Identification of differentially expressed non-coding RNAs in embryonic stem cell neural differentiation

Abstract

Protein-coding genes, guiding differentiation of ES cells into neural cells, have extensively been studied in the past. However, for the class of ncRNAs only the involvement of some specific microRNAs (miRNAs) has been described. Thus, to characterize the entire small non-coding RNA (ncRNA) transcriptome, involved in the differentiation of mouse ES cells into neural cells, we have generated three specialized ribonucleo-protein particle (RNP)-derived cDNA libraries, i.e. from pluripotent ES cells, neural progenitors and differentiated neural cells, respectively. By high-throughput sequencing and transcriptional profiling we identified several novel miRNAs to be involved in ES cell differentiation, as well as seven small nucleolar RNAs. In addition, expression of 7SL, 7SK and vault-2 RNAs was significantly up-regulated during ES cell differentiation. About half of ncRNA sequences from the three cDNA libraries mapped to intergenic or intragenic regions, designated as interRNAs and intraRNAs, respectively. Thereby, novel ncRNA candidates exhibited a predominant size of 18–30 nt, thus resembling miRNA species, but, with few exceptions, lacking canonical miRNA features. Additionally, these novel intraRNAs and interRNAs were not only found to be differentially expressed in stem-cell derivatives, but also in primary cultures of hippocampal neurons and astrocytes, strengthening their potential function in neural ES cell differentiation.

NSun2-Mediated Cytosine-5 Methylation of Vault Noncoding RNA Determines Its Processing into Regulatory Small RNAs

“…vtRNAs are ncRNAs found as part of the vault ribonucleoprotein complex of unknown function (Kedersha and Rome, 1986). Interestingly, vtRNAs are significantly upregulated during neural differentiation (Skreka et al., 2012), and NSun2 deficiency in humans causes neurodevelopmental symptoms (Abbasi-Moheb et al., 2012; Khan et al., 2012; Martinez et al., 2012). However, the role of site-specific loss of m 5 C in vtRNAs in the NSun2-mediated functions remained unclear.…”

Rn7SK small nuclear RNA is involved in neuronal differentiation

“…Recently, Rn7SK upregulation in mature neurons has been reported in in vitro experiments . Skreka et al identified differentially expressed non‐coding RNAs in neural differentiation, among them Rn7SK , which they found to be increased in mature neurons compared to neuronal progenitor cells and pluripotent stem cells.…”

‘High vault-age’: non-coding RNA control of autophagy

“…These include differentiation and development [102], cell-death signalling [103] and cell-cycle regulation [104]. For example, the levels of non-coding RNAs including vault RNAs have been reported to be highly regulated during cellular differentiation [105]. Riboregulation could therefore represent a mechanism to modulate p62 function in this context.…”