CUCUME: An RNA methylation database integrating systemic mRNAs signals, GWAS and QTL genetic regulation and epigenetics in different tissues of Cucurbitaceae
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 th...
| Main Authors: | , , , , , , , , , , , , , |
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| Format: | Article |
| Language: | English |
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Elsevier
2023-01-01
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| Series: | Computational and Structural Biotechnology Journal |
| Subjects: | |
| Online Access: | http://www.sciencedirect.com/science/article/pii/S2001037023000107 |
| _version_ | 1797384128757235712 |
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| author | 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 |
| author_facet | 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 |
| author_sort | Xiaojun Li |
| collection | DOAJ |
| description | 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. |
| first_indexed | 2024-03-08T21:31:01Z |
| format | Article |
| id | doaj.art-4e597e3b36344a08af8716329c2ad38f |
| institution | Directory Open Access Journal |
| issn | 2001-0370 |
| language | English |
| last_indexed | 2024-03-08T21:31:01Z |
| publishDate | 2023-01-01 |
| publisher | Elsevier |
| record_format | Article |
| series | Computational and Structural Biotechnology Journal |
| spelling | doaj.art-4e597e3b36344a08af8716329c2ad38f2023-12-21T07:30:44ZengElsevierComputational and Structural Biotechnology Journal2001-03702023-01-0121837846CUCUME: An RNA methylation database integrating systemic mRNAs signals, GWAS and QTL genetic regulation and epigenetics in different tissues of CucurbitaceaeXiaojun Li0Shujin Lin1Chenggang Xiang2Wenqian Liu3Xiaojing Zhang4Cuicui Wang5Xiaohong Lu6Mengshuang Liu7Tao Wang8Zixi Liu9Naonao Wang10Lihong Gao11Xiao Han12Wenna Zhang13Beijing Key Laboratory of Growth and Developmental Regulation for Protected Vegetable Crops, China Agricultural University, Beijing, ChinaCollege of Biology Science and Engineering, Fuzhou University, Fuzhou, ChinaCollege of Life Science and Technology, HongHe University, Mengzi, Yunnan, 661100, ChinaBeijing Key Laboratory of Growth and Developmental Regulation for Protected Vegetable Crops, China Agricultural University, Beijing, ChinaBeijing Key Laboratory of Growth and Developmental Regulation for Protected Vegetable Crops, China Agricultural University, Beijing, ChinaBeijing Key Laboratory of Growth and Developmental Regulation for Protected Vegetable Crops, China Agricultural University, Beijing, ChinaBeijing Key Laboratory of Growth and Developmental Regulation for Protected Vegetable Crops, China Agricultural University, Beijing, ChinaBeijing Key Laboratory of Growth and Developmental Regulation for Protected Vegetable Crops, China Agricultural University, Beijing, ChinaBeijing Key Laboratory of Growth and Developmental Regulation for Protected Vegetable Crops, China Agricultural University, Beijing, ChinaBeijing Key Laboratory of Growth and Developmental Regulation for Protected Vegetable Crops, China Agricultural University, Beijing, ChinaBeijing Key Laboratory of Growth and Developmental Regulation for Protected Vegetable Crops, China Agricultural University, Beijing, ChinaBeijing Key Laboratory of Growth and Developmental Regulation for Protected Vegetable Crops, China Agricultural University, Beijing, ChinaCollege of Biology Science and Engineering, Fuzhou University, Fuzhou, China; Corresponding authors.Beijing Key Laboratory of Growth and Developmental Regulation for Protected Vegetable Crops, China Agricultural University, Beijing, China; Corresponding authors.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.http://www.sciencedirect.com/science/article/pii/S2001037023000107RNA methylationGraft-transmissible mRNAQTLRNA motifs |
| spellingShingle | 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 CUCUME: An RNA methylation database integrating systemic mRNAs signals, GWAS and QTL genetic regulation and epigenetics in different tissues of Cucurbitaceae Computational and Structural Biotechnology Journal RNA methylation Graft-transmissible mRNA QTL RNA motifs |
| title | CUCUME: An RNA methylation database integrating systemic mRNAs signals, GWAS and QTL genetic regulation and epigenetics in different tissues of Cucurbitaceae |
| title_full | CUCUME: An RNA methylation database integrating systemic mRNAs signals, GWAS and QTL genetic regulation and epigenetics in different tissues of Cucurbitaceae |
| title_fullStr | CUCUME: An RNA methylation database integrating systemic mRNAs signals, GWAS and QTL genetic regulation and epigenetics in different tissues of Cucurbitaceae |
| title_full_unstemmed | CUCUME: An RNA methylation database integrating systemic mRNAs signals, GWAS and QTL genetic regulation and epigenetics in different tissues of Cucurbitaceae |
| title_short | CUCUME: An RNA methylation database integrating systemic mRNAs signals, GWAS and QTL genetic regulation and epigenetics in different tissues of Cucurbitaceae |
| title_sort | cucume an rna methylation database integrating systemic mrnas signals gwas and qtl genetic regulation and epigenetics in different tissues of cucurbitaceae |
| topic | RNA methylation Graft-transmissible mRNA QTL RNA motifs |
| url | http://www.sciencedirect.com/science/article/pii/S2001037023000107 |
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