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Open Access Research article

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

Amy Brock, Sui Huang and Donald E Ingber*

Author Affiliations

Vascular Biology Program, Departments of Pathology and Surgery, Harvard Medical School and Children's Hospital, Enders 1007, 300 Longwood Ave, Boston, MA 02115, USA

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BMC Cell Biology 2003, 4:6  doi:10.1186/1471-2121-4-6

Published: 8 July 2003

Abstract

Background

Interactions 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.

Results

Using 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.

Conclusions

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.

Keywords:
mRNA localization; gene expression; gene profiling; actin; cytoskeleton; post-transcriptional control; subcellular localization