MethSMRT: an integrative database for DNA N6-methyladenine and N4-methylcytosine generated by single-molecular real-time sequencing

Abstract

DNA methylation is an important type of epigenetic modifications, where 5- methylcytosine (5mC), 6-methyadenine (6mA) and 4-methylcytosine (4mC) are the most common types. Previous efforts have been largely focused on 5mC, providing invaluable insights into epigenetic regulation through DNA methylation. Recently developed single-molecule real-time (SMRT) sequencing technology provides a unique opportunity to detect the less studied DNA 6mA and 4mC modifications at single-nucleotide resolution. With a rapidly increased amount of SMRT sequencing data generated, there is an emerging demand to systematically explore DNA 6mA and 4mC modifications from these data sets. MethSMRT is the first resource hosting DNA 6mA and 4mC methylomes. All the data sets were processed using the same analysis pipeline with the same quality control. The current version of the database provides a platform to store, browse, search and download epigenome-wide methylation profiles of 156 species, including seven eukaryotes such as Arabidopsis, C. elegans, Drosophila, mouse and yeast, as well as 149 prokaryotes. It also offers a genome browser to visualize the methylation sites and related information such as single nucleotide polymorphisms (SNP) and genomic annotation. Furthermore, the database provides a quick summary of statistics of methylome of 6mA and 4mC and predicted methylation motifs for each species. MethSMRT is publicly available at http://sysbio.sysu.edu.cn/methsmrt/ without use restriction.

N6-Methyladenine DNA Modification in Human Genome

“…In this study, we used a new sequencing technology, the PacBio single-molecule real-time (SMRT) sequencing, to decode and identify the presence of 6mA in human genomic DNA, especially in the mitochondria genome (Flusberg et al, 2010;Ye et al, 2017). We found that 6mA was broadly distributed across the human genome and [G/C]AGG[C/T] was the most prevalent motif at the 6mA modification sites.…”

A Deep Neural Network for Identifying DNA N4-Methylcytosine Sites

“…After the above two steps, we obtained 15, 639 samples in C. elegans. We combine the new samples with the C. elegans benchmark dataset (Ye et al, 2017) that was used in the previous works to form a new data set with 18, 747 samples. Some of the new samples we extracted may be similar to the previous benchmark dataset.…”

SICD6mA: Identifying 6mA Sites using Deep Memory Network

“…Tolypocladium and yeast. Among them, the positive sequences of Drosophila, Tolypocladium and yeast were downloaded from the MethSMRT [29] database (http://sysbio.sysu.edu.cn/methsmrt/), and the sequences described as "6mA"were deemed as the 6mA positive sequences. The positive sequences of Rice indica were derived from the eRice websites (http://www.elabcaas.cn/rice/downloads.html), while those of Arabidopsis thaliana [9] were collected from the NCBI Gene Expression Omnibus (GEO) with accession number GSE81596 (GSM2157793), and those of Fragaria vesca [30], and Rosa chinensis [31] were obtained from the MDR database (http://mdr.xieslab.org/).…”