Changing and stable chromatin accessibility supports transcriptional overhaul during neural stem cell activation

Background

Neural stem cells (NSCs) can be functionally defined as self-renewing cells with the ability to differentiate into both glial and neural cell types. In adulthood, NSCs persist in restricted areas of the brain and can exist in both actively proliferating and non-cycling quiescent states (1). In response to intrinsic or extrinsic influences, quiescent NSCs can ‘reactivate’ and reenter the cell cycle (2,3,4). However, the molecular mechanisms that underlie this transition remain unclear. Traditionally, changes in cell fate require global resetting of histone and DNA modifications, which in turn modify DNA accessibility for gene-specific or general transcriptional machinery, enabling changes in gene expression. In this study, the authors aim to understand the chromatin accessibility in both quiescent and activated NSC states, and how this controls the ‘transcriptional overhaul’ required for activation (5,6,7).

Key findings

Maybury-Lewis et al employ a wealth of ATAC-seq, RNA-seq and ChIP-seq datasets in both in vitro and in vivo quiescent and activated NSCs to conclude that NSCs use two distinct chromatin-level mechanisms to undergo transcriptional resetting during activation.

Firstly, the authors performed ATAC-seq to assess genome-wide chromatin accessibility in quiescent, activated and reactivated neural stem and progenitor cells. This revealed that both states share similarities in chromatin conformation distinct to the neural lineage (termed ‘stable chromatin’). However, chromatin accessibility differences were also observed (termed ‘dynamic chromatin’), with chromatin opening upon activation termed ‘AA’ or ‘Accessible in Activated’ and upon quiescence termed ‘AQ’ or ‘Accessible in Quiescent’.

Findings with respect to dynamic chromatin regions

The authors used RNA-seq and ATAC-seq data to correlate transcriptional changes with chromatin accessibility. As expected, they found a gain in chromatin accessibility can lead to gene activation, with AA sites associated with gene upregulation and AQ sites associated with gene downregulation in activated NSCs. Interestingly, however, almost 70% of genes downregulated in activated NSCs only had open chromatin sites in the activated state, suggesting chromatin opening can also be associated with transcriptional repression.

The authors found dynamic changes in chromatin accessibility to occur more frequently at distal gene-specific regulatory elements, away from promoters. These regions were confirmed to contain active enhancers specific to quiescent or activated NSC states, through enrichment of the epigenomic marker H3K27ac and p300 binding. Furthermore, these enhancers were shown to be sufficient to regulate gene expression; dCas9-KRAB-targeting of the Aquaporin- 4 (Aqp4) enhancer, found to be only accessible in quiescent NSCs, resulted in downregulation of Aqp4 expression.

Analysis of the genes associated with dynamic chromatin revealed an enrichment for genes regulating neural identity, differentiation and proliferation. To understand which transcription factors bind to dynamic chromatin regions to regulate gene expression, the authors performed in silico motif analyses. While AQ sites were most enriched for NF1 motifs, AA sites were highly enriched for motifs of bHLH factors such as the pro-neurogenic factor ASCL1. Together, these findings indicate that cell-type-specific neural regulators bind to dynamically accessible active enhancers to regulate the expression of genes controlling the quiescent or activated NSC states.

Findings with respect to stable chromatin regions

Perhaps unexpectedly, genes associated with stable chromatin could also be linked to transcriptional activation in activated NSCs. In contrast to dynamic regions, these stable chromatin regions were found to occur more frequently in promoters. ChIP-seq analysis for the active promoter histone mark, H3K4me3, found profiles highly similar in quiescent and active NSCs, with H3K4me3 remaining stable at promoters of genes differentially expressed upon NSC activation. These genes were enriched for pathways regulating translation, proteostasis, metabolism, RNA polymerase II assembly, and proliferation. In keeping with this, promoters of genes differentially expressed upon NSC activation but with stable chromatin were found to be enriched with the TATA box or human TCT elements, known components of ribosomal protein and translation initiation and elongation factor gene promoters. In silico motif analysis of stable accessible chromatin revealed a distinct set of binding motifs, including enrichment for the insulator CTCF and the zinc-finger family transcription factors Sp1/5.

These findings suggest that gene expression changes can occur during NSC activation by a distinct mechanism not involving chromatin remodelling. Binding to stably open chromatin regions may function both to maintain boundaries for gene regulation and to enable rapid fine-tuning in expression of transcriptional and ribosomal machinery.

Why is this work important?

The work of Maybury-Lewis et al provides a genome-wide dataset of enhancers with dynamic chromatin that are associated with gene expression changes responsible for NSC activation. This work can be built upon to refine the relationship between changes in chromatin accessibility and the regulation of specific genes during this transition. This has potentially wide-reaching impacts in understanding the balance between NSC quiescence and activation during brain development, ageing and injury. My personal interest in understanding the mechanisms underlying NSC states lies in their applicability to brain cancer. Quiescent NSC-like cancer stem cells can evade conventional treatments and reactivate to drive tumour regrowth, therefore understanding these mechanisms may lead to therapies preventing patient relapse.

This study also provides insights into how we consider chromatin accessibility to affect NSC gene expression. It challenges the view that chromatin opening leads only to activation of gene expression by showing that enhancers with accessible chromatin only in activated NSCs (AA sites) are also associated with gene downregulation. This suggests enhancer function may be determined by the balance of transcriptional activator and repressor binding. The authors also indicate an important role for stably open chromatin at promoters during NSC activation, both in maintenance of higher order chromatin structure and transcriptional regulation through core promoter elements.

Questions for the authors

– Why do you think the reactivated NSCs still harboured closed AA and open AQ sites? Did you investigate if they would be fully ‘reset’ after a longer period in high growth factor signalling conditions?

– Did you consider performing RNA-seq on the same populations of quiescent and activated in vitro NSPCs for which you gathered ATAC-seq data?

– How would you suggest ubiquitous transcription factors with enriched binding motifs in stably open chromatin (e.g. NFY, Sp1/5) could bring about transcriptional changes between the quiescent and activated states?

– Can you conclude ASCL1 has a causal role in changing chromatin conformation? Would it be informative to monitor ASCL1 binding at AA sites at time points in the transition from quiescence to activation, to prove binding occurs before chromatin opening?

– Similarly, studies have shown that NSCs in vivo can exist along a continuum of states from quiescence to activation (7). Did you consider performing ATAC-seq analyses at intermediate time points during reactivation to observe a temporal change in chromatin dynamics?

References

(1) Codega P, Silva-Vargas V, Paul A, Maldonado-Soto AR, Deleo AM, Pastrana E & Doetsch F (2014) Prospective Identification and Purification of Quiescent Adult Neural Stem Cells from Their In Vivo Niche. Neuron 82: 545–559

(2) Parent JM, Vexler ZS, Gong C, Derugin N & Ferriero DM (2002) Rat forebrain neurogenesis and striatal neuron replacement after focal stroke. Ann Neurology 52: 802-813

(3) Zhang RL, Chopp M, Roberts C, Liu X, Wei M, Nejad-Davarani SP, Wang X & Zhang ZG (2014) Stroke increases neural stem cells and angiogenesis in the neurogenic niche of the adult mouse. PLoS One 9: e113972

(4) Villeda SA, Luo J, Mosher KI, Zou B, Britschgi M, Bieri G, Stan TM, Fainberg M, Ding Z, Eggel A et al (2011) The ageing systemic milieu negatively regulates neurogenesis and cognitive function. Nature 477: 90-94

(5) Leeman DS, Hebestreit K, Ruetz T, Webb AE, McKay A, Pollina EA, Dulken BW, Zhao X, Yeo RW, Ho TT et al (2018) Lysosome activation clears aggregates and enhances quiescent neural stem cell activation during aging. Science 359: 1277-1283

(6) Knobloch M, Pilz GA, Ghesquiere B, Kovacs WJ, Wegleiter T, Moore DL, Hruzova M, Zamboni N, Carmeliet P & Jessberger S (2017) A Fatty Acid Oxidation-Dependent Metabolic Shift Regulates Adult Neural Stem Cell Activity. Cell Rep 20: 2144-2155

(7) Dulken BW, Leeman DS, Boutet SC, Hebestreit K & Brunet A (2017) Single-Cell Transcriptomic Analysis Defines Heterogeneity and Transcriptional Dynamics in the Adult Neural Stem Cell Lineage. Cell Rep 18: 777-79

 

Tags: brain, chromatin, quiescence, stem cell

doi: https://doi.org/10.1242/prelights.19784

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