Molecular targets of chromatin repressive mark H3K9me3 in primate progenitor cells within adult neurogenic niches

Michael R Foret,Christopher T Rhodes,Richard S Sandstrom,Mitchel S Berger,Yufeng Wang,Chin-Hsing Annie Lin

doi:10.3389/fgene.2014.00252

Abstract

Histone 3 Lysine 9 (H3K9) methylation is known to be associated with pericentric heterochromatin and important in genomic stability. In this study, we show that trimethylation at H3K9 (H3K9me3) is enriched in an adult neural stem cell niche- the subventricular zone (SVZ) on the walls of the lateral ventricle in both rodent and non-human primate baboon brain. Previous studies have shown that there is significant correlation between baboon and human regarding genomic similarity and brain structure, suggesting that findings in baboon are relevant to human. To understand the function of H3K9me3 in this adult neurogenic niche, we performed genome-wide analyses using ChIP-Seq (chromatin immunoprecipitation and deep-sequencing) and RNA-Seq for in vivo SVZ cells purified from baboon brain. Through integrated analyses of ChIP-Seq and RNA-Seq, we found that H3K9me3-enriched genes associated with cellular maintenance, post-transcriptional and translational modifications, signaling pathways, and DNA replication are expressed, while genes involved in axon/neuron, hepatic stellate cell, or immune-response activation are not expressed. As neurogenesis progresses in the adult SVZ, cell fate restriction is essential to direct proper lineage commitment. Our findings highlight that H3K9me3 repression in undifferentiated SVZ cells is engaged in the maintenance of cell type integrity, implicating a role for H3K9me3 as an epigenetic mechanism to control cell fate transition within this adult germinal niche.

Highlights

Chromatin is functionally classified as euchromatin and heterochromatin, which are crucial for epigenetic controls of gene expression
H3K9 methylation is involved in pluripotency of embryonic stem cells (ESCs) and multipotency of neural precursor cells (NPCs), in which the pluripotent genes (e.g., Nanog, Oct4) and non-neural genes (e.g., GATA4, NODAL) gain H3K9me3 that lead to long-term repression during differentiation of human ESCs into NPCs (Golebiewska et al, 2009; Hirabayashi and Gotoh, 2010)
H3K9me3 IS EXPRESSED IN GERMINAL ZONES WITHIN THE ADULT BRAIN Using co-immunostaining with antibodies specific for H3K9me3 and cell type specific markers in the subventricular zone (SVZ) (Figure 1I) for the gross anatomy of 8-week (P56) old adult mouse brain (Figure 1A), we found that H3K9me3-positive cells are co-localized with Glial Fibrillary Acidic Protein (GFAP) which labels quiescent and active neural stem cells (NSCs) (Figure 1C), Vimentin positive active NSC (Figure 1D), and PSA-NCAM positive neuroblast populations as well (Figure 1E)

Summary

Introduction

Chromatin is functionally classified as euchromatin and heterochromatin, which are crucial for epigenetic controls of gene expression. Underlying the specialized chromatin structure around centromere and telomere, H3K9me was identified to be heterochromatin-enriched histone code to silence gene expression and prevent chromosomal instability (Czvitkovich et al, 2001; Lachner et al, 2001; Peters et al, 2001, 2002; Black et al, 2012). H3K9me plays a repressive role in numerous neuronal and non-neuronal genes (Roopra et al, 2004; Schaefer et al, 2009) in addition to its known function in genome stability. Studies from KMT1 knock-out mice demonstrated that loss of H3K9 methylation contributes to behavioral abnormalities and cognitive impairment (Schaefer et al, 2009) in addition to its protective role in genome stability. We found that H3K9me is enriched in the subventricular zone (SVZ), where adult neurogenesis occurs

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