Notes

The detection methods and research of DNA and RNA modification by Li Chengji and song Chunhao were reviewed.
NMN (Nicotinamide Mononucleotide),

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So far, 17 kinds of DNA modifications and more than 160 kinds of RNA modifications have been confirmed. The attention to the biological functions of these modifications has promoted the establishment and development of epigenomics and epigenetics. Understanding the exact location of specific deformations in the genome or transcriptome is the key to analyze biological function. With the development of sequencing technology, DNA / RNA modification map can be drawn, but it also leads to new problems and thinking.
Recently, Li Chengji of Peking University and song Chunhao of Oxford University jointly published the special Abstract mapping the epigenetic modification sof DNA and RNA of protein cell. This paper summarizes the current methods and discoveries of high-throughput DNA / RNA modification detection technology in detail.
DNA fertilization plays an important role in ontogeny [1], aging [2] and cancer [3]. These modifications do not hinder the Watson Crick pairing principle, but affect the binding of protein to DNA. Methylation of the fifth carbon atom of cytosine (5-methylamine, 5-methylcytosine or 5mC) in mammalian genome is the most abundant type of DNA modification, also known as the fifth base [1]. 5mC is catalyzed by DNA methylase DNMTs and is mainly concentrated in CpG island. The distribution of 5mC is tissue-specific, but 70% ~ 80% of CpG islands are modified by 5mC [4]. 5-hydroxymethylcytosine (5-hydroxymethylcytosine or 5hmc), also known as the sixth base, comes from the oxidation of Tet1 enzyme to 5mC. Further oxidation of 5hmc produced 5-porphyrin cytosine (5FC) and 5-carboxycytosine (5cac).
Like DNA, RNA has various modifications, involving all aspects of RNA metabolism. In recent years, the technology of identifying DNA / RNA modification sites by high-throughput sequence measurement has made great contributions to the research of epigenomics and epigenomics.
Identification of DNA modification sites at single base level
1.5mc site identification
Sequence analysis of sodium sulfite (BS SEQ) was considered as the gold standard for 5mC identification. Sulfite has no effect on methylated C, but its principle is to convert unmethylated C into U (uracil) and convert it into t by PCR to form methylated C and non amide. Combined with high-throughput sequencing technology, a genome-wide 5mC modification map with single base resolution can be obtained. The conversion efficiency of sulfite to methylated carbon is 99%, and the acceptance of this method is the highest [5-7]. However, sulfite treatment leads to the decomposition of DNA [8], which limits its application in rare and precious samples. In addition, unmethylated C accounting for 95% of the genome becomes T, the genome matching efficiency of sequenced fragments decreases, and the preference for coverage is also increasing. Finally, BS SEQ did not distinguish between 5mC and 5hmc.
Recently, two non bisulfite 5mC identification methods have been developed into taps (TET assisted pyridine borate sequencing) [9] and em-seq (em-seq). The false positive rate of taps was lower than that of BS SEQ, and a small amount of DNA (1ng) could be detected. Together with potassium peroxide, 5mC and 5hmc can be distinguished. EM SEQ used tet and DNA deaminase apobec3a, and its sensitivity was higher than that of BS SEQ.
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