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Open Access Research article

A tandem sequence motif acts as a distance-dependent enhancer in a set of genes involved in translation by binding the proteins NonO and SFPQ

Stefan Roepcke14, Silke Stahlberg23, Holger Klein1, Marcel H Schulz1, Lars Theobald2, Sabrina Gohlke2, Martin Vingron1 and Diego J Walther2*

Author Affiliations

1 Department of Computational Molecular Biology, Max Planck Institute for Molecular Genetics, Berlin, Germany

2 Department of Human Molecular Genetics, Max Planck Institute for Molecular Genetics, Berlin, Germany

3 Department of Biology, Chemistry, and Pharmacy, Free University Berlin, 14195 Berlin, Germany

4 Nycomed GmbH, Konstanz, Germany

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BMC Genomics 2011, 12:624  doi:10.1186/1471-2164-12-624

Published: 20 December 2011

Abstract

Background

Bioinformatic analyses of expression control sequences in promoters of co-expressed or functionally related genes enable the discovery of common regulatory sequence motifs that might be involved in co-ordinated gene expression. By studying promoter sequences of the human ribosomal protein genes we recently identified a novel highly specific Localized Tandem Sequence Motif (LTSM). In this work we sought to identify additional genes and LTSM-binding proteins to elucidate potential regulatory mechanisms.

Results

Genome-wide analyses allowed finding a considerable number of additional LTSM-positive genes, the products of which are involved in translation, among them, translation initiation and elongation factors, and 5S rRNA. Electromobility shift assays then showed specific signals demonstrating the binding of protein complexes to LTSM in ribosomal protein gene promoters. Pull-down assays with LTSM-containing oligonucleotides and subsequent mass spectrometric analysis identified the related multifunctional nucleotide binding proteins NonO and SFPQ in the binding complex. Functional characterization then revealed that LTSM enhances the transcriptional activity of the promoters in dependency of the distance from the transcription start site.

Conclusions

Our data demonstrate the power of bioinformatic analyses for the identification of biologically relevant sequence motifs. LTSM and the here found LTSM-binding proteins NonO and SFPQ were discovered through a synergistic combination of bioinformatic and biochemical methods and are regulators of the expression of a set of genes of the translational apparatus in a distance-dependent manner.