High Resolution Methylome Map of Rat Indicates Role of Intragenic DNA Methylation in Identification of Coding Region

Abstract

DNA methylation is crucial for gene regulation and maintenance of genomic stability. Rat has been a key model system in understanding mammalian systemic physiology, however detailed rat methylome remains uncharacterized till date. Here, we present the first high resolution methylome of rat liver generated using Methylated DNA immunoprecipitation and high throughput sequencing (MeDIP-Seq) approach. We observed that within the DNA/RNA repeat elements, simple repeats harbor the highest degree of methylation. Promoter hypomethylation and exon hypermethylation were common features in both RefSeq genes and expressed genes (as evaluated by proteomic approach). We also found that although CpG islands were generally hypomethylated, about 6% of them were methylated and a large proportion (37%) of methylated islands fell within the exons. Notably, we obeserved significant differences in methylation of terminal exons (UTRs); methylation being more pronounced in coding/partially coding exons compared to the non-coding exons. Further, events like alternate exon splicing (cassette exon) and intron retentions were marked by DNA methylation and these regions are retained in the final transcript. Thus, we suggest that DNA methylation could play a crucial role in marking coding regions thereby regulating alternative splicing. Apart from generating the first high resolution methylome map of rat liver tissue, the present study provides several critical insights into methylome organization and extends our understanding of interplay between epigenome, gene expression and genome stability.

Identification of reference genes for RT-qPCR in ovine mammary tissue during late pregnancy and lactation and in response to maternal nutritional programming

“…DNA methylation has been associated with imprinting (reviewed in Ref. 1), X-inactivation (43), repression of gene expression (18), and, more recently, repressing intragenic promoter activity (29), alternative splicing (13,26,33,34), and controlling transcriptional elongation (25,33). The TET enzymes convert 5-methylcytosine to 5-hydroxymethyl cytosine (36), which is then further processed to result in the regeneration of a nonmethylated cytosine (14,27).…”

Next Generation Sequencing - Advances, Applications and Challenges

“…As such the problem has much in common with other sequencing protocols, such as identifying differential expression between RNA-seq cohorts or identifying peaks from a ChIP-seq sample. This commonality opens up an abundance of methods that can be used or adapted for MeDIP-seq sample analysis, for example peak finding using MACS [42,43], or DMR finding using DESeq [44] or edgeR [45].…”

Analysis of the leaf methylomes of parents and their hybrids provides new insight into hybrid vigor in Populus deltoides

“…The fragments were end-repaired, phosphorylated, and A-tailed. The fragments were then ligated to Illumina sequencing adapters [37]. The sheared DNA was diluted in 450 µl of TE buffer, denatured in a 100°C heat block for 10 min, and snap-cooled on ice for 5 min.…”