Characterization of epitranscriptome reader proteins experimentally and in silico: Current knowledge and future perspectives beyond the YTH domain

[1]  Weimin Fan,et al.  M1ARegpred: Epitranscriptome Target Prediction of N1-methyladenosine (m1A) Regulators Based on Sequencing Features and Genomic Features. , 2022, Frontiers in bioscience.

[2]  S. Jaffrey,et al.  Small-Molecule Ebselen Binds to YTHDF Proteins Interfering with the Recognition of N6-Methyladenosine-Modified RNAs , 2022, ACS pharmacology & translational science.

[3]  A. Caflisch,et al.  Fragment Ligands of the m6A-RNA Reader YTHDF2 , 2022, ACS medicinal chemistry letters.

[4]  J. Šponer,et al.  Conformational Heterogeneity of RNA Stem-Loop Hairpins Bound to FUS RNA Recognition Motif with Disordered RGG Tail Revealed by Unbiased Molecular Dynamics Simulations , 2022, bioRxiv.

[5]  Y. Tseng,et al.  Comparative studies of AlphaFold, RoseTTAFold and Modeller: a case study involving the use of G-protein-coupled receptors , 2022, Briefings Bioinform..

[6]  Chunhua Li,et al.  Specific recognition between YTHDF3 and m6A‐modified RNA: An all‐atom molecular dynamics simulation study , 2022, Proteins.

[7]  Huaqing Yan,et al.  Roles and mechanisms of the m6A reader YTHDC1 in biological processes and diseases , 2022, Cell death discovery.

[8]  A. Caflisch,et al.  Structure-based design of ligands of the m6A-RNA reader YTHDC1 , 2022, European Journal of Medicinal Chemistry Reports.

[9]  Haoran Shi,et al.  m5CRegpred: Epitranscriptome Target Prediction of 5-Methylcytosine (m5C) Regulators Based on Sequencing Features , 2022, Genes.

[10]  Qingchuan Zheng,et al.  Theoretical investigations on the effects of mutations in important residues of NS1B on its RNA-binding using molecular dynamics simulations , 2022, Comput. Biol. Medicine.

[11]  K. Lepikhov,et al.  First Small-Molecule Inhibitors Targeting the RNA-Binding Protein IGF2BP2/IMP2 for Cancer Therapy. , 2022, ACS chemical biology.

[12]  L. Pang,et al.  Detailed resume of RNA m6A demethylases , 2022, Acta pharmaceutica Sinica. B.

[13]  Jun Li,et al.  Specific Regulation of m6A by SRSF7 Promotes the Progression of Glioblastoma , 2021, Genom. Proteom. Bioinform..

[14]  M. Sternberg,et al.  The AlphaFold Database of Protein Structures: A Biologist’s Guide , 2021, Journal of molecular biology.

[15]  Jeffrey Skolnick,et al.  AlphaFold 2: Why It Works and Its Implications for Understanding the Relationships of Protein Sequence, Structure, and Function , 2021, J. Chem. Inf. Model..

[16]  Yu Li,et al.  Protein–RNA interaction prediction with deep learning: structure matters , 2021, Briefings Bioinform..

[17]  Oriol Vinyals,et al.  Highly accurate protein structure prediction with AlphaFold , 2021, Nature.

[18]  J. Šponer,et al.  Recognition of N6-Methyladenosine by the YTHDC1 YTH Domain Studied by Molecular Dynamics and NMR Spectroscopy: The Role of Hydration. , 2021, The journal of physical chemistry. B.

[19]  Jianjun Chen,et al.  YBX1 is required for maintaining myeloid leukemia cell survival by regulating BCL2 stability in an m6A-dependent manner. , 2021, Blood.

[20]  G. Pierdominici-Sottile,et al.  Molecular Dynamics Simulations Unveil the Basis of the Sequential Binding of RsmE to the Noncoding RNA RsmZ. , 2021, The journal of physical chemistry. B.

[21]  G. Klug,et al.  The small DUF1127 protein CcaF1 from Rhodobacter sphaeroides is an RNA-binding protein involved in sRNA maturation and RNA turnover , 2021, Nucleic acids research.

[22]  A. Caflisch,et al.  Atomistic and Thermodynamic Analysis of N6-Methyladenosine (m6A) Recognition by the Reader Domain of YTHDC1. , 2021, Journal of chemical theory and computation.

[23]  J. Šponer,et al.  MD simulations reveal the basis for dynamic assembly of Hfq–RNA complexes , 2021, The Journal of biological chemistry.

[24]  A. Caflisch,et al.  Structural and Dynamic Insights into Redundant Function of YTHDF Proteins , 2020, J. Chem. Inf. Model..

[25]  Jia Meng,et al.  m6A Reader: Epitranscriptome Target Prediction and Functional Characterization of N6-Methyladenosine (m6A) Readers , 2020, Frontiers in Cell and Developmental Biology.

[26]  D. Herschlag,et al.  How to measure and evaluate binding affinities , 2020, eLife.

[27]  Qingxin Li,et al.  Application of Fragment-Based Drug Discovery to Versatile Targets , 2020, Frontiers in Molecular Biosciences.

[28]  R. Blumenthal,et al.  Biochemical and structural basis for YTH domain of human YTHDC1 binding to methylated adenine in DNA , 2020, Nucleic acids research.

[29]  Samie R. Jaffrey,et al.  A Unified Model for the Function of YTHDF Proteins in Regulating m6A-Modified mRNA , 2020, Cell.

[30]  A. Caflisch,et al.  Selectively disrupting m6A-dependent protein-RNA interactions with fragments. , 2020, ACS chemical biology.

[31]  Ilya A Vakser,et al.  How to choose templates for modeling of protein complexes: Insights from benchmarking template‐based docking , 2020, Proteins.

[32]  Manel Esteller,et al.  Writers, Readers and Erasers of RNA Modifications in Cancer. , 2020, Cancer letters.

[33]  Joseph M Jakubowski,et al.  Computational evolution of an RNA-binding protein towards enhanced oxidized-RNA binding , 2019, Computational and structural biotechnology journal.

[34]  Xuemei Chen,et al.  YTHDF2 Binds to 5-Methylcytosine in RNA and Modulates the Maturation of Ribosomal RNA. , 2019, Analytical chemistry.

[35]  Ralph E. Kleiner,et al.  YTHDF2 recognition of N1-methyladenosine (m1A)-modified RNA is associated with transcript destabilization. , 2019, ACS chemical biology.

[36]  Daniel J. Gaffney,et al.  N6-methyladenosine regulates the stability of RNA:DNA hybrids in human cells , 2019, Nature Genetics.

[37]  A. Caflisch,et al.  Flexible binding of m6A reader protein YTHDC1 to its preferred RNA motif. , 2019, Journal of chemical theory and computation.

[38]  E. Levanon,et al.  Genome-wide quantification of ADAR adenosine-to-inosine RNA editing activity , 2019, Nature Methods.

[39]  Hailing Shi,et al.  Regulation of Co-transcriptional Pre-mRNA Splicing by m6A through the Low-Complexity Protein hnRNPG. , 2019, Molecular cell.

[40]  Ralph E. Kleiner,et al.  In vitro selection with a site-specifically modified RNA library reveals the binding preferences of N6-methyladenosine (m6A) reader proteins. , 2019, Biochemistry.

[41]  L. Otterbein,et al.  Caveolin-1 selectively regulates microRNA sorting into microvesicles after noxious stimuli , 2019, The Journal of experimental medicine.

[42]  Chuan He,et al.  Where, When, and How: Context-Dependent Functions of RNA Methylation Writers, Readers, and Erasers. , 2019, Molecular cell.

[43]  Q. Lan,et al.  The Critical Role of RNA m6A Methylation in Cancer. , 2019, Cancer research.

[44]  A. Caflisch,et al.  A Reader-Based Assay for m6A Writers and Erasers. , 2019, Analytical chemistry.

[45]  Mohamed Chaabane,et al.  Comprehensive evaluation of deep learning architectures for prediction of DNA/RNA sequence binding specificities , 2019, Bioinform..

[46]  Yousheng Shu,et al.  A novel m6A reader Prrc2a controls oligodendroglial specification and myelination , 2018, Cell Research.

[47]  Hongjun Song,et al.  Fragile X mental retardation protein modulates the stability of its m6A‐marked messenger RNA targets , 2018, Human molecular genetics.

[48]  Asuka A. Orr,et al.  A high-throughput and rapid computational method for screening of RNA post-transcriptional modifications that can be recognized by target proteins. , 2018, Methods.

[49]  Z. Ignatova,et al.  Dynamic m6A methylation facilitates mRNA triaging to stress granules , 2018, Life Science Alliance.

[50]  T. Ishii,et al.  Specific binding of PCBP1 to heavily oxidized RNA to induce cell death , 2018, Proceedings of the National Academy of Sciences.

[51]  Yinsheng Wang,et al.  Identification of YTH Domain-Containing Proteins as the Readers for N1-Methyladenosine in RNA. , 2018, Analytical chemistry.

[52]  T. Pan,et al.  An additional class of m6A readers , 2018, Nature Cell Biology.

[53]  Robert M. Dirks,et al.  RNA force field with accuracy comparable to state-of-the-art protein force fields , 2018, Proceedings of the National Academy of Sciences.

[54]  S. Jaffrey,et al.  Molecular basis for the specific and multivariant recognitions of RNA substrates by human hnRNP A2/B1 , 2018, Nature Communications.

[55]  Stefan Hüttelmaier,et al.  Recognition of RNA N6-methyladenosine by IGF2BP Proteins Enhances mRNA Stability and Translation , 2018, Nature Cell Biology.

[56]  Michelle H. Moon,et al.  Measuring RNA-Ligand Interactions with Microscale Thermophoresis. , 2018, Biochemistry.

[57]  Lukas Zimmermann,et al.  A Completely Reimplemented MPI Bioinformatics Toolkit with a New HHpred Server at its Core. , 2017, Journal of molecular biology.

[58]  Jinhao Xu,et al.  Structural insights into the specific recognition of DSR by the YTH domain containing protein Mmi1. , 2017, Biochemical and biophysical research communications.

[59]  Chuan He,et al.  N6-methyladenosine (m6A) recruits and repels proteins to regulate mRNA homeostasis , 2017, Nature Structural &Molecular Biology.

[60]  Chuan He,et al.  Ythdc2 is an N6-methyladenosine binding protein that regulates mammalian spermatogenesis , 2017, Cell Research.

[61]  Alexander D. MacKerell,et al.  CHARMM‐GUI 10 years for biomolecular modeling and simulation , 2017, J. Comput. Chem..

[62]  Michal Otyepka,et al.  How to understand atomistic molecular dynamics simulations of RNA and protein–RNA complexes? , 2017, Wiley interdisciplinary reviews. RNA.

[63]  Samir Adhikari,et al.  5-methylcytosine promotes mRNA export — NSUN2 as the methyltransferase and ALYREF as an m5C reader , 2017, Cell Research.

[64]  Nian Liu,et al.  N 6-methyladenosine alters RNA structure to regulate binding of a low-complexity protein , 2017, Nucleic acids research.

[65]  Chuan He,et al.  YTHDF3 facilitates translation and decay of N6-methyladenosine-modified RNA , 2017, Cell Research.

[66]  Vijay S. Pande,et al.  OpenMM 7: Rapid development of high performance algorithms for molecular dynamics , 2016, bioRxiv.

[67]  B. L. de Groot,et al.  CHARMM36m: an improved force field for folded and intrinsically disordered proteins , 2016, Nature Methods.

[68]  Ligang Wu,et al.  YTHDF2 destabilizes m6A-containing RNA through direct recruitment of the CCR4–NOT deadenylase complex , 2016, Nature Communications.

[69]  Chengqi Yi,et al.  Transcriptome-wide mapping reveals reversible and dynamic N(1)-methyladenosine methylome. , 2016, Nature chemical biology.

[70]  T. Pan,et al.  N(6)-Methyladenosine Modification in a Long Noncoding RNA Hairpin Predisposes Its Conformation to Protein Binding. , 2016, Journal of molecular biology.

[71]  Samir Adhikari,et al.  Nuclear m(6)A Reader YTHDC1 Regulates mRNA Splicing. , 2016, Molecular cell.

[72]  Gideon Rechavi,et al.  The dynamic N1-methyladenosine methylome in eukaryotic messenger RNA , 2016, Nature.

[73]  Alexander D. MacKerell,et al.  Additive CHARMM force field for naturally occurring modified ribonucleotides , 2016, J. Comput. Chem..

[74]  K. Nishikura,et al.  A-to-I editing of coding and non-coding RNAs by ADARs , 2015, Nature Reviews Molecular Cell Biology.

[75]  Saeed Tavazoie,et al.  HNRNPA2B1 Is a Mediator of m6A-Dependent Nuclear RNA Processing Events , 2015, Cell.

[76]  Matthieu Schapira,et al.  Structural Basis for the Discriminative Recognition of N6-Methyladenosine RNA by the Human YT521-B Homology Domain Family of Proteins* , 2015, The Journal of Biological Chemistry.

[77]  B. Frey,et al.  Predicting the sequence specificities of DNA- and RNA-binding proteins by deep learning , 2015, Nature Biotechnology.

[78]  Chuan He,et al.  N 6 -methyladenosine Modulates Messenger RNA Translation Efficiency , 2015, Cell.

[79]  Michael J E Sternberg,et al.  The Phyre2 web portal for protein modeling, prediction and analysis , 2015, Nature Protocols.

[80]  Yang Zhang,et al.  I-TASSER server: new development for protein structure and function predictions , 2015, Nucleic Acids Res..

[81]  Chuan He,et al.  N6-methyladenosine-dependent RNA structural switches regulate RNA-protein interactions , 2015, Nature.

[82]  J. Šponer,et al.  Can We Execute Stable Microsecond-Scale Atomistic Simulations of Protein-RNA Complexes? , 2015, Journal of chemical theory and computation.

[83]  T. Ishii,et al.  Role of Auf1 in elimination of oxidatively damaged messenger RNA in human cells. , 2015, Free radical biology & medicine.

[84]  D. Dominissini.  Roadmap to the epitranscriptome , 2014, Science.

[85]  Jihui Wu,et al.  Structure of the YTH domain of human YTHDF2 in complex with an m6A mononucleotide reveals an aromatic cage for m6A recognition , 2014, Cell Research.

[86]  Li Wang,et al.  Crystal structure of the YTH domain of YTHDF2 reveals mechanism for recognition of N6-methyladenosine , 2014, Cell Research.

[87]  Ke Liu,et al.  Structural basis for selective binding of m6A RNA by the YTHDC1 YTH domain. , 2014, Nature chemical biology.

[88]  Liang Tong,et al.  Molecular basis for the recognition of methylated adenines in RNA by the eukaryotic YTH domain , 2014, Proceedings of the National Academy of Sciences.

[89]  Yang Zhang,et al.  Template-based structure modeling of protein-protein interactions. , 2014, Current opinion in structural biology.

[90]  Miao Yu,et al.  A METTL3-METTL14 complex mediates mammalian nuclear RNA N6-adenosine methylation , 2013, Nature chemical biology.

[91]  Zhike Lu,et al.  m6A-dependent regulation of messenger RNA stability , 2013, Nature.

[92]  Jing Huang,et al.  CHARMM36 all‐atom additive protein force field: Validation based on comparison to NMR data , 2013, J. Comput. Chem..

[93]  Peter M. Kasson,et al.  GROMACS 4.5: a high-throughput and highly parallel open source molecular simulation toolkit , 2013, Bioinform..

[94]  Karen A. Lewis,et al.  Practical strategies for the evaluation of high-affinity protein/nucleic acid interactions , 2013, Journal of nucleic acids investigation.

[95]  Alexander D. MacKerell,et al.  Automation of the CHARMM General Force Field (CGenFF) I: Bond Perception and Atom Typing , 2012, J. Chem. Inf. Model..

[96]  D. Rio.  Filter-binding assay for analysis of RNA-protein interactions. , 2012, Cold Spring Harbor protocols.

[97]  M. Kupiec,et al.  Topology of the human and mouse m6A RNA methylomes revealed by m6A-seq , 2012, Nature.

[98]  Christophe Chevalier,et al.  Molecular Dynamics Studies of the Nucleoprotein of Influenza A Virus: Role of the Protein Flexibility in RNA Binding , 2012, PloS one.

[99]  Narayanaswamy Srinivasan,et al.  iPBA: a tool for protein structure comparison using sequence alignment strategies , 2011, Nucleic Acids Res..

[100]  K. Nakayama,et al.  Human proteins that specifically bind to 8-oxoguanine-containing RNA and their responses to oxidative stress. , 2010, Biochemical and biophysical research communications.

[101]  M. Helm,et al.  Detection of RNA modifications , 2010, RNA biology.

[102]  Michael Hiller,et al.  The YTH Domain Is a Novel RNA Binding Domain* , 2010, The Journal of Biological Chemistry.

[103]  Jianpeng Ma,et al.  CHARMM: The biomolecular simulation program , 2009, J. Comput. Chem..

[104]  Alexander D. MacKerell,et al.  CHARMM general force field: A force field for drug‐like molecules compatible with the CHARMM all‐atom additive biological force fields , 2009, J. Comput. Chem..

[105]  Pedro Alexandrino Fernandes,et al.  Protein–protein docking dealing with the unknown , 2009, J. Comput. Chem..

[106]  Alexander D. MacKerell,et al.  Molecular dynamics simulations of nucleic acid-protein complexes. , 2008, Current opinion in structural biology.

[107]  L. Hellman,et al.  Electrophoretic mobility shift assay (EMSA) for detecting protein–nucleic acid interactions , 2007, Nature Protocols.

[108]  John SantaLucia,et al.  AMBER Force Field Parameters for the Naturally Occurring Modified Nucleosides in RNA. , 2007, Journal of chemical theory and computation.

[109]  Ying Zhao,et al.  Molecular dynamics simulation studies of a protein–RNA complex with a selectively modified binding interface , 2006, Biopolymers.

[110]  Holger Gohlke,et al.  The Amber biomolecular simulation programs , 2005, J. Comput. Chem..

[111]  Johannes Söding,et al.  The HHpred interactive server for protein homology detection and structure prediction , 2005, Nucleic Acids Res..

[112]  R. Russell,et al.  The relationship between sequence and interaction divergence in proteins. , 2003, Journal of molecular biology.

[113]  M. Sekiguchi,et al.  Binding capacity of human YB-1 protein for RNA containing 8-oxoguanine. , 2002, Biochemistry.

[114]  S. Stamm,et al.  YTH: a new domain in nuclear proteins. , 2002, Trends in biochemical sciences.

[115]  M. Mann,et al.  Stable Isotope Labeling by Amino Acids in Cell Culture, SILAC, as a Simple and Accurate Approach to Expression Proteomics* , 2002, Molecular & Cellular Proteomics.

[116]  M. Sekiguchi,et al.  Specific binding of 8-oxoguanine-containing RNA to polynucleotide phosphorylase protein. , 2001, Biochemistry.

[117]  K Schulten,et al.  VMD: visual molecular dynamics. , 1996, Journal of molecular graphics.

[118]  R J Roberts,et al.  Sequence specificity of the human mRNA N6-adenosine methylase in vitro. , 1990, Nucleic acids research.

[119]  B. Moss,et al.  Nucleotide sequences at the N6-methyladenosine sites of HeLa cell messenger ribonucleic acid. , 1977, Biochemistry.

[120]  F. Davis,et al.  Ribonucleic acids from yeast which contain a fifth nucleotide. , 1957, The Journal of biological chemistry.

[121]  OUP accepted manuscript , 2021, Nucleic Acids Research.

[122]  OUP accepted manuscript , 2021, Nucleic Acids Research.

[123]  S. Liao,et al.  Crystal structure of human YTHDC2 YTH domain. , 2019, Biochemical and biophysical research communications.

[124]  A. Feig.  Studying RNA-RNA and RNA-protein interactions by isothermal titration calorimetry. , 2009, Methods in enzymology.

[125]  D. Engelke,et al.  RNA affinity tags for the rapid purification and investigation of RNAs and RNA-protein complexes. , 2008, Methods in molecular biology.

[126]  Eric F Darve.  Thermodynamic Integration Using Constrained and Unconstrained Dynamics , 2007 .

[127]  Brenda L Bass,et al.  RNA editing by adenosine deaminases that act on RNA. , 2002, Annual review of biochemistry.

[128]  T. N. Bhat,et al.  The Protein Data Bank , 2000, Nucleic Acids Res..