CUCUME: An RNA methylation database integrating systemic mRNAs signals, GWAS and QTL genetic regulation and epigenetics in different tissues of Cucurbitaceae

Xiaojun Li; Shujin Lin; Chenggang Xiang; Wenqian Liu; Xiaojing Zhang; Cuicui Wang; Xiaohong Lu; Mengshuang Liu; Tao Wang; Zixi Liu; Naonao Wang; Lihong Gao; Xiao Han; Wenna Zhang

doi:10.1016/j.csbj.2023.01.012

CUCUME: An RNA methylation database integrating systemic mRNAs signals, GWAS and QTL genetic regulation and epigenetics in different tissues of Cucurbitaceae

Comput Struct Biotechnol J. 2023 Jan 10:21:837-846. doi: 10.1016/j.csbj.2023.01.012. eCollection 2023.

Authors

Affiliations

¹ Beijing Key Laboratory of Growth and Developmental Regulation for Protected Vegetable Crops, China Agricultural University, Beijing, China.
² College of Biology Science and Engineering, Fuzhou University, Fuzhou, China.
³ College of Life Science and Technology, HongHe University, Mengzi, Yunnan, 661100, China.

Abstract

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 (Cucumis sativus L.) and pumpkin (Cucurbita moschata) with high productivity worldwide. We identified mRNAs harboring 5-methylcytosine (m⁵C) and N⁶-methyladenosine (m⁶A) 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.

Keywords: Graft-transmissible mRNA; QTL; RNA methylation; RNA motifs.