Gene body methylation is popularly seen in flowering plants (Angiosperms) and animals. It has an evolutionary impact due to homeostasis. Thus it is integrated with evolution to manage the developmental process. Gene body methylation is connected with a genetic expression that is enriched with guanine and cytosine DNA methylated genes that are responsible for maintenance functions. Cytosine DNA methylation is known to a conserved modification of the chromatin structure and that contributes to the regulation of genes, structures of genomes, and integrity. They are classified into different classes according to the context of the sequence for which methylated C will be present. It includes CG, CHG, and CHH sites. All these classes of sites are established and separately maintained with various cellular pathways. According to plant genomes, methylated CG is the richest form of mCG. They are characterized and maintained with the help of Methyl Transferase 1 (MET1) a plant homolog of DNA methyltransferase 1. Gene body methylation changes are heritable and cause epigenetic variation which is revealed in the phenotypic expression. The genome of the animal and plant species is the targeted region for methylation to takes place. GMC has an impact on the evolution of the genetic material in varied invertebrate groups.
Gene Body Methylation
Gene body methylation (GbM) is the earliest epigenetic alteration which occurs at the cytosine – guanine paired nucleotide site leads to methylation as CpGs (cytosine-phospho-guanine) nucleotides. In the case of vertebrates, the CG genome methylation occurs mostly in developmental stages and cellular tissue levels.
In invertebrates reduced level of DNA methylation occurs at the transcribing units which include introns and exons. Thus gene body methylation is interconnected with active transcription in the case of plants, humans, and animals.
GBM had its origin in a model species called Arabidopsis thaliana (Brassicaceae/mustard family). Many studies have been made on this GbM to study the closely related plant species.
Methylated CG (mCG) is found in the gene bodies of angiosperms, gymnosperms, ferns, liverworts, lycopods, green algae, and moss. The levels and distribution of mCG may vary between the species.
Few enrichment tests are performed for the identification of genes with the levels of mCG and non mCG.
The majority of genes were identified only in the case of angiosperms species. There are nearly 5 different classes of methylated genes and are distinguished according to the classification of enrichment tests.
Types of Gene Body Methylation
Unmethylated gene body: In this type, during the DNA methylation, all the three site classes are absent in the transcribed regions of the gene body.
Gene body methylated (GbM): Here, there will be an enriched mCG inside the transcribed part, and with depletion in start and termination ends at the transcriptional level. A bulk of genes is made for housekeeping, constitutively to express, with a long base pair similar to the unmethylated genes.
Transcription starts/stop sites: Though the mCG genes are enriched in nature there is a limitation in their distribution which can hold in the gene expression.
CHG transposable gene: In this type, there will be enrichment in mCHG (CHG methylation) and also depletion in the mCHH (CHH methylation) inside the transcribed region part. There is no assurance for the enrichment of mCG.
CHH transposable gene: It is also known as RdDM (RNA-directed DNA methylation). Here the mCHH has some possibility for enrichment with the help of a few mCG and mCHG in the transcribed region part. But the level of the DNA methylation is not a conserved one in the case of CHG and CHH genes.
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