Temporal and spatial regulation of mRNA export: Single particle RNA‐imaging provides new tools and insights

Abstract

The transport of messenger RNAs (mRNAs) from the nucleus to cytoplasm is an essential step in the gene expression program of all eukaryotes. Recent technological advances in the areas of RNA-labeling, microscopy, and sequencing are leading to novel insights about mRNA biogenesis and export. This includes quantitative single molecule imaging (SMI) of RNA molecules in live cells, which is providing knowledge of the spatial and temporal dynamics of the export process. As this information becomes available, it leads to new questions, the reinterpretation of previous findings, and revised models of mRNA export. In this review, we will briefly highlight some of these recent findings and discuss how live cell SMI approaches may be used to further our current understanding of mRNA export and gene expression.

Imaging mRNA In Vivo, from Birth to Death

“…The formation of export-competent mRNAs starts with the cotranscriptional recruitment of the export machinery. The general mRNA export receptor NXF1 (Mex67 in yeast) interacts with members of the transcription-coupled complex (THO/TREX) and the exon junction complex deposited during splicing to transport the mRNAs through the nuclear pore complexes (NPCs) (59,137). On the basis of quantification of the number of transcribed mRNAs (2,000-3,000) and the number of nuclear pores present in the nuclear envelope of S. cerevisiae , it was estimated that each nuclear pore transports on average 10-50 mRNAs per min (59).…”

“…The general mRNA export receptor NXF1 (Mex67 in yeast) interacts with members of the transcription-coupled complex (THO/TREX) and the exon junction complex deposited during splicing to transport the mRNAs through the nuclear pore complexes (NPCs) (59,137). On the basis of quantification of the number of transcribed mRNAs (2,000-3,000) and the number of nuclear pores present in the nuclear envelope of S. cerevisiae , it was estimated that each nuclear pore transports on average 10-50 mRNAs per min (59). Diffusion of the mRNPs in the nucleoplasm brings them to the nuclear periphery, where they scan multiple NPCs before reaching the cytoplasm (50,88,110,119,122,123).…”

Agent‐Based Modeling in Molecular Systems Biology

“…Accordingly, several efforts have been made to increase the spatiotemporal resolution of experimental approaches. For instance, in the case of mRNA export, while experimental approaches such as oligo(dT) in situ hybridization assay or single molecule fluorescence in situ hybridization (smFISH) can primarily perform bulk measurements to determine the intracellular distribution of RNA, they cannot capture high‐resolution in vivo dynamics . Recent advancements in RNA labeling as well as imaging methods, however, have provided a platform to capture spatial and temporal dynamics of individual mRNAs in vivo .…”

“…For instance, in the case of mRNA export, while experimental approaches such as oligo(dT) in situ hybridization assay or single molecule fluorescence in situ hybridization (smFISH) can primarily perform bulk measurements to determine the intracellular distribution of RNA, they cannot capture highresolution in vivo dynamics. [43] Recent advancements in RNA labeling as well as imaging methods, however, have provided a platform to capture spatial and temporal dynamics of individual mRNAs in vivo. [44][45][46][47] Similarly, in contrary to ODEs or even stochastic methods like Gillespie, individual particles could be tracked in ABMs over the course of simulation.…”

The RNA export factor Mex67 functions as a mobile nucleoporin

“…Transport is mediated by transport factors that guide the mRNA through nuclear pore complexes (NPCs), which are highly specialized transport channels embedded in the nuclear envelope. Although the mRNA export machinery is highly conserved from yeast to humans, the molecular mechanisms that ensures directional mRNA transport are not well understood (Heinrich et al, 2017;Kohler and Hurt, 2007).…”