The role of RNA in the central dogma of DNA → RNA → protein has diversified greatly in the past decades, and evidence now points to a major regulatory role of non-coding RNA (ncRNA). Recent technologic advances have enabled in-depth analysis of transcriptomes that now show that most of the RNA transcribed from mammalian genomes does not code for proteins. Apart from ribosomal and transfer RNA, the ncRNAs are divided into two major classes depending on their length. Short ncRNAs are < 200 nucleotides and include microRNAs, whereas long ncRNAs (lncRNAs) are > 200 nucleotides in length and are classified according to their position of origin in the genome. The function of most lncRNAs is obscure, but available evidence implicates their involvement in a variety of cellular processes, including genomic imprinting, X chromosome inactivation, stem cell pluripotency, cell-cycle control, and pathogenesis of certain cancers and inherited disorders.
In an elegant study from the laboratory of Dr. Harvey Lodish at the Whitehead Institute/Massachusetts Institute of Technology in Cambridge, MA, the repertoire of lncRNAs involved in erythropoiesis was identified, and the functional role of a few selected samples was investigated. Dr. Alvarez-Dominguez and colleagues studied erythroid and non-erythroid cells derived from mouse fetal livers, erythroid progenitors at three stages of differentiation, and 30 murine cell and tissue types. Analysis of the transcriptome from these various categories of samples revealed a vast array of erythroid-specific lncRNAs covering the whole spectrum of lncRNA types. Several lncRNAs were differentially expressed during red cell development, and their expression levels correlated with specific chromatin signatures based on methylation status of selected histones that reflected epigenetic activation or repression of genes. To confirm that differentially expressed lncRNAs participated in erythropoiesis, the investigators demonstrated that the core erythroid transcription factors, GATA1, TAL1, and KLF1, bound to the promoters of these lncRNA genes. The binding peaks of the transcription factors coincided with DNase I hypersensitive sites, RNA polymerase II binding sites, and active chromatin marks, implying that the lncRNA genes are regulated by these factors.
To probe the erythroid-specific functions of lncRNAs, the investigators used a stringent strategy to select 12 candidates (all localized to the nucleus) and performed loss-of-function experiments. Knockdown experiments showed that the selected lncRNAs inhibited cell size reduction, enucleation, and erythrocyte maturation.
LncRNAs can regulate their target genes by acting in cis to influence a gene on the same allele from which it is transcribed, or they can interact in trans with a gene on another chromosome. Of particular interest in the current study was an anti-sense to other genes lncRNA and alncRNA-EC7, which is transcribed from an enhancer and increases expression of the neighboring SLC4A1 gene. The proposed mechanism involves in cis chromatin looping to enable the alncRNA, which remains tethered to its site of transcription, to make contact with and activate the SLC4A1 gene. This gene codes for band 3, the transmembrane anion exchanger of the red cell. It is synthesized early in erythropoiesis and serves as a focal point to recruit and stabilize the assembly of other cell membrane proteins, thus playing a crucial role in erythroid membrane biogenesis.
In Brief
This study identifies a repertoire of erythroid lncRNAs and provides evidence of another layer of regulation in the complex process of erythropoiesis. It lays the foundation for exploiting these molecules as novel diagnostic tools and therapeutic targets and provides a framework for exploring the functions and mechanisms of action of these regulatory lncRNAs. It also highlights the integration of laboratory-based scientific experiments, computational analysis, and clinical insight to advance fundamental knowledge about red blood cell development.
Competing Interests
Dr. Coetzer indicated no relevant conflicts of interest.
