Li Xiaojun, Lin Shujin, Xiang Chenggang, Liu Wenqian, Zhang Xiaojing, Wang Cuicui, Lu Xiaohong, Liu Mengshuang, Wang Tao, Liu Zixi, Wang Naonao, Gao Lihong, Han Xiao, Zhang Wenna
Beijing Key Laboratory of Growth and Developmental Regulation for Protected Vegetable Crops, China Agricultural University, Beijing, China.
College of Biology Science and Engineering, Fuzhou University, Fuzhou, China.
Comput Struct Biotechnol J. 2023 Jan 10;21:837-846. doi: 10.1016/j.csbj.2023.01.012. eCollection 2023.
As an internal modification of transcripts, RNA methylation determines RNA fate by changing RNA-protein binding affinity. In plants, RNA methylation is ubiquitous and is involved in all aspects of RNA post-transcriptional regulation. For instance, long-distance mobile RNAs, strongly influenced by their methylation status, play important roles in plant growth, development and environmental adaptation. Cucumber/pumpkin heterografts are widely used to improve stress tolerance of cucumber and to study mobile RNA signals due to their strong developed vasculature system. Here, we developed the Cucume (Cucurbit RNA methylation, http://cucume.cn/) database for these two important vegetables, cucumber ( L.) and pumpkin () with high productivity worldwide. We identified mRNAs harboring 5-methylcytosine (mC) and N-methyladenosine (mA) sites in pumpkin and cucumber at the whole genome level via Methylated RNA Immunoprecipitation sequencing (MeRIP-seq) of different tissues and the vascular exudates. In addition to RNA methylation sites, the Cucume database includes graft-transmissible systemic mRNAs identified in previous studies using cucumber/pumpkin heterografts. The further integration of cucumber genome-wide association analysis (GWAS) and quantitative trait loci (QTL) allows the study of RNA methylation-related genetic and epigenetic regulation in cucurbits. Therefore, the here developed Cucume database will promote understanding the role of cucurbit RNA methylation in RNA mobility and QTL, ultimately benefitting future breeding of agronomic crop germplasms.
作为转录本的一种内部修饰，RNA甲基化通过改变RNA与蛋白质的结合亲和力来决定RNA的命运。在植物中，RNA甲基化普遍存在，并参与RNA转录后调控的各个方面。例如，受甲基化状态强烈影响的长距离移动RNA在植物生长、发育和环境适应中发挥着重要作用。黄瓜/南瓜异种嫁接因其发达的维管系统而被广泛用于提高黄瓜的胁迫耐受性和研究移动RNA信号。在这里，我们为这两种在全球范围内具有高产量的重要蔬菜——黄瓜（Cucumis sativus L.）和南瓜（Cucurbita moschata）开发了Cucume（葫芦科RNA甲基化，http://cucume.cn/）数据库。我们通过对不同组织和维管渗出物进行甲基化RNA免疫沉淀测序（MeRIP-seq），在全基因组水平上鉴定了南瓜和黄瓜中含有5-甲基胞嘧啶（mC）和N-甲基腺苷（mA）位点的mRNA。除了RNA甲基化位点，Cucume数据库还包括先前使用黄瓜/南瓜异种嫁接研究中鉴定出的可嫁接传播的系统性mRNA。黄瓜全基因组关联分析（GWAS）和数量性状位点（QTL）的进一步整合，有助于研究葫芦科中与RNA甲基化相关的遗传和表观遗传调控。因此，这里开发的Cucume数据库将促进对葫芦科RNA甲基化在RNA移动性和QTL中的作用的理解，最终有益于未来农作物种质的育种。
