Abstract
Circular RNAs are important for many cellular processes but their mechanisms of action remain poorly understood. Here, we map circRNA inventories of mouse embryonic stem cells, neuronal progenitor cells and differentiated neurons and identify hundreds of highly expressed circRNAs. By screening several candidate circRNAs for a potential function in neuronal differentiation, we find that circZNF827 represses expression of key neuronal markers, suggesting that this molecule negatively regulates neuronal differentiation. Among 760 tested genes linked to known neuronal pathways, knockdown of circZNF827 deregulates expression of numerous genes including nerve growth factor receptor (NGFR), which becomes transcriptionally upregulated to enhance NGF signaling. We identify a circZNF827-nucleated transcription-repressive complex containing hnRNP-K/L proteins and show that knockdown of these factors strongly augments NGFR regulation. Finally, we show that the ZNF827 protein is part of the mRNP complex, suggesting a functional co-evolution of a circRNA and the protein encoded by its linear pre-mRNA host.
Highlights
The mammalian non-coding transcriptome, which includes long noncoding RNAs and circular RNAs, plays pivotal roles in biological decisions during differentiation and normal cell maintenance
We used an established differentiation model for CNS-type glutamatergic neurons, based on E14 mouse embryonic stem cells that reportedly yields a purity of glutamatergic neurons of >90% (Bibel et al, 2007)
RNA was isolated from three stages of differentiation, mouse embryonic stem cells (mESC), neuronal progenitor cells or neuronal differentiation day 8 and rRNA depleted (+/- RNase R) prior to library preparation and RNA-seq (Figure 1A)
Summary
The mammalian non-coding transcriptome, which includes long noncoding RNAs (lncRNAs) and circular RNAs (circRNAs), plays pivotal roles in biological decisions during differentiation and normal cell maintenance (reviewed in Chekulaeva and Rajewsky, 2019; Deveson et al, 2017; Kopp and Mendell, 2018). Even though circRNAs were already identified several decades ago (Capel et al, 1993; Kos et al, 1986; Nigro et al, 1991; Sanger et al, 1976), they only recently have emerged as a large class of abundant noncoding RNAs that exhibit cell-type- and tissue-specific expression patterns (Ashwal-Fluss et al, 2014; Hansen et al, 2013; Jeck et al, 2013; Memczak et al, 2013; Rybak-Wolf et al, 2015; Salzman et al, 2013; Salzman et al, 2012) (reviewed in Chekulaeva and Rajewsky, 2019; Ebbesen et al, 2017; Salzman, 2016).
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