RNA-Seq Reveals Dynamic Changes of Gene Expression in Key Stages of Intestine Regeneration in the Sea Cucumber Apostichopus japonicas

CORC > 海洋研究所 > 中国科学院海洋研究所 > 海洋生态与环境科学重点实验室

	RNA-Seq Reveals Dynamic Changes of Gene Expression in Key Stages of Intestine Regeneration in the Sea Cucumber Apostichopus japonicas
	Sun, Lina 1; Yang, Hongsheng1 ; Chen, Muyan 3; Ma, Deyou 1,2; Lin, Chenggang 1,2; Yang, HS
刊名	PLOS ONE
	2013-08-06
卷号	8 期号:8 页码:e69441
ISSN号	1932-6203
通讯作者	Yang, HS
中文摘要	Background: Sea cucumbers (Holothuroidea; Echinodermata) have the capacity to regenerate lost tissues and organs. Although the histological and cytological aspects of intestine regeneration have been extensively studied, little is known of the genetic mechanisms involved. There has, however, been a renewed effort to develop a database of Expressed Sequence Tags (ESTs) in Apostichopus japonicus, an economically-important species that occurs in China. This is important for studies on genetic breeding, molecular markers and special physiological phenomena. We have also constructed a library of ESTs obtained from the regenerative body wall and intestine of A. japonicus. The database has increased to similar to 30000 ESTs. Results: We used RNA-Seq to determine gene expression profiles associated with intestinal regeneration in A. japonicus at 3, 7, 14 and 21 days post evisceration (dpe). This was compared to profiles obtained from a normally-functioning intestine. Approximately 5 million (M) reads were sequenced in every library. Over 2400 up-regulated genes (>10%) and over 1000 down-regulated genes (similar to 5%) were observed at 3 and 7dpe (log(2)Ratio >= 1, FDR <= 0.001). Specific "Go terms" revealed that the DEGs (Differentially Expressed Genes) performed an important function at every regeneration stage. Besides some expected pathways (for example, Ribosome and Spliceosome pathway term), the "Notch signaling pathway," the "ECM-receptor interaction" and the "Cytokine-cytokine receptor interaction" were significantly enriched. We also investigated the expression profiles of developmental genes, ECM-associated genes and Cytoskeletal genes. Twenty of the most important differentially expressed genes (DEGs) were verified by Real-time PCR, which resulted in a trend concordance of almost 100% between the two techniques. Conclusion: Our studies demonstrated dynamic changes in global gene expression during intestine regeneration and presented a series of candidate genes and enriched pathways that contribute to intestine regeneration in sea cucumbers. This provides a foundation for future studies on the genetics/molecular mechanisms associated with intestine regeneration.
英文摘要	Background: Sea cucumbers (Holothuroidea; Echinodermata) have the capacity to regenerate lost tissues and organs. Although the histological and cytological aspects of intestine regeneration have been extensively studied, little is known of the genetic mechanisms involved. There has, however, been a renewed effort to develop a database of Expressed Sequence Tags (ESTs) in Apostichopus japonicus, an economically-important species that occurs in China. This is important for studies on genetic breeding, molecular markers and special physiological phenomena. We have also constructed a library of ESTs obtained from the regenerative body wall and intestine of A. japonicus. The database has increased to similar to 30000 ESTs.
学科主题	Science & Technology - Other Topics
WOS标题词	Science & Technology
类目[WOS]	Multidisciplinary Sciences
研究领域[WOS]	Science & Technology - Other Topics
关键词[WOS]	RAT-LIVER REGENERATION ; HOLOTHURIA-GLABERRIMA ; EXTRACELLULAR-MATRIX ; SKELETAL-MUSCLE ; AXON REGENERATION ; SIGNALING PATHWAY ; MOLECULAR-CLONING ; FIN REGENERATION ; LIMB MYOGENESIS ; SATELLITE CELLS
收录类别	SCI
原文出处	10.1371/journal.pone.0069441
语种	英语
WOS记录号	WOS:000324401500009
公开日期	2014-07-17
内容类型	期刊论文
源URL	[http://ir.qdio.ac.cn/handle/337002/16490]
专题	海洋研究所_海洋生态与环境科学重点实验室
通讯作者	Yang, HS
作者单位	1.Chinese Acad Sci, Inst Oceanol, Qingdao, Peoples R China 2.Univ Chinese Acad Sci, Beijing, Peoples R China 3.Ocean Univ China, Qingdao, Peoples R China
推荐引用方式 GB/T 7714	Sun, Lina,Yang, Hongsheng,Chen, Muyan,et al. RNA-Seq Reveals Dynamic Changes of Gene Expression in Key Stages of Intestine Regeneration in the Sea Cucumber Apostichopus japonicas[J]. PLOS ONE,2013,8(8):e69441.
APA	Sun, Lina,Yang, Hongsheng,Chen, Muyan,Ma, Deyou,Lin, Chenggang,&Yang, HS.(2013).RNA-Seq Reveals Dynamic Changes of Gene Expression in Key Stages of Intestine Regeneration in the Sea Cucumber Apostichopus japonicas.PLOS ONE,8(8),e69441.
MLA	Sun, Lina,et al."RNA-Seq Reveals Dynamic Changes of Gene Expression in Key Stages of Intestine Regeneration in the Sea Cucumber Apostichopus japonicas".PLOS ONE 8.8(2013):e69441.