Long non-coding RNA in stem cell pluripotency and lineage commitment: functions and evolutionary conservation

Abstract

LncRNAs have recently emerged as new and fundamental transcriptional and post-transcriptional regulators acting at multiple levels of gene expression. Indeed, lncRNAs participate in a wide variety of stem cell and developmental processes, acting in cis and/or in trans in the nuclear and/or in the cytoplasmic compartments, and generating an intricate network of interactions with RNAs, enhancers, and chromatin-modifier complexes. Given the versatility of these molecules to operate in different subcellular compartments, via different modes of action and with different target specificity, the interest in this research field is rapidly growing. Here, we review recent progress in defining the functional role of lncRNAs in stem cell biology with a specific focus on the underlying mechanisms. We also discuss recent findings on a new family of evolutionary conserved lncRNAs transcribed from ultraconserved elements, which show perfect conservation between human, mouse, and rat genomes, and that are emerging as new player in this complex scenario.

Keywords: Embryonic stem cells; LncRNAs; T-UCEs; Ultraconserved elements.

Fig. 1

Scheme representing the main mode of action of the lncRNAs localized in the nucleus. TRF2 telomeric repeat-binding factor 2, DBHS drosophila behavior human splicing proteins

Fig. 2

Scheme representing the main mode of action of the lncRNAs localized in the cytoplasm. STAU1 Staufen 1 protein

Fig. 3

T-UCEs showing dynamic expression profiles during E12.5–E18.5 of mouse brain development (top panel). T-Ucstem1 expression decreases during ESC neural differentiation (bottom panel)

Fig. 4

Scheme representing the T-UCE mode of action in ESCs