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RMDB: An Integrated Database of Single-cytosine-resolution DNA Methylation in Oryza Sativa

[ Vol. 14 , Issue. 6 ]

Author(s):

Tiansheng Zhu, Jihong Guan, Hui Liu and Shuigeng Zhou*   Pages 524 - 531 ( 8 )

Abstract:


Background: Previous studies have revealed that DNA methylation plays a crucial role in eukaryotic growth and development via involvement in the regulation of gene expression and chromosomal instability. With the advancement of biotechnology, next-generation sequencing (NGS) is emerging as a popular method to explore the functions of DNA methylation, and an increasing number of genome-scale DNA methylation datasets have been published. Several DNA methylation databases, including MethDB, NGSmethDB and MENT have been developed for storing and analyzing the DNA methylation data. However, no public resource dedicated to DNA methylation of Oryza sativa is available to date.

Methods & Results: We built a comprehensive database (RMDB) for integration and analysis of DNA methylation data of Oryza sativa. A couple of functional modules were developed to identify the connections between DNA methylation and phenotypes. Moreover, rich graphical visualization tools were employed to facilitate data presentation and interpretation.

Conclusion: RMDB is an integrated database dedicated to rice DNA methylation. To the best of our knowledge, this is the first integrated rice DNA methylation database. We believe that RMDB will be helpful to understand the epigenetic mechanisms of Oryza sativa. RMDB is freely available at http://admis.fudan.edu.cn/rmdb.

Keywords:

DNA Methylation, Oryza sativa, epigenetics, methylation pattern, methylation database, genome browser, differential methylation.

Affiliation:

Shanghai Key Lab of Intelligent Information Processing and School of Computer Science, Fudan University, Shanghai, Department of Computer Science and Technology, Tongji University, Shanghai 201804, Lab of Information Management, Changzhou University, Jiangsu 213164, Shanghai Key Lab of Intelligent Information Processing and School of Computer Science, Fudan University, Shanghai

Graphical Abstract:



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