Demethylase-assisted site-specific detection of N1-methyladenosine in RNA

Xiong, Jun; Chen, Ke-Ke; Xie, Neng-Bin; Chen, Wei; Shao, Wen-Xuan; Ji, Tong-Tong; Yu, Si-Yu; Feng, Yu-Qi; Yuan, Bi-Feng

doi:10.1016/j.cclet.2023.108953

Cited by 8 publications

(3 citation statements)

References 44 publications

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“…These advancements pave the way for elucidating distinct RNA epigenetic modification networks and hold promise for developing innovative therapeutic modalities. By leveraging chemical approaches, researchers are poised to unravel the complexities of RNA modification biology [45,46] and translate these insights into tangible clinical interventions, shaping the future of molecular biology and therapeutics.…”

Section: Discussionmentioning

confidence: 99%

Discovery of Photoexcited 2‐Chloro‐3,5‐Dinitrobenzoic Acid as a Chemical Deprenylase of i⁶A RNA

Sun,

Hui,

Liu

et al. 2024

ChemBioChem

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RNA modifications play crucial roles in regulating gene expression and cellular homeostasis. Modulating RNA modifications, particularly by targeting the enzymes responsible for their catalysis, has emerged as a promising therapeutic strategy. However, limitations, such as the lack of identified modifying enzymes and compensatory mechanisms, hinder targeted interventions. Chemical approaches independent of enzymatic activity offer an alternative strategy for RNA modification modulation. Here, we present the identification of 2‐chloro‐3,5‐dinitrobenzoic acid as a highly effective photochemical deprenylase of i6A RNA. This method demonstrates exceptional selectivity towards i6A, converting its substituent into a "N‐doped" ozonide, which upon hydrolysis releases natural adenine. We believe that this chemical approach will pave the way for a better understanding of RNA modification biology and the development of novel therapeutic modalities.

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Section: Discussionmentioning

confidence: 99%

Discovery of Photoexcited 2‐Chloro‐3,5‐Dinitrobenzoic Acid as a Chemical Deprenylase of i⁶A RNA

Sun,

Hui,

Liu

et al. 2024

ChemBioChem

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“…Beyond the four fundamental nucleobases of adenine, cytosine, guanine, and uracil that constitute the genetic code, RNA molecules are subject to a wide variety of chemical modifications. , These modifications have been identified in approximately 160 different forms across various RNA species spanning the biological three-domain system. − This diversity of modifications underscores the complexity and adaptability of RNA function beyond its canonical roles in protein synthesis and gene regulation . Similar to the way DNA modifications influence gene expression and genomic stability, modifications in RNA play crucial roles in fine-tuning a multitude of biological processes, including the regulation of mRNA stability and translation, RNA splicing, transport, and localization. − …”

Section: Introductionmentioning

confidence: 99%

Simultaneous Detection of Adenosine-to-Inosine Editing and N⁶-Methyladenosine at Identical RNA Sites through Deamination-Assisted Reverse Transcription Stalling

Min,

Shao,

et al. 2024

Anal. Chem.

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Adenosine-to-inosine (A-to-I) editing and N 6-methyladenosine (m6A) modifications are pivotal RNA modifications with widespread functional significance in physiological and pathological processes. Although significant effort has been dedicated to developing methodologies for identifying and quantifying these modifications, traditional approaches have often focused on each modification independently, neglecting the potential co-occurrence of A-to-I editing and m6A modifications at the same adenosine residues. This limitation has constrained our understanding of the intricate regulatory mechanisms governing RNA function and the interplay between different types of RNA modifications. To address this gap, we introduced an innovative technique called deamination-assisted reverse transcription stalling (DARTS), specifically designed for the simultaneous quantification of A-to-I editing and m6A at the same RNA sites. DARTS leverages the selective deamination activity of the engineered TadA–TadA8e protein, which converts adenosine residues to inosine, in combination with the unique property of Bst 2.0 DNA polymerase, which stalls when encountering inosine during reverse transcription. This approach enables the accurate quantification of A-to-I editing, m6A, and unmodified adenosine at identical RNA sites. The DARTS method is remarkable for its ability to directly quantify two distinct types of RNA modifications simultaneously, a capability that has remained largely unexplored in the field of RNA biology. By facilitating a comprehensive analysis of the co-occurrence and interaction between A-to-I editing and m6A modifications, DARTS opens new avenues for exploring the complex regulatory networks modulated by different RNA modifications.

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“…Identification and detection of DNA epigenetic modifications both in vitro and in vivo are of great significance for revealing their biological functions and mechanisms of action. − Among the various epigenetic modifications, 5-hydroxymethylcytosine (5hmC) is considered as the sixth base in the genome of higher organisms, − which is of utmost significance for gene regulation during cell development and carcinogenesis . Aberrant levels of 5hmC will lead to occurrence of many diseases, including breast cancer, papillary thyroid carcinoma, and medulloblastoma, and thus the 5hmC level is a potential indicator for cancer diagnosis. − Up to now, however, some functions of 5hmC and its role in diseases are still unclear.…”

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confidence: 99%

Selective Ligase-Based Sample Processing-Free Discrimination and Detection of Site-Specific DNA 5-Hydroxymethylcytosine

Zhao,

Yan,

et al. 2024

Anal. Chem.

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Accurate detection of site-specific 5-hydroxymethylcytosine (5hmC) in genomic DNA is of great significance, but it is technically challenging to directly distinguish very low levels of 5hmC from their abundant cytosine/5-methylcytosine (C/5mC) analogues. Herein, we wish to propose a selective ligase-mediated mechanism (SLim) that can directly discriminate 5hmC from C/ 5mC with a high specificity without the use of any sample processing protocol. In this new design, we discovered that HiFi Taq DNA Ligase can well tolerate the mismatched 5hmC/A base-pairing and then effectively ligate the associated nicking site while the mismatched 5mC/A or C/A pairs cannot be recognized by HiFi Taq DNA Ligase, providing a new way for direct and selective discriminating 5hmC from its similar analogues. Ultrasensitive and selective quantification of site-specific 5hmC is realized by coupling the SLim with polymerase chain reaction (PCR) or loop-mediated isothermal amplification (LAMP).

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Demethylase-assisted site-specific detection of N1-methyladenosine in RNA

Cited by 8 publications

References 44 publications

Discovery of Photoexcited 2‐Chloro‐3,5‐Dinitrobenzoic Acid as a Chemical Deprenylase of i⁶A RNA

Discovery of Photoexcited 2‐Chloro‐3,5‐Dinitrobenzoic Acid as a Chemical Deprenylase of i⁶A RNA

Simultaneous Detection of Adenosine-to-Inosine Editing and N⁶-Methyladenosine at Identical RNA Sites through Deamination-Assisted Reverse Transcription Stalling

Selective Ligase-Based Sample Processing-Free Discrimination and Detection of Site-Specific DNA 5-Hydroxymethylcytosine

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Demethylase-assisted site-specific detection of N1-methyladenosine in RNA

Cited by 8 publications

References 44 publications

Discovery of Photoexcited 2‐Chloro‐3,5‐Dinitrobenzoic Acid as a Chemical Deprenylase of i6A RNA

Discovery of Photoexcited 2‐Chloro‐3,5‐Dinitrobenzoic Acid as a Chemical Deprenylase of i6A RNA

Simultaneous Detection of Adenosine-to-Inosine Editing and N6-Methyladenosine at Identical RNA Sites through Deamination-Assisted Reverse Transcription Stalling

Selective Ligase-Based Sample Processing-Free Discrimination and Detection of Site-Specific DNA 5-Hydroxymethylcytosine

Contact Info

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Discovery of Photoexcited 2‐Chloro‐3,5‐Dinitrobenzoic Acid as a Chemical Deprenylase of i⁶A RNA

Discovery of Photoexcited 2‐Chloro‐3,5‐Dinitrobenzoic Acid as a Chemical Deprenylase of i⁶A RNA

Simultaneous Detection of Adenosine-to-Inosine Editing and N⁶-Methyladenosine at Identical RNA Sites through Deamination-Assisted Reverse Transcription Stalling