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Experimental characterization of the human non-sequence-specific nucleic acid interactome

Gerhard Dürnberger12, Tilmann Bürckstümmer13, Kilian Huber1, Roberto Giambruno1, Tobias Doerks4, Evren Karayel1, Thomas R Burkard15, Ines Kaupe16, André C Müller1, Andreas Schönegger1, Gerhard F Ecker7, Hans Lohninger8, Peer Bork4, Keiryn L Bennett1, Giulio Superti-Furga1* and Jacques Colinge1*

Author affiliations

1 CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Lazarettgasse 14, AKH-BT 25.3, 1090 Vienna, Austria

2 Current address: IMP - Research Institute of Molecular Pathology, Dr. Bohr-Gasse 7, 1030 Vienna, Austria

3 Current address: Haplogen GmbH, Campus Vienna Biocenter 5, Dr. Bohr-Gasse 7, 1030 Vienna, Austria

4 Structural and Computational Biology Unit, EMBL - European Molecular Biology Laboratory, Meyerhofstraße 1, 69117 Heidelberg, Germany

5 Current address: IMP/IMBA Bioinformatics Department, Dr. Bohr-Gasse 7, 1030 Vienna, Austria

6 Current address: Boehringer Ingelheim RCV GmbH & Co KG, Doktor-Böhringer-Gasse 5-11, 1121 Vienna, Austria

7 Department of Medicinal Chemistry, University of Vienna, Althanstraße 14, 1090 Vienna, Austria

8 Institute of Chemical Technologies and Analytics, Vienna University of Technology, Getreidemarkt 9/164, 1060 Vienna, Austria

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Citation and License

Genome Biology 2013, 14:R81  doi:10.1186/gb-2013-14-7-r81

Published: 31 July 2013

Abstract

Background

The interactions between proteins and nucleic acids have a fundamental function in many biological processes, including gene transcription, RNA homeostasis, protein translation and pathogen sensing for innate immunity. While our knowledge of the ensemble of proteins that bind individual mRNAs in mammalian cells has been greatly augmented by recent surveys, no systematic study on the non-sequence-specific engagement of native human proteins with various types of nucleic acids has been reported.

Results

We designed an experimental approach to achieve broad coverage of the non-sequence-specific RNA and DNA binding space, including methylated cytosine, and tested for interaction potential with the human proteome. We used 25 rationally designed nucleic acid probes in an affinity purification mass spectrometry and bioinformatics workflow to identify proteins from whole cell extracts of three different human cell lines. The proteins were profiled for their binding preferences to the different general types of nucleic acids. The study identified 746 high-confidence direct binders, 139 of which were novel and 237 devoid of previous experimental evidence. We could assign specific affinities for sub-types of nucleic acid probes to 219 distinct proteins and individual domains. The evolutionarily conserved protein YB-1, previously associated with cancer and drug resistance, was shown to bind methylated cytosine preferentially, potentially conferring upon YB-1 an epigenetics-related function.

Conclusions

The dataset described here represents a rich resource of experimentally determined nucleic acid-binding proteins, and our methodology has great potential for further exploration of the interface between the protein and nucleic acid realms.