wang,Idil Esen,Fei Chen,Stuart H Orkin

doi:10.1074/jbc.ra120.015534

Abstract

Distinct cell types emerge from embryonic stem cells through a precise and coordinated execution of gene expression programs during lineage commitment. This is established by the action of lineage specific transcription factors along with chromatin complexes. Numerous studies have focused on epigenetic factors that affect embryonic stem cells (ESC) self-renewal and pluripotency. However, the contribution of chromatin to lineage decisions at the exit from pluripotency has not been as extensively studied. Using a pooled epigenetic shRNA screen strategy, we identified chromatin-related factors critical for differentiation toward mesodermal and endodermal lineages. Here we reveal a critical role for the chromatin protein, ARID4B. Arid4b-deficient mESCs are similar to WT mESCs in the expression of pluripotency factors and their self-renewal. However, ARID4B loss results in defects in up-regulation of the meso/endodermal gene expression program. It was previously shown that Arid4b resides in a complex with SIN3A and HDACS 1 and 2. We identified a physical and functional interaction of ARID4B with HDAC1 rather than HDAC2, suggesting functionally distinct Sin3a subcomplexes might regulate cell fate decisions Finally, we observed that ARID4B deficiency leads to increased H3K27me3 and a reduced H3K27Ac level in key developmental gene loci, whereas a subset of genomic regions gain H3K27Ac marks. Our results demonstrate that epigenetic control through ARID4B plays a key role in the execution of lineage-specific gene expression programs at pluripotency exit.

Highlights

During early embryonic development, a series of differentiation and cleavage events lead to the formation of distinct cell types that later form the organism
Prior analysis of the role of the Sin3a complex in embryonic stem cells (ESC) biology has led to apparently conflicting findings
Hdac1 knockout mice are embryonic lethal, whereas Hdac2 deletion is viable [52, 62, 63]. Both HDAC1 and HDAC2 independently interact with SIN3A, it is unclear whether these proteins function within the same complex or are present in alternate Sin3a complexes [45]

Summary

Introduction

A series of differentiation and cleavage events lead to the formation of distinct cell types that later form the organism. We used a pooled shRNA library screen to identify epigenetic factors that impact mouse embryonic stem cell differentiation toward mesoderm and endoderm (Fig. 1a). Upon extension of endoderm differentiation from 5 to 8 days, we observed markedly reduced expression of Brachyury and Foxa2 in Arid4b-deleted cells (Fig. S1, h and i).

Results

Conclusion