FAQ - MethBank

Introduction

MethBank is a database that integrates whole-genome single-base nucleotide methylomes and provides an interactive browser for visualization of high-resolution DNA methylation data. Here we present an updated implementation of MethBank (http://bigd.big.ac.cn/methbank; Version 2.0) by incorporating high-quality whole-genome bisulfite sequencing methylome maps for five economically important crops (Oryza sativa, Glycine max, Manihot esculenta, Phaseolus vulgaris and Solanum lycopersicum) as well as two model animals (Danio rerio and Mus musculus). Specifically, we collected a large number of methylomes for these species (those are publicly available till May 2016), then excluded low-quality methylomes by primarily considering genome coverage and bisulfite conversion rate, and consequently obtained 90 high-quality methylomes (42 for Oryza sativa, 21 for Glycine max, 1 for Manihot esculenta, 1 for Phaseolus vulgaris, 7 for Solanum lycopersicum, 9 for Danio rerio, and 9 for Mus musculus).

In this updated version, MethBank features genome-wide profiling of methylation distributions across chromosomes, identification of differentially methylated promoters (DMPs) between a range of conditions, and visualization of methylation levels for genes, regions and CpG Islands across multiple different samples. In addition, MethBank incorporates new functionalities to browse and query the data. It provides genome-wide methylation overview and users can retrieve gene methylation profiles and regional methylation levels across all collected samples. MethBank is also equipped with more friendly and intuitive web interfaces to facilitate search of methylation levels for any given gene that is related to DMP or highly methylated CpG islands. Moreover, all related data and processed results are publicly available at http://bigd.big.ac.cn/methbank/downloads. As one of important database resources in BIG Data Center, MethBank will be continuously upgraded and ongoing developments are integration of more high-quality single-base nucleotide methylomes from a wide range of species, with the aim to serve as an important resource for epigenetic studies throughout the world.

Datasets and Methods

Database Usage

Reference

  1. Chodavarapu RK, Feng S, Ding B, Simon SA, Lopez D, Jia Y, Wang GL, Meyers BC, Jacobsen SE, Pellegrini M: Transcriptome and methylome interactions in rice hybrids. Proc Natl Acad Sci USA 2012, 109(30):12040-12045. [PMID=22778444]
  2. Hu, L., Li, N., Xu, C., Zhong, S., Lin, X., Yang, J., Zhou, T., Yuliang, A., Wu, Y., Chen, Y.R. et al. (2014) Mutation of a major CG methylase in rice causes genome-wide hypomethylation, dysregulated genome expression, and seedling lethality. Proc Natl Acad Sci USA, 111, 10642-10647.
  3. Jiang L, Zhang J, Wang JJ, Wang L, Zhang L, Li G, Yang X, Ma X, Sun X, Cai J, Huang X, Yu M, Wang X, Liu F, Wu CI, He C, Zhang B, Ci W, Liu J: Sperm, but not oocyte, DNA methylome is inherited by zebrafish early embryos. Cell 2013, 153(4):773-784. [PMID=23663777]
  4. Kim KD, El Baidouri M, Abernathy B, Iwata-Otsubo A, Chavarro C, Gonzales M, Libault M, Grimwood J, Jackson SA: A Comparative Epigenomic Analysis of Polyploidy-Derived Genes in Soybean and Common Bean. Plant Physiol 2015, 168(4):1433-1447. [PMID=26149573]
  5. Schmitz RJ, He Y, Valdes-Lopez O, Khan SM, Joshi T, Urich MA, Nery JR, Diers B, Xu D, Stacey G, Ecker JR: Epigenome-wide inheritance of cytosine methylation variants in a recombinant inbred population. Genome Res 2013, 23(10):1663-1674. [PMID=23739894]
  6. Secco D, Wang C, Shou H, Schultz MD, Chiarenza S, Nussaume L, Ecker JR, Whelan J, Lister R: Stress induced gene expression drives transient DNA methylation changes at adjacent repetitive elements. Elife 2015, 4. [PMID=26196146]
  7. Stroud, H., Ding, B., Simon, S.A., Feng, S., Bellizzi, M., Pellegrini, M., Wang, G.L., Meyers, B.C. and Jacobsen, S.E. (2013) Plants regenerated from tissue culture contain stable epigenome changes in rice. Elife, 2, e00354.
  8. Wang H, Beyene G, Zhai J, Feng S, Fahlgren N, Taylor NJ, Bart R, Carrington JC, Jacobsen SE, Ausin I: CG gene body DNA methylation changes and evolution of duplicated genes in cassava. Proc Natl Acad Sci USA 2015, 112(44):13729-13734. [PMID=26483493]
  9. Wang L, Zhang J, Duan J, Gao X, Zhu W, Lu X, Yang L, Li G, Ci W, Li W, Zhou Q, Aluru N, Tang F, He C, Huang X, Liu J: Programming and inheritance of parental DNA methylomes in mammals. Cell 2014, 157(4):979-991. [PMID=24813617]
  10. Zhong S, Fei Z, Chen YR, Zheng Y, Huang M, Vrebalov J, McQuinn R, Gapper N, Liu B, Xiang J, Shao Y, Giovannoni JJ: Single-base resolution methylomes of tomato fruit development reveal epigenome modifications associated with ripening. Nat Biotechnol 2013, 31(2):154-159. [PMID=23354102]