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Literature DB >> 25242552

Structural basis for selective binding of m6A RNA by the YTHDC1 YTH domain.

Chao Xu¹, Xiao Wang², Ke Liu³, Ian A Roundtree⁴, Wolfram Tempel⁵, Yanjun Li⁵, Zhike Lu⁶, Chuan He⁶, Jinrong Min⁷.

Abstract

N(6)-methyladenosine (m(6)A) is the most abundant internal modification of nearly all eukaryotic mRNAs and has recently been reported to be recognized by the YTH domain family proteins. Here we present the crystal structures of the YTH domain of YTHDC1, a member of the YTH domain family, and its complex with an m(6)A-containing RNA. Our structural studies, together with transcriptome-wide identification of YTHDC1-binding sites and biochemical experiments, not only reveal the specific mode of m(6)A-YTH binding but also explain the preferential recognition of the GG(m(6)A)C sequences by YTHDC1.

Entities: Chemical Gene

Mesh：

Substances：

Year: 2014 PMID： 25242552 DOI： 10.1038/nchembio.1654

Source DB: PubMed Journal: Nat Chem Biol ISSN： 1552-4450 Impact factor: 15.040

31 in total

1. Comprehensive analysis of mRNA methylation reveals enrichment in 3' UTRs and near stop codons.

Authors: Kate D Meyer; Yogesh Saletore; Paul Zumbo; Olivier Elemento; Christopher E Mason; Samie R Jaffrey
Journal: Cell Date: 2012-05-17 Impact factor: 41.582

2. ALKBH5 is a mammalian RNA demethylase that impacts RNA metabolism and mouse fertility.

Authors: Guanqun Zheng; John Arne Dahl; Yamei Niu; Peter Fedorcsak; Chun-Min Huang; Charles J Li; Cathrine B Vågbø; Yue Shi; Wen-Ling Wang; Shu-Hui Song; Zhike Lu; Ralph P G Bosmans; Qing Dai; Ya-Juan Hao; Xin Yang; Wen-Ming Zhao; Wei-Min Tong; Xiu-Jie Wang; Florian Bogdan; Kari Furu; Ye Fu; Guifang Jia; Xu Zhao; Jun Liu; Hans E Krokan; Arne Klungland; Yun-Gui Yang; Chuan He
Journal: Mol Cell Date: 2012-11-21 Impact factor: 17.970

3. How good are my data and what is the resolution?

Authors: Philip R Evans; Garib N Murshudov
Journal: Acta Crystallogr D Biol Crystallogr Date: 2013-06-13

4. N6-methyladenosine in nuclear RNA is a major substrate of the obesity-associated FTO.

Authors: Guifang Jia; Ye Fu; Xu Zhao; Qing Dai; Guanqun Zheng; Ying Yang; Chengqi Yi; Tomas Lindahl; Tao Pan; Yun-Gui Yang; Chuan He
Journal: Nat Chem Biol Date: 2011-10-16 Impact factor: 15.040

5. The ER repeat protein YT521-B localizes to a novel subnuclear compartment.

Authors: O Nayler; A M Hartmann; S Stamm
Journal: J Cell Biol Date: 2000-09-04 Impact factor: 10.539

6. MolProbity: all-atom structure validation for macromolecular crystallography.

Authors: Vincent B Chen; W Bryan Arendall; Jeffrey J Headd; Daniel A Keedy; Robert M Immormino; Gary J Kapral; Laura W Murray; Jane S Richardson; David C Richardson
Journal: Acta Crystallogr D Biol Crystallogr Date: 2009-12-21

7. High-resolution mapping reveals a conserved, widespread, dynamic mRNA methylation program in yeast meiosis.

Authors: Schraga Schwartz; Sudeep D Agarwala; Maxwell R Mumbach; Marko Jovanovic; Philipp Mertins; Alexander Shishkin; Yuval Tabach; Tarjei S Mikkelsen; Rahul Satija; Gary Ruvkun; Steven A Carr; Eric S Lander; Gerald R Fink; Aviv Regev
Journal: Cell Date: 2013-11-21 Impact factor: 41.582

8. Haematopoietic malignancies caused by dysregulation of a chromatin-binding PHD finger.

Authors: Gang G Wang; Jikui Song; Zhanxin Wang; Holger L Dormann; Fabio Casadio; Haitao Li; Jun-Li Luo; Dinshaw J Patel; C David Allis
Journal: Nature Date: 2009-06-11 Impact factor: 49.962

9. N6-methyladenosine-dependent regulation of messenger RNA stability.

Authors: Xiao Wang; Zhike Lu; Adrian Gomez; Gary C Hon; Yanan Yue; Dali Han; Ye Fu; Marc Parisien; Qing Dai; Guifang Jia; Bing Ren; Tao Pan; Chuan He
Journal: Nature Date: 2013-11-27 Impact factor: 49.962

10. Phaser crystallographic software.

Authors: Airlie J McCoy; Ralf W Grosse-Kunstleve; Paul D Adams; Martyn D Winn; Laurent C Storoni; Randy J Read
Journal: J Appl Crystallogr Date: 2007-07-13 Impact factor: 3.304

251 in total

Review 1. RNA epigenetics--chemical messages for posttranscriptional gene regulation.

Authors: Ian A Roundtree; Chuan He
Journal: Curr Opin Chem Biol Date: 2015-11-26 Impact factor: 8.822

Review 2. The Untranslated Regions of mRNAs in Cancer.

Authors: Samantha L Schuster; Andrew C Hsieh
Journal: Trends Cancer Date: 2019-03-22

3. N(6)-Methyladenosine RNA Modification Regulates Shoot Stem Cell Fate in Arabidopsis.

Authors: Lisha Shen; Zhe Liang; Xiaofeng Gu; Ying Chen; Zhi Wei Norman Teo; Xingliang Hou; Weiling Maggie Cai; Peter C Dedon; Lu Liu; Hao Yu
Journal: Dev Cell Date: 2016-07-07 Impact factor: 12.270

4. Structural Basis for the Discriminative Recognition of N6-Methyladenosine RNA by the Human YT521-B Homology Domain Family of Proteins.

Authors: Chao Xu; Ke Liu; Hazem Ahmed; Peter Loppnau; Matthieu Schapira; Jinrong Min
Journal: J Biol Chem Date: 2015-08-28 Impact factor: 5.157

5. An N⁶-methyladenosine at the transited codon 273 of p53 pre-mRNA promotes the expression of R273H mutant protein and drug resistance of cancer cells.

Authors: Mohammad B Uddin; Kartik R Roy; Salman B Hosain; Sachin K Khiste; Ronald A Hill; Seetharama D Jois; Yunfeng Zhao; Alan J Tackett; Yong-Yu Liu
Journal: Biochem Pharmacol Date: 2018-12-19 Impact factor: 5.858

Structural basis for selective binding of m6A RNA by the YTHDC1 YTH domain.

1. Comprehensive analysis of mRNA methylation reveals enrichment in 3' UTRs and near stop codons.

2. ALKBH5 is a mammalian RNA demethylase that impacts RNA metabolism and mouse fertility.

3. How good are my data and what is the resolution?

4. N6-methyladenosine in nuclear RNA is a major substrate of the obesity-associated FTO.

5. The ER repeat protein YT521-B localizes to a novel subnuclear compartment.

6. MolProbity: all-atom structure validation for macromolecular crystallography.

7. High-resolution mapping reveals a conserved, widespread, dynamic mRNA methylation program in yeast meiosis.

8. Haematopoietic malignancies caused by dysregulation of a chromatin-binding PHD finger.

9. N6-methyladenosine-dependent regulation of messenger RNA stability.

10. Phaser crystallographic software.

Review 1. RNA epigenetics--chemical messages for posttranscriptional gene regulation.

Review 2. The Untranslated Regions of mRNAs in Cancer.

3. N(6)-Methyladenosine RNA Modification Regulates Shoot Stem Cell Fate in Arabidopsis.

4. Structural Basis for the Discriminative Recognition of N6-Methyladenosine RNA by the Human YT521-B Homology Domain Family of Proteins.

5. An N⁶-methyladenosine at the transited codon 273 of p53 pre-mRNA promotes the expression of R273H mutant protein and drug resistance of cancer cells.

Review 6. The epitranscriptome and synaptic plasticity.

Review 7. Detecting and interpreting DNA methylation marks.

8. Dynamics of the human and viral m(6)A RNA methylomes during HIV-1 infection of T cells.

Review 9. How RNA-Binding Proteins Interact with RNA: Molecules and Mechanisms.

Review 10. m⁶A RNA Methylation Controls Neural Development and Is Involved in Human Diseases.

Review 1. RNA epigenetics--chemical messages for posttranscriptional gene regulation.

Review 2. The Untranslated Regions of mRNAs in Cancer.

Review 6. The epitranscriptome and synaptic plasticity.

Review 7. Detecting and interpreting DNA methylation marks.

Review 9. How RNA-Binding Proteins Interact with RNA: Molecules and Mechanisms.

Review 10. m6A RNA Methylation Controls Neural Development and Is Involved in Human Diseases.

Review 10. m⁶A RNA Methylation Controls Neural Development and Is Involved in Human Diseases.