The global identification of sequence-specific NABPs has so far been achieved through various approaches, such as chromatin immunoprecipitation (ChIP) in combination with either microarrays (ChIP-chip) or sequencing technology (ChIP-seq) as well as protein-binding microarrays and protein arrays. Transcription factors that recognize specific DNA motifs constitute only part of the nucleic acid-binding proteins (NABPs), which also include less sequence-specific interactors. Interactions between proteins and nucleic acids play a pivotal role in a wide variety of essential biological processes, such as transcription, translation, splicing, or chromatin remodeling, defects in which can cause multiple diseases. 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. 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. We could assign specific affinities for sub-types of nucleic acid probes to 219 distinct proteins and individual domains. The study identified 746 high-confidence direct binders, 139 of which were novel and 237 devoid of previous experimental evidence. The proteins were profiled for their binding preferences to the different general types of nucleic acids. 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. 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.

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.

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.

Nucleic acid sequence analysis