An Evolutionarily Conserved Long Noncoding RNA TUNA Controls Pluripotency and Neural Lineage Commitment

Abstract

SUMMARY Here, we generated the first genome-scale shRNA library targeting lincRNAs in the mouse. We performed an unbiased loss-of-function study in mouse embryonic stem cells (mESCs) and identified 20 novel lincRNAs involved in the maintenance of pluripotency. Among these, TUNA (Tcl1 Upstream Neuron-Associated lincRNA), was required for pluripotency and formed a complex with three RNA-binding proteins (RBPs). The TUNA–RBP complex was detected at the promoters of Nanog, Sox2, and Fgf4, and knockdown of TUNA or the individual RBPs inhibited neural differentiation of mESCs. TUNA showed striking evolutionary conservation of both sequence and central nervous system-restricted expression in vertebrates. Accordingly, knockdown of tuna in zebrafish caused impaired locomotor function, and TUNA expression in the brains of Huntington’s patients was significantly associated with disease grade. Our results suggest that the lincRNA TUNA plays a vital role in pluripotency and neural differentiation of ESCs and is associated with neurological function of adult vertebrates.

Decoding the noncoding: Prospective of lncRNA-mediated innate immune regulation

“…13 Although the vast majority of lncRNAs, operationally defined as being more than 200 nucleotides in length and lacking in putative coding regions, 13 have not yet been ascribed a function, they are increasingly implicated in the regulation of numerous cellular processes such as X-chromosome inactivation, 14 regulation of p53 pathway, 15 stem cell self-renewal and differentiation, 16,17 epidermal differentiation, 18 erythroid development, 19 DNA damage response, 20 chromosome architecture, 21 and maintenance of active chromatin state. 22 The low abundance and lack of sequence conservation of lncRNAs initially suggested they were of little biological significance.…”

“…Indeed, many lncRNAs discovered to date show preferences for specific loci. 15,17,28,30 It is likely that new methodology, such as RNase-protected RNA sequencing, will be needed to fully understand the structure-function relationship and molecular mechanisms underlying lncRNA-mediated regulation of gene expression.…”

Long non‐coding RNAs in brain tumours: Focus on recent epigenetic findings in glioma

“…TUNA performs a regulatory function in pluripotency and neural differentiation of ESCs, acting as a scaffold for RNA‐binding proteins. TUNA also regulates the expression of several key neurogenic genes, including SOX2, and its depletion causes down‐regulation of SOX2 and subsequent loss of neurogenesis 43. Therefore, TUNA represents another example of an lncRNA involved in both neurogenesis and brain tumour progression.…”

“…However, two dysregulated lncRNAs in glioma, linc‐RoR and TUNA, have been reported to promote reprogramming efficiency. Linc‐ROR acts as a sponge for miRNAs that target pluripotency regulators, and TUNA directly interacts with RNA‐binding proteins at the promoters of TFs, such as NANOG and SOX2, where transcription is activated by deposition of the active histone mark H3K4me3 43. Interestingly, the glioma tumour suppressor lincRNA‐p21 prevents somatic cell reprogramming by sustaining H3K9me3 and/or CpG methylation at pluripotency gene promoters or by direct association with SETDB1, a histone‐lysine N‐methyltransferase protein or DNMT1 80…”

Characterization of the hypothalamic transcriptome in response to food deprivation reveals global changes in long noncoding RNA, and cell cycle response genes

“…These indicate that lncRNAs might be involved in the energy balance regulation. In the brain, several papers have detailed the importance of lncRNA in neuronal differentiation and brain development (Aprea et al 2013;Lin et al 2014), but adult expression patterns under stress-type conditions such as fasting have not been reported.…”