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
Share
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
10.1016/S0960-9822(06)00373-3
Translational attenuation mediated by an mRNA intron
R. Chapman (1997)
10.1073/PNAS.96.16.9212
Distinctive gene expression patterns in human mammary epithelial cells and breast cancers.
C. Perou (1999)
10.1083/JCB.117.5.975
A single mRNA, transcribed from an alternative, erythroid-specific, promoter, codes for two non-myristylated forms of NADH-cytochrome b5 reductase
G. Pietrini (1992)
10.1126/SCIENCE.8342023
Signal sequence trap: a cloning strategy for secreted proteins and type I membrane proteins.
K. Tashiro (1993)
10.1016/S0076-6879(99)03003-7
Preparation of cDNA from single cells and subcellular regions.
J. E. Kacharmina (1999)
10.1016/0076-6879(87)52026-2
Isolation of messenger RNA from membrane-bound polysomes.
B. M. Mechler (1987)
10.1073/PNAS.93.14.7108
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)
10.1083/JCB.88.1.29
Membrane-bound ribosomes of myeloma cells. IV. mRNA complexity of free and membrane-bound polysomes
B. Mechler (1981)
10.1083/JCB.90.2.495
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)
10.1073/PNAS.95.17.9973
A high throughput screen to identify secreted and transmembrane proteins involved in Drosophila embryogenesis.
C. Kopczynski (1998)
10.1016/S0306-4522(97)00020-1
Evidence for Colocalization of Calcineurin and Calcium Channels in Dorsal Root Ganglion Neurons
E. Lukyanetz (1997)
10.1091/MBC.9.12.3273
Comprehensive identification of cell cycle-regulated genes of the yeast Saccharomyces cerevisiae by microarray hybridization.
P. Spellman (1998)
10.1016/S0076-6879(99)03014-1
DNA arrays for analysis of gene expression.
M. Eisen (1999)
10.1042/BST0240527
Targeting proteins to mitochondria: is there a role for mRNA localization?
R. Lightowlers (1996)
10.1126/SCIENCE.283.5398.83
The transcriptional program in the response of human fibroblasts to serum.
V. R. Iyer (1999)
10.1038/38015
Actin-dependent localization of an RNA encoding a cell-fate determinant in yeast
P. Takizawa (1997)
10.1042/BJ3220557
mRNA encoding the beta-subunit of the mitochondrial F1-ATPase complex is a localized mRNA in rat hepatocytes.
G. Egea (1997)
10.1126/SCIENCE.278.5338.680
Exploring the metabolic and genetic control of gene expression on a genomic scale.
J. DeRisi (1997)
10.1016/0076-6879(91)94004-v
Getting started with yeast.
F. Sherman (2002)
10.1093/PROTEIN/12.1.3
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)
10.1016/S0092-8674(00)80369-4
The Transmembrane Kinase Ire1p Is a Site-Specific Endonuclease That Initiates mRNA Splicing in the Unfolded Protein Response
C. Sidrauski (1997)
10.1016/0022-2836(82)90515-0
A simple method for displaying the hydropathic character of a protein.
J. Kyte (1982)
10.1093/PROTEIN/10.1.1
Identification of prokaryotic and eukaryotic signal peptides and prediction of their cleavage sites.
H. Nielsen (1997)
10.1038/NBT0698-581
Cloning of cell-specific secreted and surface proteins by subtractive antibody screening
P. Scherer (1998)



This paper is referenced by
10.1016/B978-0-12-385942-6.00034-2
Chapter 34 – Microarray Analysis of Stem Cells and Differentiation
H. Chang (2013)
10.1126/SCIENCE.291.5507.1221
Proteomics in Genomeland
S. Fields (2001)
10.1074/jbc.M109.094607
Enhancement of Procollagen Biosynthesis by p180 through Augmented Ribosome Association on the Endoplasmic Reticulum in Response to Stimulated Secretion
T. Ueno (2010)
10.1093/BFGP/3.2.103
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)
10.7554/eLife.29224
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)
10.1016/S1367-5931(00)00163-0
DNA microarrays for expression profiling.
T. Hughes (2001)
10.21236/ada443693
Identification of MMP Substrates in the Mammary Gland
Gerrit J. P. Dijkgraaf (2004)
10.1667/RR14444.1
A Molecular Profile of the Endothelial Cell Response to Ionizing Radiation
H. Himburg (2016)
10.1006/BBRC.2001.2021
Membrane-bound lecithin-retinol acyltransferase.
R. Rando (2002)
Basal Cytokeratins and HER-2 Oncogene in Breast Cancer
M. Jumppanen (2007)
10.1101/GR.709603
Analysis of mRNA with microsomal fractionation using a SAGE-based DNA microarray system facilitates identification of the genes encoding secretory proteins.
N. Toyoda (2003)
10.1261/rna.063172.117
CeFra-seq reveals broad asymmetric mRNA and noncoding RNA distribution profiles in Drosophila and human cells.
Louis Philip Benoit Bouvrette (2018)
10.1093/bioinformatics/17.6.569
AMADA: analysis of microarray data
X. Xia (2001)
10.1007/978-94-010-0448-0_6
Comprehensive gene expression analysis by transcript profiling.
J. Donson (2002)
10.1002/047001153X.G208312
Seven years of yeast microarray analysis
G. Sherlock (2005)
10.1016/j.cub.2006.06.025
Coordination of Endoplasmic Reticulum and mRNA Localization to the Yeast Bud
M. Schmid (2006)
10.1007/978-3-540-70995-4_1
Introduction Strategies in Drug Discovery and Evaluation
H. Vogel (2007)
10.1007/978-3-319-90684-3_18
Bioinformatics and In Silico 2D Gel Electrophoresis
X. Xia (2018)
10.1002/9780470015902.A0005718
Proteome Expression: The Subcellular Organisation of Protein Synthesis
Jack C.-C. Hsu (2018)
10.1038/nrm3958
Diversity and selectivity in mRNA translation on the endoplasmic reticulum
D. W. Reid (2015)
10.1101/GAD.1256904
A systems view of mRNP biology.
Haley Hieronymus (2004)
10.1007/978-3-662-04857-3
Analysis of Taste and Aroma
J. F. Jackson (2002)
Gene and Protein Expression in Human Gliomas
Oscar Persson (2008)
10.1016/j.jbior.2013.09.015
Disentangling biological signaling networks by dynamic coupling of signaling lipids to modifying enzymes.
Raymond D Blind (2014)
10.1074/jbc.M607555200
Kinectin-dependent Assembly of Translation Elongation Factor-1 Complex on Endoplasmic Reticulum Regulates Protein Synthesis*
L. Ong (2006)
10.1053/SONC.2002.32903
Challenges in developing a molecular characterization of cancer.
J. Pollack (2002)
10.1016/S0076-6879(03)65026-3
Gene trap mutagenesis in embryonic stem cells.
W. Chen (2003)
10.1016/j.tibs.2010.02.006
Addressing mRNAs to the ER: cis sequences act up!
J. Kraut-Cohen (2010)
10.1016/j.tig.2014.07.002
mRNA transport meets membrane traffic.
R. Jansen (2014)
10.1016/S0065-2164(02)51007-8
Genomics for applied microbiology.
W. Nierman (2002)
See more
Semantic Scholar Logo Some data provided by SemanticScholar