MDR: an integrative DNA N6-methyladenine and N4-methylcytosine modification database for Rosaceae

Eukaryotic DNA methylation has been receiving increasing attention for its crucial epigenetic regulatory function. The recently developed single-molecule real-time (SMRT) sequencing technology provides an efficient way to detect DNA N6-methyladenine (6mA) and N4-methylcytosine (4mC) modifications at a single-nucleotide resolution. The family Rosaceae contains horticultural plants with a wide range of economic importance. However, little is currently known regarding the genome-wide distribution patterns and functions of 6mA and 4mC modifications in the Rosaceae. In this study, we present an integrated DNA 6mA and 4mC modification database for the Rosaceae (MDR, http://mdr.xieslab.org). MDR, the first repository for displaying and storing DNA 6mA and 4mC methylomes from SMRT sequencing data sets for Rosaceae, includes meta and statistical information, methylation densities, Gene Ontology enrichment analyses, and genome search and browse for methylated sites in NCBI. MDR provides important information regarding DNA 6mA and 4mC methylation and may help users better understand epigenetic modifications in the family Rosaceae.

[1]  P. Laird.  Principles and challenges of genome-wide DNA methylation analysis , 2010, Nature Reviews Genetics.

[2]  Robert J. Schmitz,et al.  Widespread adenine N6-methylation of active genes in fungi , 2017, Nature Genetics.

[3]  Minghui He,et al.  N6-Methyladenine DNA Modification in the Human Genome. , 2018, Molecular cell.

[4]  Characterization of DNA methyltransferase and demethylase genes in Fragaria vesca , 2016, Molecular Genetics and Genomics.

[5]  A. Jeltsch,et al.  The Cytosine N4-Methyltransferase M.PvuII Also Modifies Adenine Residues , 2001, Biological chemistry.

[6]  L. Doré,et al.  N 6-Methyldeoxyadenosine Marks Active Transcription Start Sites in Chlamydomonas , 2015, Cell.

[7]  Yuke Geng,et al.  The N6-adenine methylation in yeast genome profiled by single-molecule technology. , 2018, Journal of genetics and genomics = Yi chuan xue bao.

[8]  S. Henikoff,et al.  Genome-wide analysis of Arabidopsis thaliana DNA methylation uncovers an interdependence between methylation and transcription , 2007, Nature Genetics.

[9]  Yu Zhao,et al.  Identification and analysis of adenine N6-methylation sites in the rice genome , 2018, Nature Plants.

[10]  Kun-song Chen,et al.  Downregulation of RdDM during strawberry fruit ripening , 2018, Genome Biology.

[11]  Yang Shi,et al.  DNA N6-methyladenine: a new epigenetic mark in eukaryotes? , 2015, Nature Reviews Molecular Cell Biology.

[12]  Ping Zheng,et al.  15 years of GDR: New data and functionality in the Genome Database for Rosaceae , 2018, Nucleic Acids Res..

[13]  Henry D. Priest,et al.  The genome of woodland strawberry (Fragaria vesca) , 2011, Nature Genetics.

[14]  P. Wincker,et al.  The Rosa genome provides new insights into the domestication of modern roses , 2018, Nature Genetics.

[15]  C. Bonghi,et al.  Rosaceae Fruit Development, Ripening and Post-harvest: An Epigenetic Perspective , 2017, Front. Plant Sci..

[16]  J. Cadet,et al.  High-performance liquid chromatography--tandem mass spectrometry measurement of radiation-induced base damage to isolated and cellular DNA. , 2000, Chemical research in toxicology.

[17]  Mikael Bodén,et al.  MEME Suite: tools for motif discovery and searching , 2009, Nucleic Acids Res..

[18]  Ning Ma,et al.  BLAST+: architecture and applications , 2009, BMC Bioinformatics.

[19]  A. Jeltsch,et al.  On the Substrate Specificity of DNA Methyltransferases , 1999, The Journal of Biological Chemistry.

[20]  Stephen P. Ficklin,et al.  GDR (Genome Database for Rosaceae): integrated web resources for Rosaceae genomics and genetics research , 2004, BMC Bioinform..

[21]  Richard J. Roberts,et al.  REBASE-restriction enzymes and methylases , 1993, Nucleic Acids Res..

[22]  Jeffrey P. Mower,et al.  Single-molecule sequencing and optical mapping yields an improved genome of woodland strawberry (Fragaria vesca) with chromosome-scale contiguity , 2017, GigaScience.

[23]  Coby Viner,et al.  DNAmod: the DNA modification database , 2016, bioRxiv.

[24]  M. Pellegrini,et al.  Genome-wide High-Resolution Mapping and Functional Analysis of DNA Methylation in Arabidopsis , 2006, Cell.

[25]  James A. Swenberg,et al.  DNA methylation on N6-adenine in mammalian embryonic stem cells , 2016, Nature.

[26]  Hongkun Zheng,et al.  N6-Methyladenine DNA Methylation in Japonica and Indica Rice Genomes and Its Association with Gene Expression, Plant Development, and Stress Responses. , 2018, Molecular plant.

[27]  Robert Gentleman,et al.  Software for Computing and Annotating Genomic Ranges , 2013, PLoS Comput. Biol..

[28]  Chuan He,et al.  Abundant DNA 6mA methylation during early embryogenesis of zebrafish and pig , 2016, Nature Communications.

[29]  Zhi Xie,et al.  MethSMRT: an integrative database for DNA N6-methyladenine and N4-methylcytosine generated by single-molecular real-time sequencing , 2016, Nucleic Acids Res..

[30]  Richard J. Roberts,et al.  REBASE - restriction enzymes and methylases , 2001, Nucleic Acids Res..

[31]  Peter A. Jones.  Functions of DNA methylation: islands, start sites, gene bodies and beyond , 2012, Nature Reviews Genetics.

[32]  Claude Thermes,et al.  The Third Revolution in Sequencing Technology. , 2018, Trends in genetics : TIG.

[33]  Rasko Leinonen,et al.  The sequence read archive: explosive growth of sequencing data , 2011, Nucleic Acids Res..

[34]  Julie A. Law,et al.  Establishing, maintaining and modifying DNA methylation patterns in plants and animals , 2010, Nature Reviews Genetics.

[35]  S. Turner,et al.  Real-Time DNA Sequencing from Single Polymerase Molecules , 2009, Science.

[36]  Tyson A. Clark,et al.  Direct detection of DNA methylation during single-molecule, real-time sequencing , 2010, Nature Methods.

[37]  Shunmin He,et al.  N6-Methyladenine DNA Modification in Drosophila , 2015, Cell.

[38]  Fan Liang,et al.  DNA N6-Adenine Methylation in Arabidopsis thaliana. , 2018, Developmental cell.

[39]  Aaron R. Quinlan,et al.  Bioinformatics Applications Note Genome Analysis Bedtools: a Flexible Suite of Utilities for Comparing Genomic Features , 2022 .