Identification of a distinct class of cytoskeleton-associated mRNAs using microarray technology.
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.
Brock
Amy
A
Vascular Biology Program, Department of Pathology, Harvard Medical School and Children's Hospital, Enders 1007, 300 Longwood Ave, Boston, MA 02115, USA. amybrock@fas.harvard.edu
Huang
Sui
S
Ingber
Donald E
DE
D002458:Cell Fractionation / Q000379:methods; D045744:Cell Line, Tumor; D003599:Cytoskeleton / Q000145:classification* / Q000235:genetics; D003600:Cytosol / Q000737:chemistry; D020869:Gene Expression Profiling / Q000379:methods; D015972:Gene Expression Regulation, Neoplastic; D052138:Genes, Neoplasm; D018922:HL-60 Cells / Q000737:chemistry; D006801:Humans; D020411:Oligonucleotide Array Sequence Analysis / Q000379:methods*; D012333:RNA, Messenger / Q000145:classification* / Q000235:genetics
D012333:RNA, Messenger