RNA splicing during terminal erythropoiesis

Abstract

Purpose of review Erythroid progenitors must accurately and efficiently splice thousands of pre-mRNAs as the cells undergo extensive changes in gene expression and cellular remodeling during terminal erythropoiesis. Alternative splicing choices are governed by interactions between RNA binding proteins (RBPs) and cis-regulatory binding motifs in the RNA. This review will focus on recent studies that define the genome-wide scope of splicing in erythroblasts and discuss what is known about its regulation. Recent findings RNA-seq analysis of highly purified erythroblast populations has revealed an extensive program of alternative splicing of both exons and introns. During normal erythropoiesis, stage-specific splicing transitions alter the structure and abundance of protein isoforms required for optimized red cell production. Mutation or deficiency of splicing regulators underlies hematopoietic disease in myelopdysplasia syndrome (MDS) patients via disrupting the splicing program. Summary Erythroid progenitors execute an elaborate alternative splicing program that modulates gene expression post-transcriptionally, ultimately regulating the structure and function of the proteome in a differentiation stage-specific manner during terminal erythropoiesis. This program helps drives differentiation and ensures synthesis of the proper protein isoforms required to produce mechanically stable red cells. Mutation or deficiency of key splicing regulatory proteins disrupts the splicing program to cause disease.

Dynamic changes in RNA–protein interactions and RNA secondary structure in mammalian erythropoiesis

“…Using this process, we were able to identify several proteins that could potentially be regulators of erythropoiesis. Specifically, the KEGG pathway enrichment analysis revealed an enrichment for proteins involved in splicing and RNA transport, which tracts well with the idea that RNA splicing plays a large role in terminal erythropoiesis (63), and suggests that alternative splicing would be an important regulatory process to understand for erythropoiesis. However, we were interested in identifying specific proteins that may act as regulators of this process.…”

Aberrant splicing contributes to severe α-spectrin–linked congenital hemolytic anemia

“…To gain insight into potential effects of the α LEPRA allele on mRNA processing, a series of bioinformatic studies was performed. Analysis of SPTA1 intron 30 using Sroogle, which analyzes splicing signals and the influence of mutations on splicing (16), predicted: (a) a branch point (BP1) at the expected location 31 bp 5′ of the 3′ acceptor site (3′Acc1) of exon 31; (b) an alternate we created K562 cells homozygous for the α LEPRA allele using gene editing (Supplemental Data) and treated them with the NMD inhibitors emetine or cycloheximide (24,25). In homozygous α LEPRA and to a lesser extent in WT cells, the total amount of elongated transcript increased relative to total α-spectrin transcript after NMD inhibition ( Figure 5A).…”

Length Biases in Single-Cell RNA Sequencing of pre-mRNA

“…The binary model classifying each molecule as either spliced or unspliced is computationally tractable, but unsatisfying: it is only mechanistically justified in the case where only one intermediate transcript and one protein-coding transcript are prevalent. However, differential isoform expression is well-known to be prominent [25,58], with significant biological impact [59,60]. In prin-16 ciple, a more sophisticated workflow may identify individual intermediate isoforms and fit a full splicing graph.…”