Abstract
N6-methyladenosine (6mA) DNA modification played an important role in epigenetic regulation of gene expression. And the aberrational expression of non-coding genes, as important regular elements of gene expression, was related to many diseases. However, the distribution and potential functions of 6mA modification in non-coding RNA (ncRNA) genes are still unknown. In this study, we analyzed the 6mA distribution of ncRNA genes and compared them with protein-coding genes in four species (Arabidopsis thaliana, Caenorhabditis elegans, Drosophila melanogaster, and Homo sapiens) using single-molecule real-time (SMRT) sequencing data. The results indicated that the consensus motifs of short nucleotides at 6mA location were highly conserved in four species, and the non-coding gene was less likely to be methylated compared with protein-coding gene. Especially, the 6mA-methylated lncRNA genes were expressed significant lower than genes without methylation in A. thaliana (p = 3.295e-4), D. melanogaster (p = 3.439e-11), and H. sapiens (p = 9.087e-3). The detection and distribution profiling of 6mA modification in ncRNA regions from four species reveal that 6mA modifications may have effects on their expression level.
Highlights
DNA methylation, refers to the addition of a methyl group (CH3) to the DNA molecule, plays a critical role in epigenetic regulation of genes expression
The raw DNA data sequenced by singlemolecule real-time (SMRT) PacBio RSII were used to identify DNA methylated sites (Chin et al, 2016; Seo et al, 2016), and the short reads RNA datasets from the same tissue were used to explore the gene expression in H. sapiens, D. melanogaster, C. elegans, A. thaliana (Supplementary Table S1)
The 6mA density which refers to the number of adenines with 6mA methylation over all adenines (6mA/A) ranged from 0.023% in D. melanogaster to 0.099% in A. thaliana (Table 1)
Summary
DNA methylation, refers to the addition of a methyl group (CH3) to the DNA molecule, plays a critical role in epigenetic regulation of genes expression. 6mA modifications in bacteria are involved in diverse biological processes such as DNA replication, DNA mismatch repair, host–pathogen interaction, and gene expression (Ratel et al, 2006; Wion and Casadesus, 2006). Owing to the developed high-through sequencing technologies, 6mA modifications have been detected in diverse eukaryotes such as Chlamydomonas (Fu et al, 2015), Arabidopsis thaliana (Liang et al, 2018), Caenorhabditis elegans (Greer et al, 2015), Drosophila melanogaster (Zhang et al, 2015), Mus
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