Online citations, reference lists, and bibliographies.
Please confirm you are human
(Sign Up for free to never see this)
← Back to Search

Large-scale Identification Of Secreted And Membrane-associated Gene Products Using DNA Microarrays

M. Diehn, M. Eisen, D. Botstein, P. Brown
Published 2000 · Biology, Medicine

Save to my Library
Download PDF
Analyze on Scholarcy
Membrane-associated and secreted proteins are an important class of proteins and include receptors, transporters, adhesion molecules, hormones and cytokines. Although algorithms have been developed to recognize potential amino-terminal membrane-targeting signals or transmembrane domains in protein sequences, their accuracy is limited and they require knowledge of the entire coding sequence, including the N terminus, which is not currently available for most of the genes in most organisms, including human. Several experimental approaches for identifying secreted and membrane proteins have been described, but none have taken a comprehensive genomic approach. Furthermore, none of these methods allow easy classification of clones from arrayed cDNA libraries, for which large-scale gene-expression data are now becoming available through the use of DNA microarrays. We describe here a rapid and efficient method for identifying genes that encode secreted or membrane proteins. mRNA species bound to membrane-associated polysomes were separated from other mRNAs by sedimentation equilibrium or sedimentation velocity. The distribution of individual transcripts in the ‘membrane-bound’ and ‘cytosolic’ fractions was quantitated for thousands of genes by hybridization to DNA microarrays. Transcripts known to encode secreted or membrane proteins were enriched in the membrane-bound fractions, whereas those known to encode cytoplasmic proteins were enriched in the fractions containing mRNAs associated with free and cytoplasmic ribosomes. On this basis, we identified over 275 human genes and 285 yeast genes that are likely to encode previously unrecognized secreted or membrane proteins.
This paper references
Translational attenuation mediated by an mRNA intron
R. Chapman (1997)
Distinctive gene expression patterns in human mammary epithelial cells and breast cancers.
C. Perou (1999)
A single mRNA, transcribed from an alternative, erythroid-specific, promoter, codes for two non-myristylated forms of NADH-cytochrome b5 reductase
G. Pietrini (1992)
Signal sequence trap: a cloning strategy for secreted proteins and type I membrane proteins.
K. Tashiro (1993)
Preparation of cDNA from single cells and subcellular regions.
J. E. Kacharmina (1999)
Isolation of messenger RNA from membrane-bound polysomes.
B. M. Mechler (1987)
Selection for genes encoding secreted proteins and receptors.
R. D. Klein (1996)
A powerful new technique for isolating genes encoding cell surface antigens using retroviral expression cloning.
A. Zannettino (1996)
Membrane-bound ribosomes of myeloma cells. IV. mRNA complexity of free and membrane-bound polysomes
B. Mechler (1981)
Structure and function of rat liver polysome populations. I. Complexity, frequency distribution, and degree of uniqueness of free and membrane-bound polysomal polyadenylate-containing RNA populations
M. Mueckler (1981)
A high throughput screen to identify secreted and transmembrane proteins involved in Drosophila embryogenesis.
C. Kopczynski (1998)
Evidence for Colocalization of Calcineurin and Calcium Channels in Dorsal Root Ganglion Neurons
E. Lukyanetz (1997)
Comprehensive identification of cell cycle-regulated genes of the yeast Saccharomyces cerevisiae by microarray hybridization.
P. Spellman (1998)
DNA arrays for analysis of gene expression.
M. Eisen (1999)
Targeting proteins to mitochondria: is there a role for mRNA localization?
R. Lightowlers (1996)
The transcriptional program in the response of human fibroblasts to serum.
V. R. Iyer (1999)
Actin-dependent localization of an RNA encoding a cell-fate determinant in yeast
P. Takizawa (1997)
mRNA encoding the beta-subunit of the mitochondrial F1-ATPase complex is a localized mRNA in rat hepatocytes.
G. Egea (1997)
Exploring the metabolic and genetic control of gene expression on a genomic scale.
J. DeRisi (1997)
Getting started with yeast.
F. Sherman (2002)
Machine learning approaches for the prediction of signal peptides and other protein sorting signals.
H. Nielsen (1999)
Reliable method to prepare RNA from free and membrane-bound polysomes from different yeast species.
R. Stoltenburg (1995)
The Transmembrane Kinase Ire1p Is a Site-Specific Endonuclease That Initiates mRNA Splicing in the Unfolded Protein Response
C. Sidrauski (1997)
A simple method for displaying the hydropathic character of a protein.
J. Kyte (1982)
Identification of prokaryotic and eukaryotic signal peptides and prediction of their cleavage sites.
H. Nielsen (1997)
Cloning of cell-specific secreted and surface proteins by subtractive antibody screening
P. Scherer (1998)

This paper is referenced by
Chapter 34 – Microarray Analysis of Stem Cells and Differentiation
H. Chang (2013)
Proteomics in Genomeland
S. Fields (2001)
Enhancement of Procollagen Biosynthesis by p180 through Augmented Ribosome Association on the Endoplasmic Reticulum in Response to Stimulated Secretion
T. Ueno (2010)
Translational profiling: the genome-wide measure of the nascent proteome.
T. Beilharz (2004)
The role of the budding yeast RNA-binding proteins Khd1p and Loc1p in mRNA targeting
Balaji T. Moorthy (2014)
Live-cell mapping of organelle-associated RNAs via proximity biotinylation combined with protein-RNA crosslinking
Pornchai Kaewsapsak (2017)
Polypeptide, acides nucléiques le codant, et leur utilisation pour le diagnostic du cancer
K. P. Baker (2001)
DNA microarrays for expression profiling.
T. Hughes (2001)
Identification of MMP Substrates in the Mammary Gland
Gerrit J. P. Dijkgraaf (2004)
A Molecular Profile of the Endothelial Cell Response to Ionizing Radiation
H. Himburg (2016)
Membrane-bound lecithin-retinol acyltransferase.
R. Rando (2002)
Basal Cytokeratins and HER-2 Oncogene in Breast Cancer
M. Jumppanen (2007)
Analysis of mRNA with microsomal fractionation using a SAGE-based DNA microarray system facilitates identification of the genes encoding secretory proteins.
N. Toyoda (2003)
CeFra-seq reveals broad asymmetric mRNA and noncoding RNA distribution profiles in Drosophila and human cells.
Louis Philip Benoit Bouvrette (2018)
AMADA: analysis of microarray data
X. Xia (2001)
Comprehensive gene expression analysis by transcript profiling.
J. Donson (2002)
Seven years of yeast microarray analysis
G. Sherlock (2005)
Coordination of Endoplasmic Reticulum and mRNA Localization to the Yeast Bud
M. Schmid (2006)
Introduction Strategies in Drug Discovery and Evaluation
H. Vogel (2007)
Bioinformatics and In Silico 2D Gel Electrophoresis
X. Xia (2018)
Proteome Expression: The Subcellular Organisation of Protein Synthesis
Jack C.-C. Hsu (2018)
Diversity and selectivity in mRNA translation on the endoplasmic reticulum
D. W. Reid (2015)
A systems view of mRNP biology.
Haley Hieronymus (2004)
Analysis of Taste and Aroma
J. F. Jackson (2002)
Gene and Protein Expression in Human Gliomas
Oscar Persson (2008)
Disentangling biological signaling networks by dynamic coupling of signaling lipids to modifying enzymes.
Raymond D Blind (2014)
Kinectin-dependent Assembly of Translation Elongation Factor-1 Complex on Endoplasmic Reticulum Regulates Protein Synthesis*
L. Ong (2006)
Challenges in developing a molecular characterization of cancer.
J. Pollack (2002)
Gene trap mutagenesis in embryonic stem cells.
W. Chen (2003)
Addressing mRNAs to the ER: cis sequences act up!
J. Kraut-Cohen (2010)
mRNA transport meets membrane traffic.
R. Jansen (2014)
Genomics for applied microbiology.
W. Nierman (2002)
See more
Semantic Scholar Logo Some data provided by SemanticScholar