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Transcriptome-based systematic identification of extracellular matrix proteins.

ABSTRACT: Extracellular matrix (ECM), which provides critical scaffolds for all adhesive cells, regulates proliferation, differentiation, and apoptosis. Different cell types employ customized ECMs, which are thought to play important roles in the generation of so-called niches that contribute to cell-specific functions. The molecular entities of these customized ECMs, however, have not been elucidated. Here, we describe a strategy for transcriptome-wide identification of ECM proteins based on computational screening of >60,000 full-length mouse cDNAs for secreted proteins, followed by in vitro functional assays. These assays screened the candidate proteins for ECM-assembling activities, interactions with other ECM molecules, modifications with glycosaminoglycans, and cell-adhesive activities, and were then complemented with immunohistochemical analysis. We identified 16 ECM proteins, of which seven were localized in basement membrane (BM) zones. The identification of these previously unknown BM proteins allowed us to construct a body map of BM proteins, which represents the comprehensive immunohistochemistry-based expression profiles of the tissue-specific customization of BMs.

SUBMITTER: Manabe R

PROVIDER: S-EPMC2529034 | biostudies-literature | 2008 Sep

REPOSITORIES: biostudies-literature

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Transcriptome-based systematic identification of extracellular matrix proteins.

Manabe Ri-ichiroh R Tsutsui Ko K Yamada Tomiko T Kimura Mina M Nakano Itsuko I Shimono Chisei C Sanzen Noriko N Furutani Yutaka Y Fukuda Tomohiko T Oguri Yasuko Y Shimamoto Keiko K Kiyozumi Daiji D Sato Yuya Y Sado Yoshikazu Y Senoo Haruki H Yamashina Shohei S Fukuda Shiro S Kawai Jun J Sugiura Nobuo N Kimata Koji K Hayashizaki Yoshihide Y Sekiguchi Kiyotoshi K

Proceedings of the National Academy of Sciences of the United States of America 20080829 35

Extracellular matrix (ECM), which provides critical scaffolds for all adhesive cells, regulates proliferation, differentiation, and apoptosis. Different cell types employ customized ECMs, which are thought to play important roles in the generation of so-called niches that contribute to cell-specific functions. The molecular entities of these customized ECMs, however, have not been elucidated. Here, we describe a strategy for transcriptome-wide identification of ECM proteins based on computationa ...[more]

PMID: 18757743

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Transcriptome-based systematic identification of extracellular matrix proteins.

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Transcriptome-based systematic identification of extracellular matrix proteins.

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