m6A-TSHub: unveiling the context-specific m6A methylation and m6A-affecting mutations in 23 human tissues

Huang, Daiyun; Zhang, Yuxin; Wei, Zhen; Su, Jionglong; Magalhães, João Pedro de; Rigden, Daniel J.; Meng, Jia; Chen, Kunqi

doi:10.1101/2022.01.12.476117

Cited by 4 publications

(1 citation statement)

References 127 publications

(223 reference statements)

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“…Information is provided for 23 different tissues (with approximately ∼185,000 mapped sites) and 25 tumor samples with 500,000 mapped sites. This database allows for identification of SNPs in human tissues and could be used to help users identify if variants in a specific gene could impact m 6 A sites ( Song et al 2022a ).…”

Section: Single Modification Databasesmentioning

confidence: 99%

RNA modifications: an overview of select web-based tools

Ramos

2022

RNA

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The field of epitranscriptomics has expanded dramatically in recent years, both in the number of identified RNA modifications and the number of researchers studying them. As knowledge of post-transcriptional modifications continues to expand, numerous new methods have been developed to detect these modifications. Additionally, modifications are being extended to therapeutic settings, such as with recent mRNA vaccines. With this increase in knowledge and use, the community is recognizing the necessity for user-friendly databases to 1) store information from both high- and low-throughput studies and 2) provide prediction software on how RNA modifications contribute to RNA function and disease. This mini-review highlights select RNA modification databases and their key attributes with the aim of providing a resource to researchers in the field of epitranscriptomics.

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Section: Single Modification Databasesmentioning

confidence: 99%

RNA modifications: an overview of select web-based tools

Ramos

2022

RNA

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RNA Epigenetics in Chronic Lung Diseases

Wang

Guo²,

Yan³

2022

Genes

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Chronic lung diseases are highly prevalent worldwide and cause significant mortality. Lung cancer is the end stage of many chronic lung diseases. RNA epigenetics can dynamically modulate gene expression and decide cell fate. Recently, studies have confirmed that RNA epigenetics plays a crucial role in the developing of chronic lung diseases. Further exploration of the underlying mechanisms of RNA epigenetics in chronic lung diseases, including lung cancer, may lead to a better understanding of the diseases and promote the development of new biomarkers and therapeutic strategies. This article reviews basic information on RNA modifications, including N6 methylation of adenosine (m6A), N1 methylation of adenosine (m1A), N7-methylguanosine (m7G), 5-methylcytosine (m5C), 2′O-methylation (2′-O-Me or Nm), pseudouridine (5-ribosyl uracil or Ψ), and adenosine to inosine RNA editing (A-to-I editing). We then show how they relate to different types of lung disease. This paper hopes to summarize the mechanisms of RNA modification in chronic lung disease and finds a new way to develop early diagnosis and treatment of chronic lung disease.

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Modification and Expression of mRNA m6A in the Lateral Habenular of Rats after Long-Term Exposure to Blue Light during the Sleep Period

Ren

Zhang

et al. 2023

Genes

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Artificial lighting, especially blue light, is becoming a public-health risk. Excessive exposure to blue light at night has been reported to be associated with brain diseases. However, the mechanisms underlying neuropathy induced by blue light remain unclear. An early anatomical tracing study described the projection of the retina to the lateral habenula (LHb), whereas more mechanistic reports are available on multiple brain functions and neuropsychiatric disorders in the LHb, which are rarely seen in epigenetic studies, particularly N6-methyladenosine (m6A). The purpose of our study was to first expose Sprague-Dawley rats to blue light (6.11 ± 0.05 mW/cm2, the same irradiance as 200 lx of white light in the control group) for 4 h, and simultaneously provide white light to the control group for the same time to enter a sleep period. The experiment was conducted over 12 weeks. RNA m6A modifications and different mRNA transcriptome profiles were observed in the LHb. We refer to this experimental group as BLS. High-throughput MeRIP-seq and mRNA-seq were performed, and we used bioinformatics to analyze the data. There were 188 genes in the LHb that overlapped between differentially m6A-modified mRNA and differentially expressed mRNA. The Kyoto Encyclopedia of Genes and Genomes and gene ontology analysis were used to enrich neuroactive ligand–receptor interaction, long-term depression, the cyclic guanosine monophosphate-dependent protein kinase G (cGMP-PKG) signaling pathway, and circadian entrainment. The m6A methylation level of the target genes in the BLS group was disordered. In conclusion, this study suggests that the mRNA expression and their m6A of the LHb were abnormal after blue light exposure during the sleep period, and the methylation levels of target genes related to synaptic plasticity were disturbed. This study offers a theoretical basis for the scientific use of light.

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m6A-TSHub: unveiling the context-specific m6A methylation and m6A-affecting mutations in 23 human tissues

Cited by 4 publications

References 127 publications

RNA modifications: an overview of select web-based tools

RNA modifications: an overview of select web-based tools

RNA Epigenetics in Chronic Lung Diseases

Modification and Expression of mRNA m6A in the Lateral Habenular of Rats after Long-Term Exposure to Blue Light during the Sleep Period

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