Multiplexed mRNA assembly into ribonucleoprotein particles plays an operon-like role in the control of yeast cell physiology.

Rohini R Nair,Rita Gelin-Licht,Brian J Haas,Dmitry Zabezhinsky,Chad Nusbaum,Jeffrey E Gerst,Michael Ca Dyhr,Hannah S Sperber

doi:10.7554/elife.66050

Abstract

Prokaryotes utilize polycistronic messages (operons) to co-translate proteins involved in the same biological processes. Whether eukaryotes achieve similar regulation by selectively assembling and translating monocistronic messages derived from different chromosomes is unknown. We employed transcript-specific RNA pulldowns and RNA-seq/RT-PCR to identify yeast mRNAs that co-precipitate as ribonucleoprotein (RNP) complexes. Consistent with the hypothesis of eukaryotic RNA operons, mRNAs encoding components of the mating pathway, heat shock proteins, and mitochondrial outer membrane proteins multiplex in trans, forming discrete messenger ribonucleoprotein (mRNP) complexes (called transperons). Chromatin capture and allele tagging experiments reveal that genes encoding multiplexed mRNAs physically interact; thus, RNA assembly may result from co-regulated gene expression. Transperon assembly and function depends upon histone H4, and its depletion leads to defects in RNA multiplexing, decreased pheromone responsiveness and mating, and increased heat shock sensitivity. We propose that intergenic associations and non-canonical histone H4 functions contribute to transperon formation in eukaryotic cells and regulate cell physiology.

Highlights

Prokaryotic organisms can rely on polycistronic transcription, which allows for the expression of needed mRNAs from a single promoter and enables a rapid and robust response to corresponding stimuli (Jacob and Monod, 1961)
One possibility is that eukaryotic messenger ribonucleoprotein particles, which are composed of multiple RNAs and RNA-binding proteins (RBPs) (Mitchell and Parker, 2014), effectively confer combinatorial gene expression networks similar to prokaryotic operons (Keene and Tenenbaum, 2002)
In addition to identifying the target mRNA in each pulldown, we identified non-tagged RNAs that co-precipitated with the targets (Figure 1A, Figure 1—figure supplement 1, and see Supplementary file 1 for RNA-seq data)

Summary

Introduction

Prokaryotic organisms can rely on polycistronic transcription (operons), which allows for the expression of needed mRNAs from a single promoter and enables a rapid and robust response to corresponding stimuli (e.g., lactose operon) (Jacob and Monod, 1961). One possibility is that eukaryotic messenger ribonucleoprotein (mRNP) particles, which are composed of multiple RNAs and RNA-binding proteins (RBPs) (Mitchell and Parker, 2014), effectively confer combinatorial gene expression networks similar to prokaryotic operons (Keene and Tenenbaum, 2002). In this case, the mRNP particles contain individual mRNAs that undergo co-translational control and may encode proteins involved in the same biological process or molecular complex. The latter includes motifs/structures to facilitate interactions with shared RBPs, as well as elements that

Methods

Results

Conclusion