DNA N6-Methyladenosine modification role in transmitted variations from genomic DNA to RNA in Herrania umbratica

Mei-Wei Luan,Wei Chen,Chuan-Le Xiao,Shang-Qian Xie,Jian-Feng Xing,Ying Chen

doi:10.1186/s12864-019-5776-0

Abstract

BackgroundDNA methylation is an important epigenetic modification. Recently the developed single-molecule real-time (SMRT) sequencing technology provided an efficient way to detect DNA N6-methyladenine (6mA) modification that played an important role in epigenetic and positively regulated gene expression. In addition, the gene expression was also regulated by genetic variation. However, the relationship between DNA 6mA modification and variation is still unknown.ResultsWe collected the SMRT long-reads DNA, Illumina short reads DNA and RNA datasets from the young leaves of Herrania umbratica, and used them to detect 35,654 6mA modification sites, 829,894 DNA variations and 60,672 RNA variations respectively, among which, there are 303 DNA variations and 19 RNA variations with 6mA modification, and 57,468 transmitted genetic variations from DNA to RNA. The results illustrated that the genes with 6mA modification were significant disadvantage to mutate than those genes without modification (p-value< 4.9e-08). And result from the linear regression model showed the 6mA densities of genes were associated with the transmitted variations type 0/1 to 1/1 (p-value < 0.001).ConclusionsThe variations of DNA and RNA in genes with 6mA modification were significant less than those in unmodified genes. Furthermore, the variations in 6mA modified genes were easily transmitted from DNA to RNA, especially the transmitted variation from DNA heterozygote to RNA homozygote.

Highlights

N6-methyladenine DNA modifications (6mA) refers to the DNA adenosine based with a methyl group at the nitrogen-6 position, which differed from the 5-Methylcytosine (5mC) that methylated on the carbon− 5 position of Cytosine and extensively studied in eukaryotes
The levels of gene expression were associated with genetic variation, and the variations contributed to gene expression are known as expression quantitative trait loci or single qualitative locus [15]
We explored the relationship between DNA 6mA modifications and DNA and RNA variations by using the sequencing datasets from the young leaves of Herrania umbratica, which is a species of flowering plant from the family Malvaceae

Summary

Introduction

N6-methyladenine DNA modifications (6mA) refers to the DNA adenosine based with a methyl group at the nitrogen-6 position, which differed from the 5-Methylcytosine (5mC) that methylated on the carbon− 5 position of Cytosine and extensively studied in eukaryotes. The existence of 6mA DNA methylation has been detected and confirmed in eukaryotes, The levels of gene expression were associated with genetic variation, and the variations contributed to gene expression are known as expression quantitative trait loci (eQTL) or single qualitative locus [15]. The genetic variation associated with the expression of specified gene had been investigated. Some researchers have found that gene expression was reinforced by DNA 6mA modifications in Arabidopsis thaliana, Mus musculus and Homo sapiens [5, 24, 25]. The developed single-molecule real-time (SMRT) sequencing technology provided an efficient way to detect DNA N6-methyladenine (6mA) modification that played an important role in epigenetic and positively regulated gene expression. The gene expression was regulated by genetic variation. The relationship between DNA 6mA modification and variation is still unknown

Methods

Results

Conclusion