Identification of a distinct class of cytoskeleton-associated mRNAs using microarray technology

Amy Brock,Sui Huang,Donald E Ingber

doi:10.1186/1471-2121-4-6

Abstract

BackgroundInteractions between mRNA and the cytoskeleton are critical for the localization of a number of transcripts in eukaryotic somatic cells. To characterize additional transcripts that may be subject to this form of regulation, we developed a two-step approach that utilizes biochemical fractionation of cells to isolate transcripts from different subcellular compartments followed by microarray analysis to examine and compare these subpopulations of transcripts in a massively-parallel manner.ResultsUsing this approach, mRNA was extracted from the cytoskeleton-rich and the cytosolic fractions of the promyelocytic HL-60 cell line. We identify a subset of 22 transcripts that are significantly enriched in the cytoskeleton-associated population. The majority of these encode structural proteins and/or proteins known to interact with elements of the cytoskeleton. Localization required an intact actin cytoskeleton and was largely conserved upon differentiation of precursor HL-60 cells to a macrophage-like phenotype.ConclusionsWe conclude that the association of transcripts with the actin cytoskeleton in somatic cells may be a critical post-transcriptional regulatory event that controls a larger class of genes than has previously been recognized.

Highlights

Interactions between mRNA and the cytoskeleton are critical for the localization of a number of transcripts in eukaryotic somatic cells
We conclude that the association of transcripts with the actin cytoskeleton in somatic cells may be a critical post-transcriptional regulatory event that controls a larger class of genes than has previously been recognized
Examples include the polarized localization of oocyte mRNAs which is crucial for the establishment axis formation in the embryo [1,2,3], the targeting of specific mRNAs to the synapses of nerve cells [4,5], centrosomal segregation of mRNAs in the mollusk embryo which results in asymmetric inheritance [6] and the localization of β-actin mRNA to sites of active actin polymerization at the leading edge of motile fibroblasts [7,8]

Summary

Introduction

Interactions between mRNA and the cytoskeleton are critical for the localization of a number of transcripts in eukaryotic somatic cells. Examples include the polarized localization of oocyte mRNAs which is crucial for the establishment axis formation in the embryo [1,2,3], the targeting of specific mRNAs to the synapses of nerve cells [4,5], centrosomal segregation of mRNAs in the mollusk embryo which results in asymmetric inheritance [6] and the localization of β-actin mRNA to sites of active actin polymerization at the leading edge of motile fibroblasts [7,8] In each of these cases, mRNA targeting is mediated by the cytoskeleton. Replacing the 3' UTR of the mRNA for the intermediate filament protein, vimentin, with the β-actin 3'UTR sequence results in mislocalization of vimentin transcript, altered fibroblast morphology, and impaired motility [15]

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Discussion

Conclusion