The YTH (YT521-B homology) domain was identified by sequence comparison and is found in 174 different proteins expressed in eukaryotes. It is characterized by 14 invariant residues within an ␣-helix/␤-sheet structure. Here we show that the YTH domain is a novel RNA binding domain that binds to a short, degenerated, single-stranded RNA sequence motif. The presence of the binding motif in alternative exons is necessary for YT521-B to directly influence splice site selection in vivo. Array analyses demonstrate that YT521-B predominantly regulates vertebrate-specific exons. An NMR titration experiment identified the binding surface for single-stranded RNA on the YTH domain. Structural analyses indicate that the YTH domain is related to the pseudouridine synthase and archaeosine transglycosylase (PUA) domain. Our data show that the YTH domain conveys RNA binding ability to a new class of proteins that are found in all eukaryotic organisms.The binding of proteins to RNA is a fundamental aspect of biology that interferes with most aspects of gene expression and cellular functions. The presence of various binding motifs defines the group of RNA binding proteins (1). Commonly found RNA binding domains include the RNA recognition motif (RRM), 3 the double-stranded RNA binding domain, the Piwi Argonaut and Zwille domain, and the heterogeneous nuclear ribonucleoprotein K homology domain. The most prominent RNA binding domain is the RRM that is found in ϳ2% of human proteins (2). The RRM is composed of two consensus sequences RNP2 and RNP1 that contain aromatic residues important for RNA binding. In other RNA binding motifs, such as the PUA (pseudouridine synthase and archaeosine transglycosylase) and OB-fold (oligonucleotide/oligosaccaride binding fold), the RNA interacts with the ␤-sheets that form pseudobarrels (3). The general composition of the PUA domain is reminiscent of the OB-fold, a nucleic acid binding motif that displays only a low degree of sequence similarity between its members. The OB-fold consists of two three-stranded antiparallel ␤-sheets, where strand 1 is shared by both sheets. The individual ␤-sheets can be separated by protein parts of different length, which makes the identification based on primary structure difficult (4). The ␤-sheets in the PUA and OB-folds form a ligand binding surface that can bind to nucleic acids through aromatic stacking, hydrogen bonding, as well as polar and hydrophobic interactions. The so-far unexplained RNA binding activities of proteins such as apontic (5) demonstrate that not all RNA binding domains have been described.One of the potentially new RNA binding domains is the YTH (YT521 homology) domain. The YTH domain is highly conserved during evolution and was identified by comparing all known protein sequences with the splicing factor YT521-B (6). The domain is found only in eukaryotes and is abundant in plants. The YTH domain can be between 100 and 150 amino acids in size and is characterized by 14 invariant and 19 highly conserved residues. It is predicted to contain ...

MODOMICS, a database devoted to the systems biology of RNA modification, has been subjected to substantial improvements. It provides comprehensive information on the chemical structure of modified nucleosides, pathways of their biosynthesis, sequences of RNAs containing these modifications and RNA-modifying enzymes. MODOMICS also provides cross-references to other databases and to literature. In addition to the previously available manually curated tRNA sequences from a few model organisms, we have now included additional tRNAs and rRNAs, and all RNAs with 3D structures in the Nucleic Acid Database, in which modified nucleosides are present. In total, 3460 modified bases in RNA sequences of different organisms have been annotated. New RNA-modifying enzymes have been also added. The current collection of enzymes includes mainly proteins for the model organisms Escherichia coli and Saccharomyces cerevisiae, and is currently being expanded to include proteins from other organisms, in particular Archaea and Homo sapiens. For enzymes with known structures, links are provided to the corresponding Protein Data Bank entries, while for many others homology models have been created. Many new options for database searching and querying have been included. MODOMICS can be accessed at http://genesilico.pl/modomics.