Research Collection
Journal Article
Solution structure of the YTH domain in complex with N6- methyladenosine RNA A reader of methylated RNA
Author(s): Theler, Dominik; Dominguez, Cyril; Blatter, Markus; Boudet, Julien; Allain, Frédéric H.-T.
Publication Date: 2014-12-16
Permanent Link: https://doi.org/10.3929/ethz-b-000098302
Originally published in: Nucleic Acids Research 42(22), http://doi.org/10.1093/nar/gku1116
Rights / License: Creative Commons Attribution 4.0 International
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ETH Library Published online 11 November 2014 Nucleic Acids Research, 2014, Vol. 42, No. 22 13911–13919 doi: 10.1093/nar/gku1116 Solution structure of the YTH domain in complex with N6-methyladenosine RNA: a reader of methylated RNA Dominik Theler, Cyril Dominguez, Markus Blatter, Julien Boudet and Fred´ eric´ H.-T. Allain*
Institute of Molecular Biology and Biophysics, Eidgenossische¨ Technische Hochschule (ETH) Zurich, 8093 Zurich, Switzerland Downloaded from https://academic.oup.com/nar/article-abstract/42/22/13911/2411064 by ETH Zürich user on 04 April 2019
Received September 22, 2014; Revised October 17, 2014; Accepted October 23, 2014
ABSTRACT purines). Two studies used RNA immunoprecipitation and 6 mass spectrometry to identify proteins binding selectively N A methylation is the most abundant RNA modifica- to the m6A-containing RNA sequences (7,11). Two out tion occurring within messenger RNA. Impairment of of three top confidence category proteins enriched in the methylase or demethylase functions are associated pull-downs with the methylated RNA from HepG2 cell with severe phenotypes and diseases in several or- lysates contained one YTH domain (YTHDF2, YTHDF3) ganisms. Beside writer and eraser enzymes of this (7). The top candidate from meiotic yeast lysates was the dynamic RNA epigenetic modification, reader pro- YTH domain containing protein MRB1 (11). Full-length teins that recognize this modification are involved in proteins YTHDF1, which also contains a YTH domain, numerous cellular processes. Although the precise YTHDF2 and YTHDF3 were later shown by gel shifts to characterization of these reader proteins remains un- have increased affinities for the methylated compared to known, preliminary data showed that most potential the non-methylated form of the same RNA target sequence (12). This suggested that YTH-containing proteins, whose reader proteins contained a conserved YT521-B ho- functions are generally unknown, could act as m6A readers. mology (YTH) domain. Here we define the YTH do- 6 The first protein containing a YTH domain, which was main of rat YT521-B as a N -methylated adenosine functionally characterized, is the Rattus Norvegicus protein reader domain and report its solution structure in YT521-B (alternative name YTHDC1) (Figure 1A), which complex with a N6-methylated RNA. The structure re- was identified in two yeast two hybrid studies aimed at iden- veals a binding preference for NGANNN RNA hex- tifying novel alternative splicing regulators using the SR- amer and a deep hydrophobic cleft for m6A recogni- like protein Tra2 as a bait (14,15). The protein was shown tion. These findings establish a molecular function to be able to influence alternative splicing but lacked a pre- for YTH domains as m6A reader domains and should viously known RNA-binding domain. Sequence alignment guide further studies into the biological functions of searches identified a conserved domain, which was termed YTH-containing proteins in m6A recognition. YTH domain for YT521-B homology domain (16). Subse- quently, we have shown that the YTH domain of YT521-B was indeed a RNA-binding domain with a very degener- INTRODUCTION ate sequence-specificity17 ( ). A more precisely defined bind- 6 ing sequence containing a triple A motif was later iden- Methylation of adenine at the N6 position (m A) is con- tified by biochemical and bioinformatics approaches for sidered the most abundant messenger RNA modification the Schizosaccharomyces pombe YTH-containing protein in eukaryotes besides the 5 cap structure (1,2). Functional MMI1 (18,19). impairment of methylase function leads to severe pheno- Here we show that the YTH domain of YT521-B binds types in a number of organisms such as cell death and de- sequence-specifically a GA-containing sequence with a 50- velopmental arrest (2,3). Genetic alterations in one known fold affinity increase when the adenine is N6 methylated. demethylase gene (FTO) were associated in humans with We determined the solution structure of the complex which increased body mass (4) and higher propensity for cancer provides the structural basis of the specific6 m A recognition (5,6). In recent years several thousand methylation sites by the YTH domain. On the basis of the structure, we ra- have been identified in eukaryotic transcriptomes by the tionalize why more generally YTH domains act as reader use of next-generation sequencing-based approaches (7– domains for m6A. 13). Quite consistently, m6A are embedded in a consen- sus sequence in the form 5 R-R-m6A-C 3 (where R are
*To whom correspondence should be addressed. Tel: +41 44 633 39 40; Fax: +41 44 633 12 94; Email: [email protected] Present Address: Cyril Dominguez, Department of Biochemistry, Henry Wellcome Laboratories of Structural Biology, University of Leicester, LE1 9HN Leicester, UK.