The YTH Domain Is a Novel RNA Binding Domain

Abstract

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 ...

Molecular basis for the recognition of methylated adenines in RNA by the eukaryotic YTH domain

“…S4). Other structural homologs, as identified in an earlier study based on YTHDC1 (13), include the DUF55 domain of human thymocyte nuclear protein 1 (15) and the EVE domain that is found in a collection of prokaryotic proteins (16) such as Pyrococcus horikoshii protein PH1033 (17), Agrobacterium tumefaciens Atu2648 (16), and a Leishmania major protein (18) (Fig. S4), with Z scores between 9 and 13 from the program DaliLite (19) and sequence identities between 10 and 18%.…”

“…YTHDC1 binds a degenerate unmethylated RNA sequence (13), which does not have similarity to the G(m 6 A)C consensus. The interaction between its YTH domain and an unmethylated RNA was studied by chemical-shift perturbation (13), but the structure of a complex is not available. The molecular mechanism for how the YTH domain recognizes the m 6 A modification is not known.…”

N6‐methyladenosine modification in mRNA: machinery, function and implications for health and diseases

“…The pull-down analyses revealed two novel m 6 A-binding proteins, which were subsequently identified by mass spectrometry as YTHDF2 and YTHDF3 [26]. Both of these proteins were shown to have novel RNA-binding YTH domains [85]. Subsequent studies revealed that the human genome contains at least three additional proteins: YTHDF1, YTHDC1, and YTHDC2.…”

Structure of the YTH domain of human YTHDF2 in complex with an m6A mononucleotide reveals an aromatic cage for m6A recognition

“…Two of the three residues (Trp432 and Trp486) in YTHDF2 that form the aromatic cage are completely conserved in YTH domain-containing proteins ( Figure 1E). The third aromatic cage residue (Trp491 in YTHDF2) is replaced by Tyr237 in PHO92, the only known YTH domain-containing protein in Saccharomyces cerevisiae (S. cerevisiae) [9], and a leucine residue in YTHDC1/2 which have been reported to bind to a degenerate unmethylated RNA sequence [10] (Figure 1E). During the preparation of this manuscript, structures of the YTH domains of human YTHDC1 [11] and ZrMRB1 (the ortholog of S. cerevisiae PHO92 in Zygosaccharomyces rouxii) [12] were reported.…”