Identification and characterization of microRNAs involved in ascidian larval metamorphosis

doi:10.1186/s12864-018-4566-4

IOCAS-IR > 实验海洋生物学重点实验室

	Identification and characterization of microRNAs involved in ascidian larval metamorphosis
	Zhang, Xiaoming 1,2; Liu, Xiaozhuo 1; Liu, Chengzhang 2,3; Wei, Jiankai1,2 ; Yu, Haiyan 1; Dong, Bo 1,2,4
	2018-03-01
发表期刊	BMC GENOMICS
ISSN	1471-2164
卷号	19 页码:12
通讯作者	Dong, Bo(bodong@ouc.edu.cn)
摘要	Background: Metamorphosis takes place within the life cycle of most marine invertebrates. The marine ascidian is a classical model to study complex cellular processes and underlying molecular mechanisms involved in its larval metamorphosis. The detailed molecular signaling pathways remain elusive, though extracellular signal-regulated kinases (ERKs) and c-Jun N-terminal kinase (JNK) have been revealed to regulate cell migration, differentiation, and apoptosis in ascidian larval organ regression and juvenile organ development. MicroRNAs (miRNAs) are small non-coding RNAs that modulate gene expression at the post-transcriptional level. Large numbers of miRNAs have been demonstrated to be involved in many developmental and metamorphic processes. However, the identification of miRNAs in ascidian larval metamorphosis has not yet been investigated. Results: Totally, 106 known and 59 novel miRNAs were screened out through RNA-sequencing of three small RNA libraries from 18 to 21 h post fertilization (hpf) tailbud embryos as well as from 42 hpf larvae (after tail regression) in Ciona savignyi. Expression profiling of miRNAs was confirmed by quantitative real-time PCR, showing that the expression levels of csa-miR-4040, csa-miR-4086, csa-miR-4055, csa-miR-4060, csa-miR-216a, csa-miR-216b, csa-miR-217, csa-miR-183, and csa-miR-92c were significantly higher in 42 hpf larvae, whereas those of csa-miR-4018a, csa-miR-4018b, and csa-miR-4000f were higher in 18 and 21 hpf embryos; then, their expression in 42 hpf larvae became significantly low. For these 12 miRNAs, whose expression levels significantly changed, we predicted their target genes through the combination of miRanda and TargetScan. This prediction analysis revealed 332 miRNA-target gene pairs that were associated with the ERK, JNK, and transforming growth factor beta signaling pathways, suggesting that the identified miRNAs are involved in the regulation of C. savignyi larval metamorphosis via controlling the expression of their target genes. Furthermore, we validated the expression of five selected miRNAs by northern blotting. Among the selected miRNAs, the expression patterns of csa-miR-4018a, csa-miR-4018b, and csa-miR-4000f were further examined by whole-mount in situ hybridization. The results showed that all three miRNAs were specifically expressed in a cell population resembling mesenchymal cells at the head and trunk part in swimming larvae but not in metamorphic larvae. Utilizing the luciferase assay, we also confirmed that miR-4000f targeted Mapk1, suggesting that the csa-miR-4018a/csa-miR-4018b/csa-miR-4000f cluster regulates larval metamorphosis through the Mapk1-mediated signaling pathway. Conclusions: Totally, 165 miRNAs, including 59 novel ones, were identified from the embryos and larvae of C. savignyi. Twelve of them showed significant changes in expression before and during metamorphosis. In situ hybridization and northern blotting results revealed that three miRNAs are potentially involved in the signaling regulatory network for the migration and differentiation of mesenchymal cells in larval metamorphosis. Furthermore, the luciferase reporter assay revealed that Mapk1 is a target of csa-miR-4000f. Our results not only present a list and profile of miRNAs involved in Ciona metamorphosis but also provide informative cues to further understand their function in ascidian larval metamorphosis.
关键词	microRNAs Ciona savignyi Metamorphosis Mesenchyme Signaling pathways
DOI	10.1186/s12864-018-4566-4
收录类别	SCI
语种	英语
资助项目	National Natural Science Foundation of China[31572352] ; National Natural Science Foundation of China[41706153] ; National Natural Science Foundation of China[31771649] ; Qingdao National Laboratory for Marine Science and Technology[QNLM2016ORP0301] ; Taishan Scholar Program of Shandong Province, China[201502035] ; National Natural Science Foundation of China[31572352] ; National Natural Science Foundation of China[41706153] ; National Natural Science Foundation of China[31771649] ; Qingdao National Laboratory for Marine Science and Technology[QNLM2016ORP0301] ; Taishan Scholar Program of Shandong Province, China[201502035]
WOS研究方向	Biotechnology & Applied Microbiology ; Genetics & Heredity
WOS类目	Biotechnology & Applied Microbiology ; Genetics & Heredity
WOS记录号	WOS:000427127300003
出版者	BIOMED CENTRAL LTD
引用统计	被引频次：11[WOS] [WOS记录] [WOS相关记录]
文献类型	期刊论文
条目标识符	http://ir.qdio.ac.cn/handle/337002/154492
专题	实验海洋生物学重点实验室
通讯作者	Dong, Bo
作者单位	1.Ocean Univ China, Coll Marine Life Sci, Minist Educ, Key Lab Marine Genet & Breeding, Qingdao 266003, Peoples R China 2.Qingdao Natl Lab Marine Sci & Technol, Lab Marine Biol & Biotechnol, Qingdao 266237, Peoples R China 3.Chinese Acad Sci, Inst Oceanol, Key Lab Expt Marine Biol, Qingdao 266071, Peoples R China 4.Ocean Univ China, Inst Evolut & Marine Biodivers, 5 Yushan Rd, Qingdao 266003, Peoples R China
推荐引用方式 GB/T 7714	Zhang, Xiaoming,Liu, Xiaozhuo,Liu, Chengzhang,et al. Identification and characterization of microRNAs involved in ascidian larval metamorphosis[J]. BMC GENOMICS,2018,19:12.
APA	Zhang, Xiaoming,Liu, Xiaozhuo,Liu, Chengzhang,Wei, Jiankai,Yu, Haiyan,&Dong, Bo.(2018).Identification and characterization of microRNAs involved in ascidian larval metamorphosis.BMC GENOMICS,19,12.
MLA	Zhang, Xiaoming,et al."Identification and characterization of microRNAs involved in ascidian larval metamorphosis".BMC GENOMICS 19(2018):12.

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