Epitranscriptome
Secondly, this mark is enriched in specific regions of the transcriptome; it is mostly found close to stop codons, in 3’-UTRs and in long internal exons.
Notably, in vertebrates, the presence of proteins categorized as 'Erasers' is suggested to facilitate the removal of m6A, which enables a dynamic regulation of m6A deposition on mRNAs.
[11] Discovery of the METTL3 complex indicated that m6A installation might be a regulated process, which was pivotal for the advancement and interest in the field of epitranscriptomics.
[12] It has been shown that three members of the human YTH domain family of proteins have higher binding affinities to methylated mRNA.
It also causes a 1.5-fold increase in the amount of GTP hydrolyzed per peptidyl transfer, which indicates that a lot of proofreading is required.
[19] The "reader" YTHDF2 binds to m6A-containing mRNAs and decreases their stability by recruiting them to P-bodies, in a process called methylation-dependent mRNA decay.
Evidence supporting this claim identified that decreased m6A levels in the transcriptome lead to significantly reduced hnRNPC binding.
Splicing is affected in Mettl3 knock-out mice, resulting in increased frequency of exon skipping and intron retention.
Reduced m6A levels due to down regulation of METTL3 and/or METTL14 lead to the activation of a number of oncogenes, such as the gene encoding ADAM metallopeptidase domain 19 (ADAM19).
[14] In addition, single nucleotide polymorphisms (SNPs) on the gene encoding FTO have been associated with increased risk of breast and pancreatic cancer.
[22] All things considered, "writers" and "erasers" of the m6A mark may be good potential drug targets in cancer therapy.
[14] Current research of the m6a epitranscriptome is continuing to uncover the implications of m6a and its post-physiological effects on ischemic stroke incidents.
N1-methyladenosine modification is thought to regulate tRNA and rRNA stability, as well as potentially alter protein-RNA interactions or RNA secondary structures.
A computational tool based on the data generated from these methods called RAMPed has been developed to try to identify these particular modifications.
Involvement of m1a may be organized under the categories of proliferation, invasion, cell death, tumor microenvironment, or cancer metabolism.
For example, the regulator TRMT6 has been found to be overexpressed in individuals with glioma, a cancer marked by the inappropriate proliferation of glial cells of the brain or spinal cord.
It is important to note that DNMT-2 is a protein that falls under the DNMT family, which contains three other DNMTs (1, 3a, and 3b) known to demonstrate methylation activity in relation to the genome.
[27] While these writers have been identified, as of now, there are no known m5C "erasers"; in a broader sense, this means that reamination, or the conversion of 5-methylcytosine back into cytosine, has not been observed in RNA.
[28] On the other hand, m5C modifications could possibly be associated with the regulation of genes involved in energy and lipid metabolism, through modulation of the overall RNA translational fate.
These modifications are very common in tissues and cells of the nervous system, and malfunctions in this deamination can result in a variety of different human diseases.
Other similar modifications to nucleotides impact the ability of tRNA to initiate translation, thus impeding gene expression.
[31] This modification is particularly widespread and found amongst a variety of organisms, indicating that perhaps convergent evolution took place in the development of this nucleoside.
[28][29] The artificial process of pseudouridylation has an effect on the function of mRNA: it changes the genetic code by making non-canonical base pairing possible in the ribosome decoding center.
For instance, PUS4 (also known as TruB pseudouridine synthase family member 1, TRUB1) and PUS7, which are responsible for most of the mRNA pseudouridylation, are located in the nucleus or the cytoplasm.
Even if CMCT can form covalent bonds with U, G and Ψ residues, only Ψ-CMC is resistant to alkaline hydrolysis (U-CMC and G-CMC get hydrolyzed).
[29] Other pseudouridine detection methods include site-specific cleavage and radioactive-labeling followed by ligation-assisted extraction and thin-layer chromatography (SCARLET) and mass spectrometry.
Examples include methylation of cytosine groups by tRNA methyltransferase (Trm4) in response to the depletion of nutrients in the body.
[40] Modifications can also happen in short non-coding RNAs, including small nuclear RNA (snRNA) and microRNA (miRNA).
[37] Even if m6A-marked viral transcripts are involved in regulating gene expression of a number of different viruses, the mechanisms by which this happens have not been identified.
[46] The ENCyclOpedia of Rna Epitranscriptome (ENCORE) is an upgraded version of RMBase that a comprehensive epitranscriptome platform with tens of new software and tools, to decode the distribution pattern, metagene profile, biogenesis mechanisms, regulatory functions, interactome, evolutional conservation and novel reader proteins of more than 70 different types of RNA modifications by analyzing thousands of high-throughput sequencing data.
