title: Experimental characterization of the human non-sequence-specific nucleic acid interactome.
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.
authors.forename: Gerhard
authors.initials: G
authors.lastname: Dürnberger
authors.forename: Tilmann
authors.initials: T
authors.lastname: Bürckstümmer
authors.forename: Kilian
authors.initials: K
authors.lastname: Huber
authors.forename: Roberto
authors.initials: R
authors.lastname: Giambruno
authors.forename: Tobias
authors.initials: T
authors.lastname: Doerks
authors.forename: Evren
authors.initials: E
authors.lastname: Karayel
authors.forename: Thomas R
authors.initials: TR
authors.lastname: Burkard
authors.forename: Ines
authors.initials: I
authors.lastname: Kaupe
authors.forename: André C
authors.initials: AC
authors.lastname: Müller
authors.forename: Andreas
authors.initials: A
authors.lastname: Schönegger
authors.forename: Gerhard F
authors.initials: GF
authors.lastname: Ecker
authors.forename: Hans
authors.initials: H
authors.lastname: Lohninger
authors.forename: Peer
authors.initials: P
authors.lastname: Bork
authors.forename: Keiryn L
authors.initials: KL
authors.lastname: Bennett
authors.forename: Giulio
authors.initials: G
authors.lastname: Superti-Furga
authors.forename: Jacques
authors.initials: J
authors.lastname: Colinge
mesh_terms: D001483:Base Sequence; D002460:Cell Line; D030562:Databases, Protein; D004194:Disease; D006801:Humans; D009696:Nucleic Acids / Q000378:metabolism*; D011485:Protein Binding; D025941:Protein Interaction Mapping; D017434:Protein Structure, Tertiary; D015203:Reproducibility of Results; D013379:Substrate Specificity
chemical_list: D009696:Nucleic Acids
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