弓形虫三个主要基因型虫株mRNA m6A甲基化修饰的差异分析

doi:10.1016/j.jia.2024.03.072

摘要/Abstract

摘要： 刚地弓形虫（Toxoplasma gondii）呈全球性分布，可感染人和几乎所有的温血动物，引起人兽共患弓形虫病。弓形虫仅有一个种，但存在有200多种基因型，不同基因型虫株具有不同的地理分布和毒力差异。N⁶-腺苷酸甲基化（N⁶-methyladenosine, m⁶A）是mRNAs中丰度最高的表观遗传修饰形式，其涉及mRNAs生物学的多种方面，然而目前尚不清楚弓形虫不同基因型之间的mRNA m⁶A甲基化修饰的差异。因此，本研究采用RNA测序（RNA-seq）和m⁶A甲基化测序（MeRIP-seq）技术，来探索弓形虫三个主要克隆谱系（I型、II型和III型）之间mRNA m⁶A甲基化修饰的差异，并鉴定不同基因型之间主要的差异性表达的甲基化基因。结果表明，在弓形虫RH（I型）、ME49（II型）和VEG（III型）虫株速殖子的5211、5607和4974个基因上分别鉴定出7650、8359和7264个m⁶A甲基化修饰峰；大多数的m⁶A甲基化修饰发生在3'UTR区，其次是CDS区，且在3'UTR区发生m⁶A甲基化修饰的基因具有较高的mRNA丰度。通过RH vs. ME49、RH vs. VEG和ME49 vs. VEG组间对比，在676、168和553个基因上分别鉴定出735、192和615个差异甲基化峰。进一步结合不同基因型之间的RNA-seq数据分析发现，在RH vs. ME49、RH vs. VEG和ME49 vs. VEG三个比较组中分别鉴定出172、41和153个差异性表达的甲基化基因，且大多数差异性表达的甲基化基因的m⁶A修饰水平与mRNA丰度之间呈正相关性。对这些差异性表达的甲基化基因进行GO注释分析发现，其主要参与Golgi apparatus、plasma membrane、signal transduction、RNA processing和catalytic step 2 spliceosome等生物学途径；对这些差异性表达的甲基化基因进行KEGG通路富集分析表明，其主要参与endocytosis、systemic lupus erythematosus和mTOR signaling pathway等信号通路。这些发现揭示了m⁶A甲基化修饰在弓形虫不同基因型虫株之间存在特异性差异，有助于更好地研究m⁶A甲基化修饰在弓形虫病理生物学中的作用，阐明弓形虫不同基因型虫株之间毒力差异的分子机制。

Abstract: Toxoplasma gondii is an important zoonotic parasite which has over 200 genotypes worldwide. N⁶-methyladenosine (m⁶A) methylation is a common epigenetic modification in messenger RNAs (mRNAs), and has been implicated in many aspects of mRNA biology. However, little is known about the difference in m⁶A methylation among different genotypes of T. gondii. In the present study, we employed methylated RNA immunoprecipitation sequencing (MeRIP-seq) technology to identify key genes exhibiting m⁶A methylation in the three major clonal lineages (Types I, II and III) of T. gondii tachyzoites. A total of 7650, 8359 and 7264 m⁶A peaks were identified in 5211, 5607 and 4974 genes in tachyzoites of RH strain (Type I), ME49 strain (Type II) and VEG strain (Type III), respectively. By comparing RH vs. ME49, RH vs. VEG, and ME49 vs. VEG, 735, 192 and 615 differentially methylated peaks (DMPs) were identified in 676, 168 and 553 genes, respectively. A combined MeRIP-seq and RNA-seq analysis revealed 172, 41 and 153 differentially methylated genes (DMGs) at both the m⁶A methylation and transcriptional level. Gene ontology term enrichment analysis of the DMPs identified differences related to Golgi apparatus, plasma membrane, signal transduction, RNA processing and catalytic step 2 spliceosome. KEGG pathway enrichment analysis showed that the DMGs are mainly involved in endocytosis, systemic lupus erythematosus and mTOR signaling pathway. These findings reveal genotype-specific differences in m⁶A methylation, which provide new resources for further investigations of the role of m⁶A in the pathobiology of T. gondii.

Key words: Toxoplasma gondii , , toxoplasmosis , , MeRIP-seq , , RNA-seq , , N⁶-methyladenosine

. 弓形虫三个主要基因型虫株mRNA m⁶A甲基化修饰的差异分析[J]. Journal of Integrative Agriculture, DOI: 10.1016/j.jia.2024.03.072.

Changning Wei, Hui Cao, Chenxu Li, Hongyu Song, Qing Liu, Xingquan Zhu, Wenbin Zheng. Differences in N⁶-methyladenosine (m⁶A) methylation among the three major clonal lineages of Toxoplasma gondii tachyzoites[J]. Journal of Integrative Agriculture, DOI: 10.1016/j.jia.2024.03.072.

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弓形虫三个主要基因型虫株mRNA m⁶A甲基化修饰的差异分析

Differences in N⁶-methyladenosine (m⁶A) methylation among the three major clonal lineages of Toxoplasma gondii tachyzoites

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