Csde1 binds transcripts involved in protein homeostasis and controls their expression in an erythroid cell line

Kat S Moore,Emile Van Den Akker,Nahuel A Paolini,Alexander B Meijer,Marieke Von Lindern,Floris Van Alphen,Riekelt H Houtkooper,Ntsiki M Held,Rastislav Horos,Nurcan Yagci,Peter A C ‘T Hoen

doi:10.1038/s41598-018-20518-7

Abstract

Expression of the RNA-binding protein Csde1 (Cold shock domain protein e1) is strongly upregulated during erythropoiesis compared to other hematopoietic lineages. Csde1 expression is impaired in the severe congenital anemia Diamond Blackfan Anemia (DBA), and reduced expression of Csde1 in healthy erythroblasts impaired their proliferation and differentiation. To investigate the cellular pathways controlled by Csde1 in erythropoiesis, we identified the transcripts that physically associate with Csde1 in erythroid cells. These mainly encoded proteins involved in ribogenesis, mRNA translation and protein degradation, but also proteins associated with the mitochondrial respiratory chain and mitosis. Crispr/Cas9-mediated deletion of the first cold shock domain of Csde1 affected RNA expression and/or protein expression of Csde1-bound transcripts. For instance, protein expression of Pabpc1 was enhanced while Pabpc1 mRNA expression was reduced indicating more efficient translation of Pabpc1 followed by negative feedback on mRNA stability. Overall, the effect of reduced Csde1 function on mRNA stability and translation of Csde1-bound transcripts was modest. Clones with complete loss of Csde1, however, could not be generated. We suggest that Csde1 is involved in feed-back control in protein homeostasis and that it dampens stochastic changes in mRNA expression.

Highlights

RNA binding proteins (RBP) regulate transcript stability and translation
To identify its function in erythropoiesis, we aimed to identify the transcripts that are bound by Csde[1] in erythroblasts, and to evaluate the effect Csde[1] on transcript stability and translation
Comparison showed that 53 of the 274 transcripts we identified as Csde1-associated transcripts were identified as a Csde[1] target in melanoma cells using iCLIP18

Summary

Introduction

RBPs can cooperate with protein complexes of the general mRNA translation machinery, or with protein complexes that control mRNA location and/ or degradation Deregulated expression of such RBPs affects protein synthesis from a set of transcripts dependent on that specific RBP. The RNA regulon may define a set of ubiquitously expressed transcripts whose translation is modified by cell type specific expression of RBP. In Diamond Blackfan Anemia (DBA), a ribosomopathy due to haploinsufficiency of ribosomal proteins, this upregulation was impaired[4] This raised our interest in the role of Csde[1] in erythropoiesis. The role of Csde[1] in control of mRNA stability and translation may be diverse as it binds transcripts through distinct sites[12,13]. We suggest that the function of Csde[1] is involved in feed-back control during protein homeostasis and that it may dampen stochastic changes in gene expression

Objectives

Methods

Results

Conclusion